Sodium in PDB 9mg3: Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
Enzymatic activity of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
All present enzymatic activity of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp:
2.1.1.56;
Protein crystallography data
The structure of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp, PDB code: 9mg3
was solved by
D.J.Nilson,
E.Fedorov,
A.Ghosh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.96 /
1.42
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.043,
92.611,
101.298,
90,
90,
90
|
|
R / Rfree (%)
|
17.4 /
20.1
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
(pdb code 9mg3). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the
Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp, PDB code: 9mg3:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 1 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:22.1
occ:1.00
|
O
|
A:HOH773
|
2.6
|
23.1
|
1.0
|
|
HE2
|
A:PHE418
|
2.7
|
18.4
|
1.0
|
|
O
|
A:ARG353
|
2.8
|
15.1
|
1.0
|
|
HG3
|
A:ARG353
|
2.8
|
20.5
|
1.0
|
|
HB2
|
A:ASP357
|
2.9
|
22.7
|
1.0
|
|
O
|
A:MET361
|
2.9
|
16.8
|
1.0
|
|
HA
|
A:GLU362
|
3.0
|
18.7
|
1.0
|
|
HB3
|
A:ALA356
|
3.0
|
19.5
|
1.0
|
|
HG2
|
A:ARG353
|
3.1
|
20.5
|
1.0
|
|
HD2
|
A:PHE418
|
3.2
|
17.8
|
1.0
|
|
H
|
A:ASP357
|
3.3
|
19.9
|
1.0
|
|
CG
|
A:ARG353
|
3.4
|
17.1
|
1.0
|
|
CE2
|
A:PHE418
|
3.4
|
15.3
|
1.0
|
|
HA
|
A:ARG353
|
3.4
|
17.8
|
1.0
|
|
N
|
A:ASP357
|
3.5
|
16.6
|
1.0
|
|
H
|
A:LEU363
|
3.6
|
18.6
|
1.0
|
|
CD2
|
A:PHE418
|
3.7
|
14.8
|
1.0
|
|
C
|
A:ARG353
|
3.7
|
15.2
|
1.0
|
|
CB
|
A:ASP357
|
3.7
|
18.9
|
1.0
|
|
HA
|
A:ASP357
|
3.7
|
19.9
|
1.0
|
|
CA
|
A:GLU362
|
3.8
|
15.6
|
1.0
|
|
HB2
|
A:LEU363
|
3.8
|
19.7
|
1.0
|
|
N
|
A:LEU363
|
3.8
|
15.5
|
1.0
|
|
CB
|
A:ALA356
|
3.9
|
16.2
|
1.0
|
|
HE
|
A:ARG353
|
3.9
|
27.9
|
1.0
|
|
CA
|
A:ASP357
|
3.9
|
16.6
|
1.0
|
|
HB1
|
A:ALA356
|
3.9
|
19.5
|
1.0
|
|
C
|
A:MET361
|
3.9
|
17.4
|
1.0
|
|
CA
|
A:ARG353
|
3.9
|
14.8
|
1.0
|
|
C
|
A:GLU362
|
4.1
|
14.6
|
1.0
|
|
C
|
A:ALA356
|
4.2
|
14.0
|
1.0
|
|
HB3
|
A:ASP357
|
4.2
|
22.7
|
1.0
|
|
N
|
A:GLU362
|
4.3
|
15.7
|
1.0
|
|
CB
|
A:ARG353
|
4.3
|
15.8
|
1.0
|
|
HA
|
A:LEU363
|
4.5
|
16.8
|
1.0
|
|
HG2
|
A:GLU362
|
4.5
|
23.9
|
1.0
|
|
NE
|
A:ARG353
|
4.5
|
23.2
|
1.0
|
|
CA
|
A:ALA356
|
4.5
|
13.8
|
1.0
|
|
CD
|
A:ARG353
|
4.6
|
18.0
|
1.0
|
|
HB2
|
A:ALA356
|
4.6
|
19.5
|
1.0
|
|
CA
|
A:LEU363
|
4.6
|
14.0
|
1.0
|
|
CB
|
A:LEU363
|
4.6
|
16.4
|
1.0
|
|
CZ
|
A:PHE418
|
4.7
|
14.4
|
1.0
|
|
OD1
|
A:ASP357
|
4.7
|
27.3
|
1.0
|
|
CG
|
A:ASP357
|
4.7
|
26.5
|
1.0
|
|
HB2
|
A:ARG353
|
4.8
|
19.0
|
1.0
|
|
H
|
A:ALA356
|
4.8
|
17.2
|
1.0
|
|
HA
|
A:SER354
|
4.8
|
19.2
|
0.6
|
|
N
|
A:SER354
|
4.9
|
15.8
|
0.4
|
|
N
|
A:SER354
|
4.9
|
15.7
|
0.6
|
|
HZ
|
A:PHE418
|
4.9
|
17.3
|
1.0
|
|
O
|
A:ALA356
|
4.9
|
14.2
|
1.0
|
|
CB
|
A:GLU362
|
4.9
|
16.9
|
1.0
|
|
O
|
A:HOH808
|
5.0
|
30.6
|
1.0
|
|
HB3
|
A:ARG353
|
5.0
|
19.0
|
1.0
|
|
HA
|
A:SER354
|
5.0
|
19.2
|
0.4
|
|
N
|
A:ALA356
|
5.0
