Sodium in PDB 4ubg: Resting State of Rat Cysteine Dioxygenase C93G Variant
Enzymatic activity of Resting State of Rat Cysteine Dioxygenase C93G Variant
All present enzymatic activity of Resting State of Rat Cysteine Dioxygenase C93G Variant:
1.13.11.20;
Protein crystallography data
The structure of Resting State of Rat Cysteine Dioxygenase C93G Variant, PDB code: 4ubg
was solved by
M.Fellner,
E.P.Tchesnokov,
G.N.Jameson,
S.M.Wilbanks,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
42.10 /
1.90
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.840,
57.840,
122.730,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.2 /
24.1
|
Other elements in 4ubg:
The structure of Resting State of Rat Cysteine Dioxygenase C93G Variant also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Resting State of Rat Cysteine Dioxygenase C93G Variant
(pdb code 4ubg). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the
Resting State of Rat Cysteine Dioxygenase C93G Variant, PDB code: 4ubg:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Sodium binding site 1 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 1 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na302
b:30.0
occ:1.00
|
N
|
A:ASP54
|
2.8
|
13.8
|
1.0
|
|
O
|
A:ARG57
|
2.9
|
12.2
|
1.0
|
|
O
|
A:ASP54
|
2.9
|
10.7
|
1.0
|
|
O
|
A:CYS76
|
3.0
|
11.6
|
1.0
|
|
CA
|
A:PHE53
|
3.6
|
13.8
|
1.0
|
|
O
|
A:HOH503
|
3.6
|
16.7
|
1.0
|
|
C
|
A:ASP54
|
3.7
|
18.6
|
1.0
|
|
C
|
A:PHE53
|
3.7
|
17.6
|
1.0
|
|
CD1
|
A:PHE53
|
3.7
|
15.9
|
1.0
|
|
CA
|
A:ASP54
|
3.7
|
13.5
|
1.0
|
|
CB
|
A:PHE53
|
3.8
|
10.7
|
1.0
|
|
ND1
|
A:HIS81
|
3.8
|
11.8
|
1.0
|
|
CA
|
A:TYR58
|
3.8
|
9.2
|
1.0
|
|
C
|
A:ARG57
|
3.8
|
9.4
|
1.0
|
|
C
|
A:CYS76
|
3.9
|
13.0
|
1.0
|
|
CG2
|
A:THR59
|
3.9
|
10.0
|
1.0
|
|
N
|
A:GLY78
|
4.0
|
11.1
|
1.0
|
|
CE1
|
A:HIS81
|
4.0
|
14.2
|
1.0
|
|
N
|
A:THR59
|
4.0
|
7.7
|
1.0
|
|
CB
|
A:ASP54
|
4.1
|
12.7
|
1.0
|
|
CG
|
A:PHE53
|
4.1
|
13.1
|
