Iron in PDB 3nvv: Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
All present enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite:
1.17.1.4;
1.17.3.2;
Protein crystallography data
The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite, PDB code: 3nvv
was solved by
H.Cao,
R.Hille,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
131.80 /
1.82
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.766,
73.418,
138.158,
90.00,
96.93,
90.00
|
R / Rfree (%)
|
19.3 /
22.9
|
Other elements in 3nvv:
The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
(pdb code 3nvv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite, PDB code: 3nvv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 1 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:13.6
occ:1.00
|
FE1
|
A:FES601
|
0.0
|
13.6
|
1.0
|
S1
|
A:FES601
|
2.2
|
14.5
|
1.0
|
S2
|
A:FES601
|
2.2
|
15.6
|
1.0
|
SG
|
A:CYS150
|
2.4
|
12.3
|
1.0
|
SG
|
A:CYS113
|
2.4
|
12.1
|
1.0
|
FE2
|
A:FES601
|
2.7
|
14.7
|
1.0
|
CB
|
A:CYS113
|
3.3
|
13.6
|
1.0
|
CB
|
A:CYS150
|
3.3
|
13.0
|
1.0
|
N
|
A:CYS113
|
3.5
|
12.5
|
1.0
|
O
|
C:HOH136
|
3.7
|
13.0
|
1.0
|
CA
|
A:CYS113
|
3.8
|
12.3
|
1.0
|
N
|
A:GLY114
|
3.8
|
10.8
|
1.0
|
N
|
A:CYS150
|
4.1
|
12.5
|
1.0
|
C
|
A:CYS113
|
4.2
|
11.7
|
1.0
|
CA
|
A:CYS150
|
4.3
|
12.7
|
1.0
|
N
|
A:PHE115
|
4.4
|
10.3
|
1.0
|
SG
|
A:CYS148
|
4.5
|
13.1
|
1.0
|
SG
|
A:CYS116
|
4.6
|
12.8
|
1.0
|
C
|
A:GLN112
|
4.7
|
12.1
|
1.0
|
N
|
A:ARG149
|
4.8
|
12.0
|
1.0
|
CB
|
A:GLN112
|
4.8
|
10.8
|
1.0
|
CA
|
A:GLY114
|
4.9
|
10.3
|
1.0
|
N
|
A:CYS116
|
4.9
|
9.9
|
1.0
|
|
Iron binding site 2 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 2 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:14.7
occ:1.00
|
FE2
|
A:FES601
|
0.0
|
14.7
|
1.0
|
S2
|
A:FES601
|
2.2
|
15.6
|
1.0
|
S1
|
A:FES601
|
2.2
|
14.5
|
1.0
|
SG
|
A:CYS116
|
2.3
|
12.8
|
1.0
|
SG
|
A:CYS148
|
2.5
|
13.1
|
1.0
|
FE1
|
A:FES601
|
2.7
|
13.6
|
1.0
|
CB
|
A:CYS116
|
3.4
|
9.3
|
1.0
|
CB
|
A:CYS148
|
3.4
|
12.5
|
1.0
|
CA
|
A:CYS148
|
3.6
|
13.2
|
1.0
|
N
|
A:ARG149
|
4.1
|
12.0
|
1.0
|
N
|
A:CYS116
|
4.2
|
9.9
|
1.0
|
O
|
A:HOH166
|
4.2
|
13.0
|
1.0
|
C
|
A:CYS148
|
4.3
|
12.1
|
1.0
|
N
|
A:CYS150
|
4.4
|
12.5
|
1.0
|
CA
|
A:CYS116
|
4.4
|
11.1
|
1.0
|
SG
|
A:CYS150
|
4.5
|
12.3
|
1.0
|
CB
|
A:CYS150
|
4.5
|
13.0
|
1.0
|
SG
|
A:CYS113
|
4.8
|
12.1
|
1.0
|
CG2
|
A:THR151
|
4.8
|
12.9
|
1.0
|
O
|
A:LEU147
|
4.9
|
13.8
|
1.0
|
N
|
A:CYS148
|
4.9
|
12.6
|
1.0
|
C
|
A:CYS116
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 3 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 3 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:15.3
occ:1.00
|
FE1
|
A:FES602
|
0.0
|
15.3
|
1.0
|
S2
|
A:FES602