|
14.3
|
1.0
|
|
Sodium binding site 2 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 2 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:21.2
occ:1.00
|
HB2
|
A:PRO281
|
2.4
|
14.1
|
1.0
|
|
HA
|
A:VAL346
|
2.5
|
14.5
|
1.0
|
|
O
|
A:TYR345
|
2.7
|
15.8
|
1.0
|
|
O
|
A:HOH758
|
2.8
|
13.0
|
1.0
|
|
HG2
|
A:PRO281
|
2.8
|
17.0
|
1.0
|
|
OH
|
A:TYR331
|
2.8
|
13.8
|
1.0
|
|
HE1
|
A:TYR331
|
3.0
|
15.2
|
1.0
|
|
HG22
|
A:ILE347
|
3.1
|
19.1
|
1.0
|
|
H
|
A:ILE347
|
3.1
|
14.9
|
1.0
|
|
CB
|
A:PRO281
|
3.2
|
11.7
|
1.0
|
|
CA
|
A:VAL346
|
3.4
|
12.1
|
1.0
|
|
CG
|
A:PRO281
|
3.4
|
14.2
|
1.0
|
|
HH
|
A:TYR331
|
3.4
|
16.6
|
1.0
|
|
HB2
|
A:HIS250
|
3.4
|
24.1
|
1.0
|
|
HD2
|
A:PRO281
|
3.5
|
15.0
|
1.0
|
|
C
|
A:TYR345
|
3.5
|
14.4
|
1.0
|
|
HB3
|
A:PRO281
|
3.6
|
14.1
|
1.0
|
|
N
|
A:ILE347
|
3.6
|
12.4
|
1.0
|
|
HB3
|
A:HIS250
|
3.7
|
24.1
|
1.0
|
|
CE1
|
A:TYR331
|
3.7
|
12.6
|
1.0
|
|
HD2
|
A:HIS250
|
3.7
|
21.7
|
1.0
|
|
CZ
|
A:TYR331
|
3.7
|
15.4
|
1.0
|
|
HD11
|
A:ILE286
|
3.7
|
17.4
|
1.0
|
|
N
|
A:VAL346
|
3.8
|
13.5
|
1.0
|
|
C
|
A:VAL346
|
3.8
|
14.2
|
1.0
|
|
CB
|
A:HIS250
|
3.9
|
20.1
|
1.0
|
|
HD12
|
A:ILE286
|
3.9
|
17.4
|
1.0
|
|
CD
|
A:PRO281
|
4.0
|
12.5
|
1.0
|
|
CG2
|
A:ILE347
|
4.0
|
15.9
|
1.0
|
|
HD13
|
A:ILE286
|
4.0
|
17.4
|
1.0
|
|
CD2
|
A:HIS250
|
4.1
|
18.1
|
1.0
|
|
CD1
|
A:ILE286
|
4.1
|
14.4
|
1.0
|
|
CG
|
A:HIS250
|
4.2
|
17.1
|
1.0
|
|
HG3
|
A:GLU344
|
4.2
|
17.0
|
1.0
|
|
HG3
|
A:PRO281
|
4.2
|
17.0
|
1.0
|
|
HG13
|
A:VAL346
|
4.3
|
17.8
|
1.0
|
|
HG23
|
A:ILE347
|
4.4
|
19.1
|
1.0
|
|
HG22
|
A:VAL346
|
4.4
|
17.0
|
1.0
|
|
CA
|
A:PRO281
|
4.4
|
12.4
|
1.0
|
|
O
|
A:PRO281
|
4.5
|
12.1
|
1.0
|
|
HG21
|
A:ILE347
|
4.5
|
19.1
|
1.0
|
|
CB
|
A:VAL346
|
4.5
|
13.6
|
1.0
|
|
H
|
A:VAL346
|
4.6
|
16.2
|
1.0
|
|
OE2
|
A:GLU344
|
4.6
|
14.6
|
1.0
|
|
C
|
A:PRO281
|
4.7
|
13.2
|
1.0
|
|
HB
|
A:ILE347
|
4.7
|
16.6
|
1.0
|
|
N
|
A:PRO281
|
4.7
|
12.2
|
1.0
|
|
HD3
|
A:PRO281
|
4.7
|
15.0
|
1.0
|
|
H
|
A:TYR345
|
4.7
|
17.7
|
1.0
|
|
CB
|
A:ILE347
|
4.8
|
13.8
|
1.0
|
|
CA
|
A:ILE347
|
4.8
|
15.1
|
1.0
|
|
CA
|
A:TYR345
|
4.8
|
15.3
|
1.0
|
|
O
|
A:VAL346
|
4.8
|
13.8
|
1.0
|
|
CG1
|
A:VAL346
|
4.8
|
14.8
|
1.0
|
|
CG2
|
A:VAL346
|
4.9
|
14.1
|
1.0
|
|
N
|
A:TYR345
|
4.9
|
14.7
|
1.0
|
|
Sodium binding site 3 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 3 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:17.9
occ:1.00
|
H
|
A:SER283
|
2.1
|
14.8
|
1.0
|
|
O
|
A:PRO281
|
2.8
|
12.1
|
1.0
|
|
O
|
A:ILE347
|
2.8
|
14.9
|
1.0
|
|
HG23
|
A:ILE347
|
2.9
|
19.1
|
1.0
|
|
O
|
A:HOH639
|
2.9
|
19.9
|
1.0
|
|
N
|
A:SER283
|
2.9
|
12.3
|
1.0
|
|
HA
|
A:ASP282
|
2.9
|
15.8
|
1.0
|
|
HD1
|
A:PHE349
|
3.0
|
21.4
|
1.0
|
|
HB3
|
A:SER283
|
3.2
|
17.3
|
1.0
|
|
HD12
|
A:ILE280
|
3.2
|
16.5
|
1.0
|
|
HB2
|
A:PHE349
|
3.3
|
16.1
|
1.0
|
|
OG
|
A:SER283
|
3.3
|
14.0
|
1.0
|
|
HD11
|
A:ILE280
|
3.5
|
16.5
|
1.0
|
|
CB
|
A:SER283
|
3.6
|
14.4
|
1.0
|
|
HG13
|
A:ILE280
|
3.7
|
13.8
|
1.0
|
|
HG21
|
A:THR414
|
3.7
|
15.6
|
1.0