1.0
|
|
OG1
|
A:THR59
|
4.2
|
16.8
|
1.0
|
|
C
|
A:TYR58
|
4.2
|
12.3
|
1.0
|
|
N
|
A:TYR58
|
4.3
|
13.8
|
1.0
|
|
CB
|
A:CYS76
|
4.4
|
10.2
|
1.0
|
|
N
|
A:TRP77
|
4.5
|
11.9
|
1.0
|
|
CB
|
A:THR59
|
4.6
|
10.0
|
1.0
|
|
CA
|
A:TRP77
|
4.6
|
11.6
|
1.0
|
|
C
|
A:TRP77
|
4.6
|
11.2
|
1.0
|
|
CE1
|
A:PHE53
|
4.7
|
14.6
|
1.0
|
|
CA
|
A:GLY78
|
4.7
|
12.7
|
1.0
|
|
CA
|
A:CYS76
|
4.8
|
10.0
|
1.0
|
|
O
|
A:PHE53
|
4.9
|
12.8
|
1.0
|
|
CA
|
A:THR59
|
4.9
|
10.3
|
1.0
|
|
CB
|
A:TYR58
|
4.9
|
9.5
|
1.0
|
|
N
|
A:PHE53
|
4.9
|
11.7
|
1.0
|
|
N
|
A:GLN55
|
5.0
|
14.5
|
1.0
|
|
Sodium binding site 2 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 2 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na303
b:30.0
occ:1.00
|
O
|
A:GLY138
|
2.6
|
21.6
|
1.0
|
|
OD1
|
A:ASP135
|
2.6
|
13.9
|
1.0
|
|
ND1
|
A:HIS88
|
2.8
|
19.2
|
1.0
|
|
CA
|
A:ASP135
|
3.5
|
20.4
|
1.0
|
|
N
|
A:HIS88
|
3.5
|
15.7
|
1.0
|
|
CA
|
A:ASP87
|
3.6
|
15.8
|
1.0
|
|
N
|
A:ASP135
|
3.7
|
13.9
|
1.0
|
|
O
|
A:ASN134
|
3.7
|
14.0
|
1.0
|
|
CE1
|
A:HIS88
|
3.7
|
19.1
|
1.0
|
|
C
|
A:ASN134
|
3.7
|
15.5
|
1.0
|
|
C
|
A:GLY138
|
3.7
|
16.9
|
1.0
|
|
CG
|
A:ASP135
|
3.7
|
13.3
|
1.0
|
|
C
|
A:ASP87
|
3.8
|
14.2
|
1.0
|
|
CG
|
A:HIS88
|
3.8
|
18.3
|
1.0
|
|
CB
|
A:HIS88
|
4.1
|
16.8
|
1.0
|
|
CA
|
A:LEU139
|
4.1
|
22.0
|
1.0
|
|
O
|
A:HIS86
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ASP87
|
4.2
|
12.8
|
1.0
|
|
CB
|
A:ASP135
|
4.2
|
13.2
|
1.0
|
|
CG1
|
A:ILE133
|
4.3
|
26.7
|
1.0
|
|
N
|
A:LEU139
|
4.3
|
16.6
|
1.0
|
|
CD2
|
A:LEU139
|
4.4
|
18.4
|
1.0
|
|
CA
|
A:HIS88
|
4.4
|
15.9
|
1.0
|
|
CA
|
A:ASN134
|
4.6
|
16.3
|
1.0
|
|
C
|
A:ASP135
|
4.6
|
21.6
|
1.0
|
|
CD1
|
A:ILE133
|
4.6
|
21.0
|
1.0
|
|
N
|
A:ASP87
|
4.7
|
15.6
|
1.0
|
|
O
|
A:ASP87
|
4.7
|
11.8
|
1.0
|
|
OD2
|
A:ASP135
|
4.8
|
18.0
|
1.0
|
|
O
|
A:ASP135
|
4.8
|
20.0
|
1.0
|
|
CA
|
A:GLY138
|
4.9
|
18.5
|
1.0
|
|
C
|
A:HIS86
|
4.9
|
16.1
|
1.0
|
|
NE2
|
A:HIS88
|
4.9
|
