Sodium in PDB 9k72: Crystal Structure of Tsabgl Using Merged Datasets
Enzymatic activity of Crystal Structure of Tsabgl Using Merged Datasets
All present enzymatic activity of Crystal Structure of Tsabgl Using Merged Datasets:
3.2.1.21;
Protein crystallography data
The structure of Crystal Structure of Tsabgl Using Merged Datasets, PDB code: 9k72
was solved by
K.H.Nam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
57.86 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.21,
71.12,
99.49,
90,
90,
90
|
R / Rfree (%)
|
20.1 /
23.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Tsabgl Using Merged Datasets
(pdb code 9k72). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of Tsabgl Using Merged Datasets, PDB code: 9k72:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 9k72
Go back to
Sodium Binding Sites List in 9k72
Sodium binding site 1 out
of 5 in the Crystal Structure of Tsabgl Using Merged Datasets
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:22.8
occ:1.00
|
O
|
A:GLY49
|
2.7
|
15.2
|
1.0
|
O
|
A:HOH715
|
2.7
|
16.8
|
1.0
|
N
|
A:GLY21
|
2.8
|
15.7
|
1.0
|
O
|
A:TYR17
|
2.9
|
13.4
|
1.0
|
CA
|
A:GLY21
|
3.5
|
13.9
|
1.0
|
C
|
A:TYR17
|
3.6
|
14.0
|
1.0
|
C
|
A:GLY49
|
3.7
|
13.9
|
1.0
|
CA
|
A:TYR17
|
3.7
|
14.0
|
1.0
|
N
|
A:GLU20
|
3.8
|
17.9
|
1.0
|
O
|
A:SER16
|
3.9
|
13.8
|
1.0
|
CD1
|
A:TYR17
|
3.9
|
15.4
|
1.0
|
C
|
A:GLU20
|
3.9
|
14.8
|
1.0
|
CA
|
A:GLY49
|
3.9
|
14.2
|
1.0
|
O
|
A:GLY21
|
4.0
|
13.9
|
1.0
|
CB
|
A:ALA52
|
4.0
|
13.8
|
1.0
|
CA
|
A:GLU20
|
4.2
|
13.9
|
1.0
|
C
|
A:GLY21
|
4.2
|
16.1
|
1.0
|
CE1
|
A:TYR17
|
4.2
|
16.1
|
1.0
|
CB
|
A:GLU20
|
4.3
|
13.8
|
1.0
|
CG
|
A:TYR17
|
4.3
|
15.5
|
1.0
|
C
|
A:VAL19
|
4.5
|
13.2
|
1.0
|
CB
|
A:TYR17
|
4.6
|
12.8
|
1.0
|
N
|
A:GLN18
|
4.7
|
14.3
|
1.0
|
N
|
A:VAL19
|
4.7
|
13.5
|
1.0
|
C
|
A:SER16
|
4.7
|
15.2
|
1.0
|
N
|
A:TYR17
|
4.8
|
12.3
|
1.0
|
O
|
A:HOH646
|
4.8
|
20.1
|
1.0
|
N
|
A:ASP50
|
4.9
|
15.3
|
1.0
|
CZ
|
A:TYR17
|
5.0
|
16.0
|
1.0
|
C
|
A:GLN18
|
5.0
|
13.5
|
1.0
|
CD2
|
A:TYR17
|
5.0
|
15.8
|
1.0
|
|
Sodium binding site 2 out
of 5 in 9k72
Go back to
Sodium Binding Sites List in 9k72
Sodium binding site 2 out
of 5 in the Crystal Structure of Tsabgl Using Merged Datasets
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:27.3