|
|
CA
|
A:ASP282
|
3.7
|
13.2
|
1.0
|
|
CD1
|
A:ILE280
|
3.7
|
13.7
|
1.0
|
|
O
|
A:HOH758
|
3.8
|
13.0
|
1.0
|
|
C
|
A:ASP282
|
3.8
|
12.9
|
1.0
|
|
CG2
|
A:ILE347
|
3.8
|
15.9
|
1.0
|
|
CA
|
A:SER283
|
3.8
|
15.0
|
1.0
|
|
C
|
A:PRO281
|
3.9
|
13.2
|
1.0
|
|
HG
|
A:SER283
|
3.9
|
16.8
|
1.0
|
|
CD1
|
A:PHE349
|
3.9
|
17.8
|
1.0
|
|
H
|
A:PHE349
|
4.0
|
15.7
|
1.0
|
|
HG22
|
A:THR414
|
4.0
|
15.6
|
1.0
|
|
C
|
A:ILE347
|
4.0
|
13.2
|
1.0
|
|
HA
|
A:PHE349
|
4.1
|
15.4
|
1.0
|
|
CB
|
A:PHE349
|
4.1
|
13.4
|
1.0
|
|
N
|
A:PHE349
|
4.2
|
13.1
|
1.0
|
|
HG21
|
A:ILE347
|
4.2
|
19.1
|
1.0
|
|
HG22
|
A:ILE347
|
4.2
|
19.1
|
1.0
|
|
HG12
|
A:ILE347
|
4.2
|
20.1
|
1.0
|
|
CG1
|
A:ILE280
|
4.2
|
11.5
|
1.0
|
|
N
|
A:ASP282
|
4.3
|
11.4
|
1.0
|
|
CG2
|
A:THR414
|
4.3
|
13.0
|
1.0
|
|
HA
|
A:SER283
|
4.4
|
18.0
|
1.0
|
|
CA
|
A:PHE349
|
4.4
|
12.8
|
1.0
|
|
OD1
|
A:ASP282
|
4.5
|
15.5
|
1.0
|
|
HB2
|
A:SER283
|
4.5
|
17.3
|
1.0
|
|
CG
|
A:PHE349
|
4.5
|
16.4
|
1.0
|
|
H
|
A:ILE347
|
4.5
|
14.9
|
1.0
|
|
HB
|
A:ILE280
|
4.6
|
13.4
|
1.0
|
|
H
|
A:GLU284
|
4.6
|
15.5
|
1.0
|
|
HD13
|
A:ILE280
|
4.6
|
16.5
|
1.0
|
|
HA
|
A:PRO348
|
4.6
|
16.4
|
1.0
|
|
HG23
|
A:THR414
|
4.7
|
15.6
|
1.0
|
|
CB
|
A:ILE347
|
4.7
|
13.8
|
1.0
|
|
CA
|
A:ILE347
|
4.8
|
15.1
|
1.0
|
|
C
|
A:PRO348
|
4.8
|
15.2
|
1.0
|
|
HB3
|
A:PHE349
|
4.8
|
16.1
|
1.0
|
|
CG1
|
A:ILE347
|
4.9
|
16.7
|
1.0
|
|
CB
|
A:ASP282
|
5.0
|
14.5
|
1.0
|
|
HE1
|
A:PHE349
|
5.0
|
24.9
|
1.0
|
|
CE1
|
A:PHE349
|
5.0
|
20.7
|
1.0
|
|
HG12
|
A:ILE280
|
5.0
|
13.8
|
1.0
|
|
N
|
A:PRO348
|
5.0
|
14.9
|
1.0
|
|
Sodium binding site 4 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 4 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:24.7
occ:1.00
|
H
|
A:ASN313
|
2.5
|
26.2
|
1.0
|
|
HB3
|
A:SER312
|
2.7
|
24.2
|
1.0
|
|
O
|
A:MET330
|
2.8
|
15.3
|
1.0
|
|
HD2
|
A:PHE311
|
2.8
|
17.0
|
1.0
|
|
O
|
A:HOH765
|
2.8
|
23.1
|
1.0
|
|
O
|
A:HOH641
|
2.9
|
22.1
|
1.0
|
|
H
|
A:SER312
|
2.9
|
20.3
|
1.0
|
|
H
|
A:MET330
|
3.1
|
18.6
|
1.0
|
|
N
|
A:ASN313
|
3.2
|
21.8
|
1.0
|
|
N
|
A:SER312
|
3.4
|
16.9
|
1.0
|
|
OD1
|
A:ASN313
|
3.5
|
21.0
|
1.0
|
|
HD21
|
A:ASN313
|
3.5
|
27.4
|
1.0
|
|
CB
|
A:SER312
|
3.6
|
20.1
|
1.0
|
|
HB3
|
A:PHE311
|
3.6
|
18.4
|
1.0
|
|
CG
|
A:ASN313
|
3.6
|
22.1
|
1.0
|
|
N
|
A:MET330
|
3.6
|
15.4
|
1.0
|
|
ND2
|
A:ASN313
|
3.6
|
22.8
|
1.0
|
|
CD2
|
A:PHE311
|
3.7
|
14.2
|
1.0
|
|
C
|
A:MET330
|
3.8
|
15.5
|
1.0
|
|
O
|
A:ASN313
|
3.8
|
17.4
|
1.0
|
|
CA
|
A:SER312
|
3.8
|
15.4
|
1.0
|
|
HB2
|
A:SER312
|
3.9
|
24.2
|
1.0
|
|
C
|
A:SER312
|
3.9
|
19.1
|
1.0
|
|
HA
|
A:GLN329
|
4.0
|
20.3
|
1.0
|
|
HD22
|
A:ASN313
|
4.0
|
27.4
|
1.0
|
|
CA
|
A:ASN313
|
4.1
|
20.7
|
1.0
|
|
CA
|
A:MET330
|
4.2
|
15.4
|
1.0
|
|
HB3
|
A:MET330
|
4.2
|
23.1
|
1.0
|
|
C
|
A:GLN329
|
4.2
|
13.9
|
1.0
|
|
CB
|
A:PHE311
|
4.3
|
15.3
|
1.0
|
|
C
|
A:PHE311
|
4.3
|
17.1
|
1.0
|
|
HA
|
A:PHE311
|
4.3
|
17.8
|
1.0
|
|
C
|
A:ASN313
|
4.3
|
19.4
|
1.0
|
|
CB
|
A:ASN313
|
4.3
|
22.6
|
1.0
|
|
O
|
A:HOH729
|
4.3
|
18.3
|