20.7
|
1.0
|
|
CZ2
|
A:TRP109
|
4.9
|
18.5
|
1.0
|
|
C
|
A:LEU139
|
4.9
|
15.7
|
1.0
|
|
N
|
A:GLY138
|
4.9
|
18.4
|
1.0
|
|
CD2
|
A:HIS88
|
5.0
|
19.2
|
1.0
|
|
N
|
A:ASN134
|
5.0
|
22.4
|
1.0
|
|
Sodium binding site 3 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 3 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na304
b:30.0
occ:1.00
|
OD1
|
A:ASN144
|
2.7
|
13.8
|
1.0
|
|
O
|
A:HOH414
|
2.9
|
18.7
|
1.0
|
|
O
|
A:GLU149
|
2.9
|
16.5
|
1.0
|
|
O
|
A:ASN101
|
3.2
|
12.2
|
1.0
|
|
N
|
A:ASN101
|
3.2
|
15.8
|
1.0
|
|
CG
|
A:ASN144
|
3.5
|
11.9
|
1.0
|
|
CB
|
A:SER146
|
3.5
|
12.3
|
1.0
|
|
ND2
|
A:ASN144
|
3.7
|
12.4
|
1.0
|
|
CB
|
A:ALA151
|
3.7
|
10.8
|
1.0
|
|
CA
|
A:GLY100
|
3.8
|
14.4
|
1.0
|
|
C
|
A:GLU149
|
3.9
|
14.7
|
1.0
|
|
CB
|
A:GLU149
|
3.9
|
18.9
|
1.0
|
|
O
|
A:PRO150
|
4.0
|
16.9
|
1.0
|
|
C
|
A:GLY100
|
4.0
|
12.8
|
1.0
|
|
C
|
A:ASN101
|
4.0
|
13.9
|
1.0
|
|
CA
|
A:ASN101
|
4.1
|
15.6
|
1.0
|
|
C
|
A:PRO150
|
4.1
|
11.3
|
1.0
|
|
OG
|
A:SER146
|
4.1
|
13.6
|
1.0
|
|
N
|
A:ALA151
|
4.2
|
12.5
|
1.0
|
|
CA
|
A:ALA151
|
4.2
|
13.6
|
1.0
|
|
O
|
A:HOH427
|
4.3
|
14.9
|
1.0
|
|
CA
|
A:GLU149
|
4.5
|
18.0
|
1.0
|
|
CB
|
A:ASN101
|
4.5
|
16.4
|
1.0
|
|
ND2
|
A:ASN101
|
4.6
|
15.5
|
1.0
|
|
CB
|
A:ASN144
|
4.8
|
15.5
|
1.0
|
|
N
|
A:PRO150
|
4.8
|
11.2
|
1.0
|
|
O
|
A:HOH458
|
4.8
|
24.6
|
1.0
|
|
CA
|
A:SER146
|
4.8
|
10.0
|
1.0
|
|
CA
|
A:PRO150
|
4.9
|
17.1
|
1.0
|
|
N
|
A:SER146
|
4.9
|
18.6
|
1.0
|
|
Sodium binding site 4 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 4 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na305
b:30.0
occ:1.00
|
OG1
|
A:THR105
|
2.6
|
19.0
|
1.0
|
|
OE1
|
A:GLU143
|
2.6
|
27.7
|
1.0
|
|
O
|
A:LYS103
|
3.0
|
14.9
|
1.0
|
|
CG
|
A:GLU143
|
3.3
|
18.5
|
1.0
|
|
O
|
A:ARG141
|
3.3
|
15.2
|
1.0
|
|
CD
|
A:GLU143
|
3.4
|
26.8
|
1.0
|
|
O
|
A:HOH520
|
3.4
|
40.9
|
1.0
|
|
N
|
A:THR105
|
3.4
|
15.8
|
1.0
|
|
CB
|
A:THR105
|
3.5
|
15.8
|
1.0
|
|
C
|