occ:1.00
|
O
|
A:HOH1030
|
2.7
|
31.2
|
1.0
|
O
|
A:SER46
|
2.7
|
18.0
|
1.0
|
ND2
|
A:ASN48
|
2.9
|
17.0
|
1.0
|
O
|
A:SER37
|
3.0
|
17.9
|
0.4
|
O
|
A:SER37
|
3.0
|
17.9
|
0.6
|
C
|
A:SER37
|
3.6
|
17.7
|
0.4
|
C
|
A:SER37
|
3.6
|
17.7
|
0.6
|
C
|
A:SER46
|
3.7
|
19.2
|
1.0
|
CB
|
A:ASN48
|
3.8
|
17.7
|
1.0
|
CG
|
A:ASN48
|
3.8
|
17.2
|
1.0
|
CG
|
A:ARG38
|
3.9
|
19.4
|
1.0
|
CA
|
A:ARG38
|
3.9
|
21.4
|
1.0
|
O
|
A:HIS47
|
4.0
|
13.8
|
1.0
|
N
|
A:ARG38
|
4.0
|
15.7
|
1.0
|
CB
|
A:SER46
|
4.0
|
22.8
|
1.0
|
CA
|
A:SER46
|
4.2
|
17.8
|
1.0
|
C
|
A:HIS47
|
4.2
|
15.1
|
1.0
|
OG
|
A:SER37
|
4.2
|
16.4
|
0.6
|
CB
|
A:SER37
|
4.3
|
17.7
|
0.6
|
CB
|
A:SER37
|
4.4
|
17.7
|
0.4
|
CB
|
A:ARG38
|
4.5
|
19.1
|
1.0
|
N
|
A:ASN48
|
4.5
|
13.4
|
1.0
|
O
|
A:HOH941
|
4.6
|
39.0
|
1.0
|
CA
|
A:SER37
|
4.6
|
16.0
|
0.4
|
CA
|
A:SER37
|
4.6
|
16.0
|
0.6
|
N
|
A:HIS47
|
4.7
|
17.9
|
1.0
|
CA
|
A:ASN48
|
4.7
|
12.9
|
1.0
|
CA
|
A:HIS47
|
4.9
|
15.3
|
1.0
|
OD1
|
A:ASN48
|
4.9
|
16.6
|
1.0
|
|
Sodium binding site 3 out
of 5 in 9k72
Go back to
Sodium Binding Sites List in 9k72
Sodium binding site 3 out
of 5 in the Crystal Structure of Tsabgl Using Merged Datasets
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:27.2
occ:1.00
|
O
|
A:HOH618
|
2.7
|
31.9
|
1.0
|
N
|
A:LEU286
|
2.9
|
15.2
|
1.0
|
O
|
A:HOH852
|
3.0
|
27.7
|
1.0
|
CE
|
A:MET345
|
3.3
|
27.6
|
1.0
|
CD
|
A:LYS285
|
3.5
|
21.4
|
1.0
|
CA
|
A:LYS285
|
3.6
|
16.2
|
1.0
|
CE1
|
A:PHE253
|
3.6
|
24.3
|
1.0
|
C
|
A:LYS285
|
3.7
|
17.6
|
1.0
|
O
|
A:HOH883
|
3.7
|
36.9
|
1.0
|
CB
|
A:LEU286
|
3.7
|
15.2
|
1.0
|
CD1
|
A:PHE253
|
3.8
|
20.2
|
1.0
|
CA
|
A:LEU286
|
3.8
|
13.9
|
1.0
|
CG
|
A:LEU286
|
3.9
|
17.5
|
1.0
|
O
|
A:GLN284
|
4.0
|
16.7
|
1.0
|
O
|
A:LEU286
|
4.2
|
16.3
|
1.0
|
CE
|
A:LYS285
|
4.3
|
30.2
|
1.0
|
CG
|
A:LYS285
|
4.4
|
18.9
|
1.0
|
NZ
|
A:LYS285
|
4.4
|
24.1
|
1.0
|
C
|
A:LEU286
|
4.5
|
15.2
|
1.0
|
N
|
A:LYS285
|
4.5
|
17.6
|
1.0
|
CB
|
A:LYS285
|
4.5
|
18.7
|
1.0
|
SD
|
A:MET345
|
4.5
|
25.1
|
1.0
|
CD1
|
A:LEU286
|
4.6
|
14.7
|
1.0
|
C
|
A:GLN284
|
4.6
|
16.0
|
1.0
|
O
|
A:LEU252
|
4.9
|
16.0
|
1.0
|
CZ
|
A:PHE253
|
4.9
|
20.8
|
1.0
|
O
|
A:LYS285
|
4.9
|
17.0
|
1.0
|
|
Sodium binding site 4 out
of 5 in 9k72
Go back to
Sodium Binding Sites List in 9k72