1.0
|
|
HE2
|
A:PHE311
|
4.5
|
17.8
|
1.0
|
|
CG
|
A:PHE311
|
4.5
|
14.6
|
1.0
|
|
HB3
|
A:GLN329
|
4.5
|
19.2
|
1.0
|
|
O
|
A:HOH719
|
4.5
|
27.9
|
1.0
|
|
HB3
|
A:ASN313
|
4.5
|
27.2
|
1.0
|
|
CA
|
A:PHE311
|
4.6
|
14.8
|
1.0
|
|
CE2
|
A:PHE311
|
4.6
|
14.8
|
1.0
|
|
CA
|
A:GLN329
|
4.6
|
16.9
|
1.0
|
|
OG
|
A:SER312
|
4.6
|
23.6
|
1.0
|
|
O
|
A:HOH735
|
4.7
|
27.1
|
1.0
|
|
CB
|
A:MET330
|
4.7
|
19.2
|
1.0
|
|
HA
|
A:SER312
|
4.8
|
18.5
|
1.0
|
|
OE1
|
A:GLN329
|
4.9
|
21.5
|
1.0
|
|
N
|
A:TYR331
|
5.0
|
15.4
|
1.0
|
|
Sodium binding site 5 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 5 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na507
b:23.5
occ:1.00
|
H
|
A:GLN329
|
2.1
|
20.1
|
1.0
|
|
HB2
|
A:GLN329
|
2.6
|
19.2
|
1.0
|
|
O
|
A:PRO326
|
2.8
|
17.4
|
1.0
|
|
O
|
A:VAL346
|
2.8
|
13.8
|
1.0
|
|
HG2
|
A:GLN329
|
2.9
|
22.6
|
1.0
|
|
N
|
A:GLN329
|
2.9
|
16.7
|
1.0
|
|
HB
|
A:VAL346
|
3.0
|
16.4
|
1.0
|
|
HA
|
A:PHE327
|
3.0
|
21.1
|
1.0
|
|
HB3
|
A:TYR345
|
3.1
|
17.2
|
1.0
|
|
H
|
A:GLY328
|
3.2
|
17.6
|
1.0
|
|
H
|
A:VAL346
|
3.2
|
16.2
|
1.0
|
|
CB
|
A:GLN329
|
3.2
|
16.0
|
1.0
|
|
N
|
A:GLY328
|
3.3
|
14.6
|
1.0
|
|
C
|
A:PHE327
|
3.4
|
17.0
|
1.0
|
|
CG
|
A:GLN329
|
3.5
|
18.8
|
1.0
|
|
N
|
A:VAL346
|
3.5
|
13.5
|
1.0
|
|
CA
|
A:PHE327
|
3.5
|
17.5
|
1.0
|
|
C
|
A:PRO326
|
3.5
|
17.9
|
1.0
|
|
CA
|
A:GLN329
|
3.6
|
16.9
|
1.0
|
|
C
|
A:VAL346
|
3.6
|
14.2
|
1.0
|
|
HD3
|
A:PRO348
|
3.7
|
18.1
|
1.0
|
|
HB3
|
A:PHE253
|
3.7
|
18.9
|
1.0
|
|
HG3
|
A:GLN329
|
3.8
|
22.6
|
1.0
|
|
CB
|
A:VAL346
|
3.8
|
13.6
|
1.0
|
|
N
|
A:PHE327
|
3.8
|
16.1
|
1.0
|
|
CA
|
A:VAL346
|
3.8
|
12.1
|
1.0
|
|
O
|
A:GLN329
|
3.9
|
16.5
|
1.0
|
|
C
|
A:GLY328
|
3.9
|
17.7
|
1.0
|
|
CB
|
A:TYR345
|
4.0
|
14.3
|
1.0
|
|
O
|
A:PHE327
|
4.1
|
18.2
|
1.0
|
|
HB3
|
A:GLN329
|
4.1
|
19.2
|
1.0
|
|
CA
|
A:GLY328
|
4.1
|
16.4
|
1.0
|
|
O
|
A:PHE253
|
4.1
|
16.4
|
1.0
|
|
C
|
A:GLN329
|
4.2
|
13.9
|
1.0
|
|
C
|
A:TYR345
|
4.2
|
14.4
|
1.0
|
|
HB2
|
A:TYR345
|
4.3
|
17.2
|
1.0
|
|
HD2
|
A:PHE253
|
4.3
|
21.2
|
1.0
|
|
HG23
|
A:VAL346
|
4.4
|
17.0
|
1.0
|
|
HA
|
A:TYR345
|
4.4
|
18.4
|
1.0
|
|
HA
|
A:GLN329
|
4.4
|
20.3
|
1.0
|
|
HA2
|
A:GLY328
|
4.5
|
19.7
|
1.0
|
|
CA
|
A:TYR345
|
4.5
|
15.3
|
1.0
|
|
H
|
A:PHE327
|
4.5
|
19.3
|
1.0
|
|
CD
|
A:PRO348
|
4.6
|
15.1
|
1.0
|
|
HE21
|
A:GLN329
|
4.6
|
24.6
|
1.0
|
|
HG12
|
A:VAL346
|
4.7
|
17.8
|
1.0
|
|
CB
|
A:PHE253
|
4.7
|
15.8
|
1.0
|
|
CG2
|
A:VAL346
|
4.7
|
14.1
|
1.0
|
|
HD2
|
A:PRO348
|
4.7
|
18.1
|
1.0
|
|
HA
|
A:PRO326
|
4.8
|
22.6
|
1.0
|
|
CD
|
A:GLN329
|
4.8
|
20.7
|
1.0
|
|
CA
|
A:PRO326
|
4.8
|
18.8
|
1.0
|
|
N
|
A:ILE347
|
4.8
|
12.4
|
1.0
|
|
HA
|
A:VAL346
|
4.8
|
14.5
|
1.0
|
|
HA
|
A:ILE347
|
4.8
|
18.2
|
1.0
|
|
CG1
|
A:VAL346
|
4.8
|
14.8
|
1.0
|
|
O
|
A:SER325
|
4.9
|
19.3
|
1.0
|
|
HB2
|
A:PHE253
|
4.9
|
18.9
|
1.0
|
|
HG3
|
A:PRO348
|
4.9
|
18.0
|
1.0
|
|
HA3
|
A:GLY328
|
4.9
|
19.7
|
1.0
|
|
HD1
|
A:TYR345
|
4.9
|
17.8
|
1.0
|
|
HG2
|
A:PRO348
|
4.9
|
18.0
|
1.0
|
|
CB
|
A:PHE327
|
5.0
|