A:LYS103
|
3.7
|
15.8
|
1.0
|
|
CE
|
A:LYS103
|
3.7
|
29.9
|
1.0
|
|
C
|
A:ARG141
|
3.8
|
16.0
|
1.0
|
|
CG
|
A:LYS103
|
3.9
|
16.0
|
1.0
|
|
CB
|
A:GLU143
|
3.9
|
14.8
|
1.0
|
|
C
|
A:GLU104
|
4.0
|
14.0
|
1.0
|
|
N
|
A:GLU143
|
4.0
|
11.7
|
1.0
|
|
CB
|
A:ARG141
|
4.1
|
18.2
|
1.0
|
|
CA
|
A:THR105
|
4.1
|
17.3
|
1.0
|
|
CA
|
A:GLU104
|
4.1
|
9.1
|
1.0
|
|
CD
|
A:ARG141
|
4.2
|
19.0
|
1.0
|
|
CB
|
A:LYS103
|
4.2
|
15.5
|
1.0
|
|
N
|
A:GLU104
|
4.2
|
13.4
|
1.0
|
|
N
|
A:VAL142
|
4.3
|
10.8
|
1.0
|
|
CA
|
A:VAL142
|
4.3
|
11.7
|
1.0
|
|
C
|
A:VAL142
|
4.3
|
11.8
|
1.0
|
|
CD
|
A:LYS103
|
4.4
|
23.1
|
1.0
|
|
CG
|
A:ARG141
|
4.5
|
25.6
|
1.0
|
|
CA
|
A:ARG141
|
4.5
|
8.3
|
1.0
|
|
CA
|
A:LYS103
|
4.6
|
16.4
|
1.0
|
|
OE2
|
A:GLU143
|
4.6
|
37.5
|
1.0
|
|
CA
|
A:GLU143
|
4.6
|
13.6
|
1.0
|
|
NZ
|
A:LYS103
|
4.7
|
30.1
|
1.0
|
|
O
|
A:HOH522
|
4.8
|
39.8
|
1.0
|
|
O
|
A:GLU104
|
4.8
|
13.5
|
1.0
|
|
CG2
|
A:THR105
|
4.8
|
20.6
|
1.0
|
|
NE
|
A:ARG141
|
4.9
|
22.6
|
1.0
|
|
Sodium binding site 5 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 5 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na306
b:30.0
occ:1.00
|
O
|
A:HOH516
|
2.8
|
32.0
|
1.0
|
|
N
|
A:ALA13
|
2.8
|
17.4
|
1.0
|
|
O
|
A:HOH532
|
2.9
|
31.2
|
1.0
|
|
N
|
A:LEU12
|
3.2
|
20.1
|
1.0
|
|
CB
|
A:THR11
|
3.4
|
13.4
|
1.0
|
|
CB
|
A:ALA13
|
3.5
|
22.3
|
1.0
|
|
OG1
|
A:THR11
|
3.5
|
20.0
|
1.0
|
|
CB
|
A:LEU12
|
3.5
|
14.3
|
1.0
|
|
CA
|
A:LEU12
|
3.7
|
20.0
|
1.0
|
|
CG
|
A:GLU46
|
3.7
|
20.6
|
1.0
|
|
CD
|
A:GLU46
|
3.7
|
19.0
|
1.0
|
|
C
|
A:LEU12
|
3.7
|
13.3
|
1.0
|
|
CA
|
A:ALA13
|
3.7
|
15.3
|
1.0
|
|
OE1
|
A:GLU46
|
3.8
|
15.8
|
1.0
|
|
CB
|
A:GLU46
|
3.9
|
14.2
|
1.0
|
|
C
|
A:THR11
|
4.0
|
18.0
|
1.0
|
|
O
|
A:HOH517
|
4.0
|
35.8
|
1.0
|
|
OE2
|
A:GLU46
|
4.2
|
23.9
|
1.0
|
|
CA
|
A:THR11
|
4.2
|
15.6
|
1.0
|
|
O
|
A:HOH611
|
4.3
|
21.4
|
1.0
|
|
CG2
|
A:THR11
|
4.5
|
15.4
|
1.0
|
|
CG
|
A:LEU12
|
4.6
|
18.1
|
1.0
|
|
O
|
A:LEU12
|