Sodium binding site 4 out
of 5 in the Crystal Structure of Tsabgl Using Merged Datasets
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:33.5
occ:1.00
|
O
|
A:ASP287
|
3.0
|
16.2
|
1.0
|
O
|
A:HOH637
|
3.3
|
32.0
|
1.0
|
C
|
A:ASP287
|
3.7
|
18.7
|
1.0
|
CG
|
A:PRO346
|
3.8
|
18.8
|
1.0
|
CB
|
A:ASP287
|
3.9
|
15.0
|
1.0
|
CB
|
A:PRO346
|
3.9
|
21.2
|
1.0
|
CG
|
A:LYS214
|
4.0
|
25.7
|
1.0
|
CB
|
A:PHE288
|
4.1
|
13.9
|
1.0
|
CD
|
A:LYS214
|
4.1
|
34.3
|
1.0
|
O
|
A:HOH815
|
4.1
|
23.3
|
1.0
|
CD2
|
A:PHE288
|
4.3
|
12.6
|
1.0
|
CA
|
A:ASP287
|
4.3
|
15.2
|
1.0
|
CB
|
A:LYS214
|
4.4
|
14.7
|
1.0
|
N
|
A:PHE288
|
4.5
|
15.0
|
1.0
|
CE
|
A:LYS214
|
4.6
|
36.6
|
1.0
|
CD
|
A:PRO346
|
4.6
|
18.7
|
1.0
|
CG
|
A:PHE288
|
4.7
|
15.0
|
1.0
|
CA
|
A:PHE288
|
4.7
|
12.7
|
1.0
|
O
|
A:HOH788
|
4.8
|
25.5
|
1.0
|
OH
|
A:TYR348
|
4.9
|
23.3
|
1.0
|
NZ
|
A:LYS214
|
4.9
|
29.7
|
1.0
|
CE1
|
A:TYR348
|
5.0
|
22.1
|
1.0
|
|
Sodium binding site 5 out
of 5 in 9k72
Go back to
Sodium Binding Sites List in 9k72
Sodium binding site 5 out
of 5 in the Crystal Structure of Tsabgl Using Merged Datasets
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Tsabgl Using Merged Datasets within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:27.2
occ:1.00
|
N
|
A:GLU328
|
2.9
|
23.6
|
1.0
|
CG
|
A:GLU328
|
3.0
|
27.6
|
1.0
|
CB
|
A:GLU328
|
3.1
|
23.7
|
1.0
|
N
|
A:PRO327
|
3.4
|
16.8
|
1.0
|
CD
|
A:PRO327
|
3.5
|
19.7
|
1.0
|
CD1
|
A:TYR326
|
3.5
|
19.1
|
1.0
|
C
|
A:TYR326
|
3.6
|
16.4
|
1.0
|
CA
|
A:GLU328
|
3.6
|
18.7
|
1.0
|
CE1
|
A:TYR326
|
3.6
|
25.8
|
1.0
|
CG
|
A:TYR326
|
3.7
|
18.0
|
1.0
|
CA
|
A:TYR326
|
3.9
|
17.0
|
1.0
|
CZ
|
A:TYR326
|
3.9
|
28.9
|
1.0
|
CG
|
A:PRO327
|
4.0
|
19.8
|
1.0
|
C
|
A:PRO327
|
4.0
|
19.0
|
1.0
|
CD2
|
A:TYR326
|
4.0
|
15.9
|
1.0
|
CE2
|
A:TYR326
|
4.1
|
19.6
|
1.0
|
CA
|
A:PRO327
|
4.1
|
15.2
|
1.0
|
CD
|
A:GLU328
|
4.2
|
51.3
|
1.0
|
O
|
A:TYR326
|
4.2
|
14.1
|
1.0
|
CB
|
A:TYR326
|
4.4
|
18.7
|
1.0
|
CB
|
A:PRO327
|
4.6
|
20.2
|
1.0
|
O
|
A:HOH1005
|
4.6
|
31.5
|
1.0
|
OE1
|
A:GLU328
|
4.6
|
51.8
|
1.0
|
OH
|
A:TYR326
|
4.7
|
27.5
|
1.0
|
C
|
A:GLU328
|
4.8
|
17.9
|
1.0
|
N
|
A:SER329
|
4.9
|
17.9
|
1.0
|
OE2
|
A:GLU328
|
5.0
|
65.0
|
1.0
|
|
Reference:
K.H.Nam,
K.H.Nam.
N/A N/A.
Page generated: Wed Nov 13 13:11:52 2024
|