16.5
|
1.0
|
|
Sodium binding site 6 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 6 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:18.9
occ:1.00
|
H
|
B:SER283
|
2.1
|
14.5
|
1.0
|
|
O
|
B:PRO281
|
2.8
|
11.8
|
1.0
|
|
HG23
|
B:ILE347
|
2.8
|
17.7
|
1.0
|
|
O
|
B:ILE347
|
2.8
|
13.9
|
1.0
|
|
HA
|
B:ASP282
|
2.9
|
13.4
|
1.0
|
|
N
|
B:SER283
|
3.0
|
12.1
|
1.0
|
|
O
|
B:HOH664
|
3.0
|
20.0
|
1.0
|
|
HD1
|
B:PHE349
|
3.1
|
21.9
|
1.0
|
|
HD12
|
B:ILE280
|
3.1
|
16.8
|
1.0
|
|
HB3
|
B:SER283
|
3.1
|
17.3
|
1.0
|
|
HB2
|
B:PHE349
|
3.2
|
18.2
|
1.0
|
|
HD11
|
B:ILE280
|
3.4
|
16.8
|
1.0
|
|
OG
|
B:SER283
|
3.4
|
13.2
|
1.0
|
|
CB
|
B:SER283
|
3.6
|
14.4
|
1.0
|
|
CD1
|
B:ILE280
|
3.6
|
14.0
|
1.0
|
|
HG13
|
B:ILE280
|
3.7
|
14.0
|
1.0
|
|
HG21
|
B:THR414
|
3.7
|
16.3
|
1.0
|
|
CA
|
B:ASP282
|
3.7
|
11.2
|
1.0
|
|
O
|
B:HOH768
|
3.7
|
13.3
|
1.0
|
|
CG2
|
B:ILE347
|
3.8
|
14.8
|
1.0
|
|
C
|
B:ASP282
|
3.8
|
11.6
|
1.0
|
|
CA
|
B:SER283
|
3.9
|
11.2
|
1.0
|
|
C
|
B:PRO281
|
3.9
|
12.1
|
1.0
|
|
H
|
B:PHE349
|
3.9
|
17.3
|
1.0
|
|
CD1
|
B:PHE349
|
3.9
|
18.2
|
1.0
|
|
HG22
|
B:THR414
|
4.0
|
16.3
|
1.0
|
|
C
|
B:ILE347
|
4.0
|
13.5
|
1.0
|
|
HG
|
B:SER283
|
4.1
|
15.8
|
1.0
|
|
CB
|
B:PHE349
|
4.1
|
15.1
|
1.0
|
|
HA
|
B:PHE349
|
4.1
|
14.7
|
1.0
|
|
HG22
|
B:ILE347
|
4.1
|
17.7
|
1.0
|
|
N
|
B:PHE349
|
4.1
|
14.4
|
1.0
|
|
HG21
|
B:ILE347
|
4.2
|
17.7
|
1.0
|
|
CG1
|
B:ILE280
|
4.2
|
11.6
|
1.0
|
|
HG12
|
B:ILE347
|
4.2
|
17.0
|
1.0
|
|
N
|
B:ASP282
|
4.2
|
11.2
|
1.0
|
|
CG2
|
B:THR414
|
4.3
|
13.6
|
1.0
|
|
CA
|
B:PHE349
|
4.4
|
12.2
|
1.0
|
|
HA
|
B:SER283
|
4.4
|
13.5
|
1.0
|
|
HB
|
B:ILE280
|
4.5
|
14.8
|
1.0
|
|
HB2
|
B:SER283
|
4.5
|
17.3
|
1.0
|
|
HD13
|
B:ILE280
|
4.5
|
16.8
|
1.0
|
|
CG
|
B:PHE349
|
4.5
|
14.2
|
1.0
|
|
H
|
B:ILE347
|
4.6
|
15.6
|
1.0
|
|
OD1
|
B:ASP282
|
4.6
|
13.0
|
1.0
|
|
H
|
B:GLU284
|
4.6
|
14.3
|
1.0
|
|
HG23
|
B:THR414
|
4.6
|
16.3
|
1.0
|
|
CB
|
B:ILE347
|
4.7
|
14.8
|
1.0
|
|
HA
|
B:PRO348
|
4.7
|
17.9
|
1.0
|
|
CA
|
B:ILE347
|
4.8
|
14.6
|
1.0
|
|
C
|
B:PRO348
|
4.8
|
16.2
|
1.0
|
|
HB3
|
B:PHE349
|
4.8
|
18.2
|
1.0
|
|
CG1
|
B:ILE347
|
4.9
|
14.1
|
1.0
|
|
CB
|
B:ILE280
|
4.9
|
12.3
|
1.0
|
|
HG12
|
B:ILE280
|
5.0
|
14.0
|
1.0
|
|
CB
|
B:ASP282
|
5.0
|
12.0
|
1.0
|
|
N
|
B:PRO348
|
5.0
|
12.3
|
1.0
|
|
Sodium binding site 7 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 7 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na504
b:23.7
occ:1.00
|
H
|
B:ASN313
|
2.5
|
23.3
|
1.0
|
|
HB3
|
B:SER312
|
2.7
|
22.4
|
1.0
|
|
O
|
B:MET330
|
2.8
|
14.7
|
1.0
|
|
HD2
|
B:PHE311
|
2.8
|
19.7
|
1.0
|
|
O
|
B:HOH654
|
2.8
|
20.3
|
1.0
|
|
H
|
B:SER312
|
2.9
|
20.8
|
1.0
|
|
O
|
B:HOH783
|
2.9
|
21.7
|
1.0
|
|
H
|
B:MET330
|
3.2
|
19.0
|
1.0
|
|
N
|
B:ASN313
|
3.2
|
19.4
|
1.0
|
|
N
|
B:SER312
|
3.4
|
17.3
|
1.0
|
|
OD1
|
B:ASN313
|
3.5
|
18.9
|
1.0
|
|
CG
|
B:ASN313
|
3.5
|
18.4
|
1.0
|
|
HB3
|
B:PHE311
|
3.5
|
20.0
|
1.0
|
|
HD21
|
B:ASN313
|
3.6
|
28.2
|
1.0
|
|
CB
|
B:SER312
|
3.6
|
18.6
|
1.0
|
|
ND2