4.9
|
12.8
|
1.0
|
|
CA
|
A:GLU46
|
4.9
|
11.3
|
1.0
|
|
O
|
A:THR11
|
4.9
|
11.4
|
1.0
|
|
C
|
A:ALA13
|
4.9
|
17.6
|
1.0
|
|
N
|
A:ASP14
|
4.9
|
16.2
|
1.0
|
|
O
|
A:HOH535
|
5.0
|
30.2
|
1.0
|
|
O
|
A:GLU46
|
5.0
|
9.7
|
1.0
|
|
Sodium binding site 6 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 6 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na307
b:30.0
occ:1.00
|
N
|
A:ARG60
|
2.9
|
9.2
|
0.5
|
|
N
|
A:ARG60
|
2.9
|
9.2
|
0.5
|
|
O
|
A:THR180
|
3.1
|
23.7
|
1.0
|
|
CA
|
A:THR59
|
3.5
|
10.3
|
1.0
|
|
N
|
A:HIS182
|
3.6
|
16.0
|
1.0
|
|
CB
|
A:HIS182
|
3.6
|
13.0
|
1.0
|
|
C
|
A:THR59
|
3.7
|
12.0
|
1.0
|
|
CB
|
A:ARG60
|
3.7
|
9.7
|
0.5
|
|
CB
|
A:ARG60
|
3.7
|
9.8
|
0.5
|
|
CA
|
A:ARG60
|
3.8
|
11.2
|
0.5
|
|
CA
|
A:ARG60
|
3.8
|
11.0
|
0.5
|
|
CG
|
A:ARG60
|
3.9
|
14.5
|
0.5
|
|
O
|
A:ARG60
|
3.9
|
12.8
|
0.5
|
|
O
|
A:ARG60
|
3.9
|
13.0
|
0.5
|
|
CG
|
A:ARG60
|
4.0
|
14.6
|
0.5
|
|
NH2
|
A:ARG57
|
4.1
|
30.2
|
1.0
|
|
CA
|
A:HIS182
|
4.1
|
14.6
|
1.0
|
|
CB
|
A:THR59
|
4.2
|
10.0
|
1.0
|
|
C
|
A:THR180
|
4.2
|
29.6
|
1.0
|
|
O
|
A:TYR58
|
4.2
|
9.4
|
1.0
|
|
CD
|
A:ARG60
|
4.2
|
16.9
|
0.5
|
|
C
|
A:ARG60
|
4.3
|
12.6
|
0.5
|
|
C
|
A:ARG60
|
4.3
|
12.7
|
0.5
|
|
C
|
A:PHE181
|
4.3
|
20.5
|
1.0
|
|
OG1
|
A:THR180
|
4.5
|
44.1
|
1.0
|
|
CA
|
A:PHE181
|
4.6
|
18.9
|
1.0
|
|
CZ
|
A:ARG57
|
4.7
|
34.7
|
1.0
|
|
N
|
A:THR59
|
4.7
|
7.7
|
1.0
|
|
CG
|
A:HIS182
|
4.7
|
13.9
|
1.0
|
|
CG2
|
A:THR59
|
4.7
|
10.0
|
1.0
|
|
CD
|
A:ARG60
|
4.8
|
14.9
|
0.5
|
|
N
|
A:PHE181
|
4.8
|
28.7
|
1.0
|
|
O
|
A:THR59
|
4.8
|
9.9
|
1.0
|
|
C
|
A:TYR58
|
4.9
|
12.3
|
1.0
|
|
ND1
|
A:HIS182
|
5.0
|
22.4
|
1.0
|
|
Sodium binding site 7 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 7 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na308
b:30.0
occ:1.00
|
N
|
A:GLY186
|
2.8
|
15.0
|
1.0
|
|
OG
|
A:SER183
|
2.8
|
14.6
|
1.0
|
|
O
|
A:LEU62
|
2.9
|
11.7
|
1.0
|
|
N
|
A:PHE185
|
3.2
|
14.7
|
1.0
|
|
CD1
|
A:TYR50
|
3.4
|
17.3
|
1.0
|
|
CA
|
A:GLY186
|
3.5
|
15.8
|
1.0
|
|
C
|
A:LYS184
|
3.6
|
16.4
|
1.0
|
|
C
|
A:SER183
|
3.6
|
18.1
|
1.0
|
|
CB
|
A:SER183
|
3.6
|
11.8
|
1.0
|
|
N
|
A:LYS184
|
3.6
|
13.6
|
1.0
|
|
O
|
A:SER183
|
3.7
|
12.9
|
1.0
|
|
CA
|
A:LYS184
|
3.7
|
17.3
|
1.0
|
|
C
|
A:PHE185
|
3.8
|
21.0
|
1.0
|
|
CA
|
A:PHE185
|
3.9
|
16.0
|
1.0
|
|
C
|
A:LEU62
|
3.9
|
10.8
|
1.0
|
|
CB
|
A:ASN61
|
3.9
|
9.8
|
1.0
|
|
N
|
A:LEU62
|
3.9
|
16.1
|
1.0
|
|
C
|
A:ASN61
|
4.0
|
17.0
|
1.0
|
|
CE1
|
A:TYR50
|
4.1
|
14.7
|
1.0
|
|
CA
|
A:ASN61
|
4.2
|
10.3
|
1.0
|
|
CA
|
A:SER183
|
4.2
|
16.0
|
1.0
|
|
CG
|
A:TYR50
|
4.3
|
11.9
|
1.0
|
|
CB
|
A:TYR50
|
4.3
|
12.5
|
1.0
|
|
C
|
A:GLY186
|
4.3
|
14.8
|
1.0
|
|
O
|
A:LYS184
|
4.3
|
14.5
|
1.0
|
|
CA
|
A:TYR50
|
4.4
|
15.8
|
1.0
|
|
O
|
A:ASN61
|
4.4
|
14.6
|
1.0
|
|
N
|
A:ILE187
|
4.4
|
15.2
|
1.0
|
|
CA
|
A:LEU62
|
4.5
|
13.4
|
1.0
|
|
OD1
|
A:ASN61
|
4.8
|
14.5
|
1.0
|
|
CG
|
A:ASN61
|
4.8
|
15.3
|
1.0
|
|
CE
|
A:LYS52
|
4.9
|
19.1
|
1.0
|
|
N
|
A:VAL63
|
4.9
|
10.2
|
1.0
|
|
O
|
A:PHE185
|
4.9
|
20.6
|
1.0
|
|
O
|
A:TYR50
|
5.0
|
15.7
|
1.0
|
|
Sodium binding site 8 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 8 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na309
b:30.0
occ:1.00
|
O
|
A:GLY82
|
2.9
|
13.2
|
1.0
|
|
O
|
A:HOH482
|
3.0
|
20.1
|
1.0
|
|
N
|
A:TYR58
|
3.0
|
13.8
|
1.0
|
|
CD2
|
A:TYR58
|
3.3
|
9.7
|
1.0
|
|
CB
|
A:ARG57
|
3.3
|
15.4
|
1.0
|
|
CA
|
A:ARG57
|
3.4
|
12.5
|
1.0
|
|
N
|
A:GLY82
|
3.4
|
14.9
|
1.0
|
|
CB
|
A:HIS81
|
3.5
|
13.2
|
1.0
|
|
C
|
A:ARG57
|
3.7
|
9.4
|
1.0
|
|
C
|
A:GLY82
|
3.8
|
14.5
|
1.0
|
|
CA
|
A:HIS81
|
3.9
|
13.2
|
1.0
|
|
O
|
A:HOH528
|
3.9
|
28.8
|
1.0
|
|
CG
|
A:HIS81
|
3.9
|
8.6
|
1.0
|
|
C
|
A:HIS81
|
4.0
|
10.4
|
1.0
|
|
O
|
A:HOH546
|
4.0
|
29.4
|
1.0
|
|
CB
|
A:TYR58
|
4.2
|
9.5
|
1.0
|
|
CA
|
A:TYR58
|
4.2
|
9.2
|
1.0
|
|
CE2
|
A:TYR58
|
4.2
|
15.4
|
1.0
|
|
CA
|
A:GLY82
|
4.2
|
14.0
|
1.0
|
|
CG