|
B:ASN313
|
3.6
|
23.5
|
1.0
|
|
N
|
B:MET330
|
3.6
|
15.8
|
1.0
|
|
CD2
|
B:PHE311
|
3.7
|
16.4
|
1.0
|
|
C
|
B:MET330
|
3.8
|
14.5
|
1.0
|
|
O
|
B:ASN313
|
3.8
|
17.1
|
1.0
|
|
CA
|
B:SER312
|
3.8
|
16.8
|
1.0
|
|
HB2
|
B:SER312
|
3.9
|
22.4
|
1.0
|
|
C
|
B:SER312
|
3.9
|
17.9
|
1.0
|
|
HA
|
B:GLN329
|
4.0
|
18.0
|
1.0
|
|
HD22
|
B:ASN313
|
4.0
|
28.2
|
1.0
|
|
HB3
|
B:MET330
|
4.1
|
18.6
|
1.0
|
|
CA
|
B:ASN313
|
4.1
|
17.7
|
1.0
|
|
CA
|
B:MET330
|
4.2
|
14.1
|
1.0
|
|
C
|
B:GLN329
|
4.2
|
15.6
|
1.0
|
|
HA
|
B:PHE311
|
4.3
|
17.6
|
1.0
|
|
CB
|
B:PHE311
|
4.3
|
16.6
|
1.0
|
|
C
|
B:PHE311
|
4.3
|
15.0
|
1.0
|
|
CB
|
B:ASN313
|
4.3
|
21.0
|
1.0
|
|
C
|
B:ASN313
|
4.3
|
15.0
|
1.0
|
|
HB3
|
B:GLN329
|
4.4
|
20.9
|
1.0
|
|
O
|
B:HOH727
|
4.4
|
17.5
|
1.0
|
|
CG
|
B:PHE311
|
4.5
|
14.4
|
1.0
|
|
HE2
|
B:PHE311
|
4.5
|
17.2
|
1.0
|
|
CA
|
B:PHE311
|
4.5
|
14.6
|
1.0
|
|
CA
|
B:GLN329
|
4.6
|
15.0
|
1.0
|
|
HB3
|
B:ASN313
|
4.6
|
25.2
|
1.0
|
|
CE2
|
B:PHE311
|
4.6
|
14.3
|
1.0
|
|
O
|
B:HOH719
|
4.6
|
26.2
|
1.0
|
|
OG
|
B:SER312
|
4.7
|
21.9
|
1.0
|
|
CB
|
B:MET330
|
4.7
|
15.5
|
1.0
|
|
HG
|
B:SER312
|
4.7
|
26.3
|
1.0
|
|
HA
|
B:SER312
|
4.8
|
20.2
|
1.0
|
|
OE1
|
B:GLN329
|
4.8
|
20.4
|
1.0
|
|
O
|
B:HOH803
|
5.0
|
32.1
|
1.0
|
|
N
|
B:TYR331
|
5.0
|
12.5
|
1.0
|
|
Sodium binding site 8 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 8 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na505
b:20.9
occ:1.00
|
H
|
B:GLN329
|
2.1
|
17.2
|
1.0
|
|
O
|
B:VAL346
|
2.7
|
14.9
|
1.0
|
|
O
|
B:PRO326
|
2.8
|
16.1
|
1.0
|
|
HB2
|
B:GLN329
|
2.8
|
20.9
|
1.0
|
|
N
|
B:GLN329
|
3.0
|
14.3
|
1.0
|
|
HB3
|
B:TYR345
|
3.0
|
19.5
|
1.0
|
|
HA
|
B:PHE327
|
3.0
|
18.8
|
1.0
|
|
HG2
|
B:GLN329
|
3.0
|
18.7
|
1.0
|
|
HB
|
B:VAL346
|
3.1
|
16.0
|
1.0
|
|
H
|
B:GLY328
|
3.1
|
18.1
|
1.0
|
|
H
|
B:VAL346
|
3.3
|
15.8
|
1.0
|
|
N
|
B:GLY328
|
3.3
|
15.0
|
1.0
|
|
CB
|
B:GLN329
|
3.4
|
17.4
|
1.0
|
|
C
|
B:PHE327
|
3.4
|
17.0
|
1.0
|
|
N
|
B:VAL346
|
3.5
|
13.2
|
1.0
|
|
CA
|
B:PHE327
|
3.5
|
15.6
|
1.0
|
|
C
|
B:VAL346
|
3.6
|
13.7
|
1.0
|
|
HB3
|
B:PHE253
|
3.6
|
17.5
|
1.0
|
|
C
|
B:PRO326
|
3.6
|
16.6
|
1.0
|
|
CG
|
B:GLN329
|
3.6
|
15.6
|
1.0
|
|
CA
|
B:GLN329
|
3.7
|
15.0
|
1.0
|
|
HD3
|
B:PRO348
|
3.7
|
16.5
|
1.0
|
|
CA
|
B:VAL346
|
3.8
|
12.7
|
1.0
|
|
CB
|
B:TYR345
|
3.8
|
16.2
|
1.0
|
|
CB
|
B:VAL346
|
3.9
|
13.3
|
1.0
|
|
N
|
B:PHE327
|
3.9
|
16.8
|
1.0
|
|
O
|
B:GLN329
|
3.9
|
14.8
|
1.0
|
|
C
|
B:GLY328
|
3.9
|
15.2
|
1.0
|
|
O
|
B:PHE253
|
3.9
|
15.8
|
1.0
|
|
HG3
|
B:GLN329
|
4.0
|
18.7
|
1.0
|
|
HB2
|
B:TYR345
|
4.1
|
19.5
|
1.0
|
|
CA
|
B:GLY328
|
4.1
|
16.1
|
1.0
|
|
O
|
B:PHE327
|
4.1
|
16.5
|
1.0
|
|
C
|
B:TYR345
|
4.2
|
12.3
|
1.0
|
|
C
|
B:GLN329
|
4.2
|
15.6
|
1.0
|
|
HB3
|
B:GLN329
|
4.3
|
20.9
|
1.0
|
|
HA
|
B:TYR345
|
4.4
|
16.4
|
1.0
|
|
CA
|
B:TYR345
|
4.4
|
13.6
|
1.0
|
|
HG23
|
B:VAL346
|
4.4
|
19.8
|
1.0
|
|
HA2
|
B:GLY328
|
4.4
|
19.4
|
1.0
|
|
HD2
|
B:PHE253
|
4.4
|
19.8
|
1.0
|
|
HA
|
B:GLN329
|
4.5
|
18.0
|
1.0
|
|
CB
|