|
A:TYR58
|
4.2
|
12.5
|
1.0
|
|
CD2
|
A:HIS81
|
4.5
|
9.2
|
1.0
|
|
ND1
|
A:HIS81
|
4.6
|
11.8
|
1.0
|
|
O
|
A:TYR56
|
4.6
|
17.4
|
1.0
|
|
CG
|
A:ARG57
|
4.7
|
15.1
|
1.0
|
|
N
|
A:ARG57
|
4.7
|
13.3
|
1.0
|
|
NE
|
A:ARG57
|
4.8
|
26.4
|
1.0
|
|
O
|
A:ARG57
|
4.9
|
12.2
|
1.0
|
|
CD
|
A:ARG57
|
5.0
|
26.1
|
1.0
|
|
N
|
A:SER83
|
5.0
|
11.7
|
1.0
|
|
Sodium binding site 9 out
of 9 in 4ubg
Go back to
Sodium Binding Sites List in 4ubg
Sodium binding site 9 out
of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na310
b:30.0
occ:1.00
|
O
|
A:PRO9
|
2.5
|
16.0
|
1.0
|
|
N
|
A:GLU41
|
2.9
|
13.0
|
1.0
|
|
O
|
A:HOH501
|
3.0
|
22.7
|
1.0
|
|
NZ
|
A:LYS8
|
3.3
|
29.4
|
1.0
|
|
CB
|
A:GLU41
|
3.6
|
24.2
|
1.0
|
|
CD1
|
A:TYR40
|
3.7
|
14.3
|
1.0
|
|
CE
|
A:LYS8
|
3.7
|
41.3
|
1.0
|
|
O
|
A:ARG10
|
3.7
|
23.3
|
1.0
|
|
C
|
A:PRO9
|
3.7
|
17.9
|
1.0
|
|
CA
|
A:GLU41
|
3.8
|
17.3
|
1.0
|
|
CA
|
A:TYR40
|
3.8
|
17.4
|
1.0
|
|
C
|
A:TYR40
|
3.8
|
17.5
|
1.0
|
|
O
|
A:ALA39
|
3.9
|
14.3
|
1.0
|
|
C
|
A:ARG10
|
4.0
|
15.2
|
1.0
|
|
O
|
A:GLU41
|
4.0
|
12.5
|
1.0
|
|
CA
|
A:ARG10
|
4.2
|
22.3
|
1.0
|
|
CG
|
A:GLU41
|
4.2
|
31.0
|
1.0
|
|
CE1
|
A:TYR40
|
4.3
|
13.0
|
1.0
|
|
C
|
A:GLU41
|
4.4
|
13.6
|
1.0
|
|
N
|
A:ARG10
|
4.4
|
11.3
|
1.0
|
|
CG
|
A:TYR40
|
4.5
|
17.1
|
1.0
|
|
CG
|
A:LYS8
|
4.5
|
17.0
|
1.0
|
|
CB
|
A:TYR40
|
4.6
|
15.2
|
1.0
|
|
N
|
A:THR11
|
4.7
|
16.1
|
1.0
|
|
CD
|
A:LYS8
|
4.8
|
28.4
|
1.0
|
|
C
|
A:ALA39
|
4.8
|
13.8
|
1.0
|
|
CD
|
A:GLU41
|
4.8
|
57.4
|
1.0
|
|
N
|
A:TYR40
|
4.8
|
13.4
|
1.0
|
|
CA
|
A:PRO9
|
4.8
|
18.4
|
1.0
|
|
OE2
|
A:GLU41
|
4.9
|
54.4
|
1.0
|
|
O
|
A:TYR40
|
5.0
|
14.6
|
1.0
|
|
O
|
A:HOH510
|
5.0
|
21.8
|
1.0
|
|
Reference:
C.G.Davies,
M.Fellner,
E.P.Tchesnokov,
S.M.Wilbanks,
G.N.Jameson.
The Cys-Tyr Crosslink of Cysteine Dioxygenase Changes the Optimum pH of Reaction Without Structural Change Biochemistry 2014.
ISSN: ISSN 0006-2960
Page generated: Mon Oct 7 18:36:42 2024
|