B:PHE253
|
4.5
|
14.6
|
1.0
|
|
CD
|
B:PRO348
|
4.6
|
13.8
|
1.0
|
|
H
|
B:PHE327
|
4.6
|
20.2
|
1.0
|
|
HE21
|
B:GLN329
|
4.7
|
22.5
|
1.0
|
|
HG12
|
B:VAL346
|
4.7
|
18.2
|
1.0
|
|
HB2
|
B:PHE253
|
4.7
|
17.5
|
1.0
|
|
HD2
|
B:PRO348
|
4.8
|
16.5
|
1.0
|
|
CG2
|
B:VAL346
|
4.8
|
16.5
|
1.0
|
|
N
|
B:ILE347
|
4.8
|
13.0
|
1.0
|
|
HA
|
B:VAL346
|
4.8
|
15.3
|
1.0
|
|
HA
|
B:ILE347
|
4.8
|
17.5
|
1.0
|
|
HD1
|
B:TYR345
|
4.8
|
16.2
|
1.0
|
|
HA
|
B:PRO326
|
4.8
|
19.9
|
1.0
|
|
C
|
B:PHE253
|
4.9
|
13.6
|
1.0
|
|
CA
|
B:PRO326
|
4.9
|
16.6
|
1.0
|
|
CG1
|
B:VAL346
|
4.9
|
15.1
|
1.0
|
|
HA3
|
B:GLY328
|
4.9
|
19.4
|
1.0
|
|
HG3
|
B:PRO348
|
4.9
|
17.7
|
1.0
|
|
CD
|
B:GLN329
|
4.9
|
18.1
|
1.0
|
|
HG2
|
B:PRO348
|
5.0
|
17.7
|
1.0
|
|
CG
|
B:TYR345
|
5.0
|
15.0
|
1.0
|
|
CB
|
B:PHE327
|
5.0
|
17.2
|
1.0
|
|
Sodium binding site 9 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 9 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na506
b:19.5
occ:1.00
|
HB2
|
B:PRO281
|
2.5
|
12.8
|
1.0
|
|
HA
|
B:VAL346
|
2.5
|
15.3
|
1.0
|
|
O
|
B:TYR345
|
2.7
|
13.4
|
1.0
|
|
O
|
B:HOH768
|
2.8
|
13.3
|
1.0
|
|
HG2
|
B:PRO281
|
2.8
|
12.8
|
1.0
|
|
OH
|
B:TYR331
|
2.8
|
13.2
|
1.0
|
|
HG22
|
B:ILE347
|
3.0
|
17.7
|
1.0
|
|
HE2
|
B:TYR331
|
3.1
|
13.4
|
1.0
|
|
H
|
B:ILE347
|
3.1
|
15.6
|
1.0
|
|
CB
|
B:PRO281
|
3.2
|
10.6
|
1.0
|
|
HB2
|
B:HIS250
|
3.4
|
21.9
|
1.0
|
|
CA
|
B:VAL346
|
3.4
|
12.7
|
1.0
|
|
CG
|
B:PRO281
|
3.4
|
10.6
|
1.0
|
|
HH
|
B:TYR331
|
3.4
|
15.8
|
1.0
|
|
HD2
|
B:PRO281
|
3.5
|
15.1
|
1.0
|
|
C
|
B:TYR345
|
3.5
|
12.3
|
1.0
|
|
N
|
B:ILE347
|
3.6
|
13.0
|
1.0
|
|
HB3
|
B:HIS250
|
3.6
|
21.9
|
1.0
|
|
HB3
|
B:PRO281
|
3.7
|
12.8
|
1.0
|
|
CE2
|
B:TYR331
|
3.7
|
11.2
|
1.0
|
|
CZ
|
B:TYR331
|
3.7
|
11.6
|
1.0
|
|
HD11
|
B:ILE286
|
3.7
|
17.4
|
1.0
|
|
N
|
B:VAL346
|
3.8
|
13.2
|
1.0
|
|
C
|
B:VAL346
|
3.8
|
13.7
|
1.0
|
|
HD2
|
B:HIS250
|
3.9
|
23.6
|
1.0
|
|
CB
|
B:HIS250
|
3.9
|
18.2
|
1.0
|
|
HD12
|
B:ILE286
|
4.0
|
17.4
|
1.0
|
|
CD
|
B:PRO281
|
4.0
|
12.5
|
1.0
|
|
CG2
|
B:ILE347
|
4.0
|
14.8
|
1.0
|
|
HD13
|
B:ILE286
|
4.1
|
17.4
|
1.0
|
|
CD1
|
B:ILE286
|
4.1
|
14.4
|
1.0
|
|
CD2
|
B:HIS250
|
4.2
|
19.6
|
1.0
|
|
CG
|
B:HIS250
|
4.2
|
16.8
|
1.0
|
|
HG3
|
B:PRO281
|
4.2
|
12.8
|
1.0
|
|
HG13
|
B:VAL346
|
4.2
|
18.2
|
1.0
|
|
HG3
|
B:GLU344
|
4.2
|
14.4
|
1.0
|
|
HG22
|
B:VAL346
|
4.3
|
19.8
|
1.0
|
|
HG21
|
B:ILE347
|
4.4
|
17.7
|
1.0
|
|
HG23
|
B:ILE347
|
4.4
|
17.7
|
1.0
|
|
CA
|
B:PRO281
|
4.4
|
10.7
|
1.0
|
|
O
|
B:PRO281
|
4.4
|
11.8
|
1.0
|
|
CB
|
B:VAL346
|
4.6
|
13.3
|
1.0
|
|
H
|
B:VAL346
|
4.6
|
15.8
|
1.0
|
|
OE2
|
B:GLU344
|
4.6
|
13.0
|
1.0
|
|
HB
|
B:ILE347
|
4.6
|
17.8
|
1.0
|
|
C
|
B:PRO281
|
4.7
|
12.1
|
1.0
|
|
N
|
B:PRO281
|
4.7
|
10.1
|
1.0
|
|
H
|
B:TYR345
|
4.7
|
15.8
|
1.0
|
|
HD3
|
B:PRO281
|
4.7
|
15.1
|
1.0
|
|
CB
|
B:ILE347
|
4.7
|
14.8
|
1.0
|
|
CA
|
B:ILE347
|
4.8
|
14.6
|
1.0
|
|
CG1
|
B:VAL346
|
4.8
|
15.1
|
1.0
|
|
CA
|
B:TYR345
|
4.8
|
13.6
|
1.0
|
|
O
|
B:VAL346
|
4.8
|
14.9
|
1.0
|
|
CG2
|
B:VAL346
|
4.9
|
16.5
|
1.0
|
|
N
|
B:TYR345
|
4.9
|
13.2
|
1.0
|
|
Sodium binding site 10 out
of 10 in 9mg3
Go back to
Sodium Binding Sites List in 9mg3
Sodium binding site 10 out
of 10 in the Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp
 Mono view
 Stereo pair view
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A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure of Kluyveromyces Lactis Mrna Cap (Guanine-N7) Methyltransferase, ABD1, in Complex with Sinefungin and Gtp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na507
b:22.1
occ:1.00
|
O
|
B:HOH771
|
2.7
|
22.5
|
1.0
|
|
HE2
|
B:PHE418
|
2.7
|
18.6
|
1.0
|
|
O
|
B:MET361
|
2.8
|
16.6
|
1.0
|
|
O
|
B:ARG353
|
2.8
|
15.6
|
1.0
|
|
HG3
|
B:ARG353
|
2.8
|
23.3
|
1.0
|
|
HA
|
B:GLU362
|
2.9
|
19.5
|
1.0
|
|
HB2
|
B:ASP357
|
2.9
|
18.2
|
1.0
|
|
HB3
|
B:ALA356
|
3.0
|
17.3
|
1.0
|
|
HD2
|
B:PHE418
|
3.1
|
16.6
|
1.0
|
|
HG2
|
B:ARG353
|
3.2
|
23.3
|
1.0
|
|
H
|
B:ASP357
|
3.2
|
17.9
|
1.0
|
|
CE2
|
B:PHE418
|
3.4
|
15.5
|
1.0
|
|
CG
|
B:ARG353
|
3.4
|
19.4
|
1.0
|
|
N
|
B:ASP357
|
3.5
|
14.8
|
1.0
|
|
HA
|
B:ARG353
|
3.5
|
18.8
|
1.0
|
|
H
|
B:LEU363
|
3.5
|
16.3
|
1.0
|
|
CD2
|
B:PHE418
|
3.6
|
13.8
|
1.0
|
|
HA
|
B:ASP357
|
3.6
|
19.8
|
1.0
|
|
C
|
B:ARG353
|
3.7
|
16.3
|
1.0
|
|
CA
|
B:GLU362
|
3.7
|
16.2
|
1.0
|
|
CB
|
B:ASP357
|
3.7
|
15.2
|
1.0
|
|
C
|
B:MET361
|
3.8
|
16.7
|
1.0
|
|
N
|
B:LEU363
|
3.8
|
13.6
|
1.0
|
|
CB
|
B:ALA356
|
3.8
|
14.4
|
1.0
|
|
HE
|
B:ARG353
|
3.8
|
26.9
|
1.0
|
|
CA
|
B:ASP357
|
3.8
|
16.5
|
1.0
|
|
HB1
|
B:ALA356
|
3.9
|
17.3
|
1.0
|
|
HB2
|
B:LEU363
|
3.9
|
18.6
|
1.0
|
|
CA
|
B:ARG353
|
4.0
|
15.6
|
1.0
|
|
C
|
B:GLU362
|
4.1
|
12.0
|
1.0
|
|
C
|
B:ALA356
|
4.1
|
15.1
|
1.0
|
|
N
|
B:GLU362
|
4.2
|
15.1
|
1.0
|
|
CB
|
B:ARG353
|
4.3
|
15.3
|
1.0
|
|
HB3
|
B:ASP357
|
4.3
|
18.2
|
1.0
|
|
CA
|
B:ALA356
|
4.5
|
15.4
|
1.0
|
|
NE
|
B:ARG353
|
4.5
|
22.4
|
1.0
|
|
HA
|
B:LEU363
|
4.5
|
15.3
|
1.0
|
|
HB2
|
B:ALA356
|
4.5
|
17.3
|
1.0
|
|
HG2
|
B:GLU362
|
4.6
|
23.1
|
1.0
|
|
CD
|
B:ARG353
|
4.6
|
20.3
|
1.0
|
|
CA
|
B:LEU363
|
4.6
|
12.8
|
1.0
|
|
CZ
|
B:PHE418
|
4.7
|
14.0
|
1.0
|
|
OD1
|
B:ASP357
|
4.7
|
26.3
|
1.0
|
|
CB
|
B:LEU363
|
4.7
|
15.5
|
1.0
|
|
CG
|
B:ASP357
|
4.7
|
26.6
|
1.0
|
|
HB2
|
B:ARG353
|
4.8
|
18.4
|
1.0
|
|
H
|
B:ALA356
|
4.8
|
18.4
|
1.0
|
|
HB2
|
B:MET361
|
4.8
|
18.9
|
1.0
|
|
O
|
B:ALA356
|
4.8
|
15.6
|
1.0
|
|
HA
|
B:SER354
|
4.9
|
19.4
|
0.4
|
|
N
|
B:SER354
|
4.9
|
15.0
|
1.0
|
|
HZ
|
B:PHE418
|
4.9
|
16.8
|
1.0
|
|
CG
|
B:PHE418
|
4.9
|
13.4
|
1.0
|
|
CB
|
B:GLU362
|
4.9
|
16.6
|
1.0
|
|
HA
|
B:SER354
|
4.9
|
19.3
|
0.6
|
|
N
|
B:ALA356
|
4.9
|
15.3
|
1.0
|
|
Reference:
D.J.Nilson,
B.Schwer,
S.Shuman,
S.C.Almo.
Structural Basis For Sensitivity and Acquired Resistance of Fungal Cap Guanine-N7 Methyltransferases to the Antifungal Antibiotic Sinefungin Nucleic Acids Res. 2025.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAF538
Page generated: Mon Aug 18 17:25:13 2025
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