|
2.2
|
16.8
|
1.0
|
S1
|
A:FES602
|
2.2
|
16.8
|
1.0
|
SG
|
A:CYS51
|
2.3
|
14.4
|
1.0
|
SG
|
A:CYS73
|
2.3
|
15.8
|
1.0
|
FE2
|
A:FES602
|
2.8
|
14.8
|
1.0
|
CB
|
A:CYS73
|
3.1
|
17.5
|
1.0
|
CB
|
A:CYS51
|
3.4
|
13.3
|
1.0
|
CB
|
A:ASN71
|
4.1
|
17.7
|
1.0
|
N
|
A:CYS73
|
4.2
|
17.2
|
1.0
|
CA
|
A:CYS73
|
4.2
|
17.6
|
1.0
|
N
|
A:CYS51
|
4.3
|
14.7
|
1.0
|
N
|
A:GLY46
|
4.3
|
18.2
|
1.0
|
OD1
|
A:ASN71
|
4.4
|
18.8
|
1.0
|
CG
|
A:ASN71
|
4.4
|
18.6
|
1.0
|
SG
|
A:CYS43
|
4.5
|
13.5
|
1.0
|
CA
|
A:CYS51
|
4.5
|
13.8
|
1.0
|
N
|
A:GLY44
|
4.5
|
15.0
|
1.0
|
CA
|
A:GLY46
|
4.5
|
17.5
|
1.0
|
SG
|
A:CYS48
|
4.6
|
14.3
|
1.0
|
CA
|
A:GLY44
|
4.8
|
17.2
|
1.0
|
N
|
A:GLY49
|
4.9
|
14.3
|
1.0
|
CA
|
A:ASN71
|
4.9
|
17.9
|
1.0
|
N
|
A:GLU45
|
4.9
|
17.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 4 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:14.8
occ:1.00
|
FE2
|
A:FES602
|
0.0
|
14.8
|
1.0
|
S1
|
A:FES602
|
2.2
|
16.8
|
1.0
|
SG
|
A:CYS48
|
2.2
|
14.3
|
1.0
|
S2
|
A:FES602
|
2.2
|
16.8
|
1.0
|
SG
|
A:CYS43
|
2.4
|
13.5
|
1.0
|
FE1
|
A:FES602
|
2.8
|
15.3
|
1.0
|
CB
|
A:CYS48
|
3.3
|
15.0
|
1.0
|
N
|
A:CYS43
|
3.4
|
14.4
|
1.0
|
CB
|
A:CYS43
|
3.5
|
14.3
|
1.0
|
N
|
A:CYS48
|
3.6
|
15.3
|
1.0
|
CA
|
A:CYS48
|
3.9
|
15.3
|
1.0
|
N
|
A:GLY49
|
3.9
|
14.3
|
1.0
|
CA
|
A:CYS43
|
3.9
|
14.9
|
1.0
|
N
|
A:GLY44
|
3.9
|
15.0
|
1.0
|
C
|
A:GLY42
|
4.0
|
15.4
|
1.0
|
CA
|
A:GLY42
|
4.2
|
15.2
|
1.0
|
N
|
A:GLY42
|
4.2
|
13.9
|
1.0
|
C
|
A:CYS48
|
4.2
|
14.7
|
1.0
|
C
|
A:CYS43
|
4.4
|
15.6
|
1.0
|
N
|
A:GLY47
|
4.4
|
17.3
|
1.0
|
N
|
A:ALA50
|
4.4
|
13.5
|
1.0
|
SG
|
A:CYS73
|
4.4
|
15.8
|
1.0
|
N
|
A:GLY46
|
4.4
|
18.2
|
1.0
|
SG
|
A:CYS51
|
4.6
|
14.4
|
1.0
|
C
|
A:GLY47
|
4.7
|
16.9
|
1.0
|
N
|
A:GLU45
|
4.7
|
17.9
|
1.0
|
C
|
A:GLY46
|
4.8
|
18.5
|
1.0
|
CA
|
A:GLY46
|
4.8
|
17.5
|
1.0
|
CA
|
A:GLY49
|
4.9
|
14.1
|
1.0
|
O
|
A:GLY42
|
4.9
|
15.8
|
1.0
|
CB
|
A:ALA50
|
4.9
|
13.2
|
1.0
|
CA
|
A:GLY44
|
4.9
|
17.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 5 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe601
b:14.6
occ:1.00
|
FE1
|
J:FES601
|
0.0
|
14.6
|
1.0
|
S1
|
J:FES601
|
2.2
|
16.2
|
1.0
|
S2
|
J:FES601
|
2.2
|
16.5
|
1.0
|
SG
|
J:CYS150
|
2.3
|
14.4
|
1.0
|
SG
|
J:CYS113
|
2.4
|
15.7
|
1.0
|
FE2
|
J:FES601
|
2.6
|
14.6
|
1.0
|
CB
|
J:CYS150
|
3.2
|
14.8
|
1.0
|
CB
|
J:CYS113
|
3.3
|
14.5
|
1.0
|
N
|
J:CYS113
|
3.6
|
13.0
|
1.0
|
O
|
L:HOH384
|
3.7
|
15.1
|
1.0
|
CA
|
J:CYS113
|
3.9
|
13.0
|
1.0
|
N
|
J:GLY114
|
4.0
|
11.9
|
1.0
|
N
|
J:CYS150
|
4.0
|
16.0
|
1.0
|
CA
|
J:CYS150
|
4.2
|
14.7
|
1.0
|
SG
|
J:CYS148
|
4.3
|
17.4
|
1.0
|
C
|
J:CYS113
|
4.3
|
13.6
|
1.0
|
N
|
J:PHE115
|
4.5
|
13.2
|
1.0
|
SG
|
J:CYS116
|
4.6
|
14.7
|
1.0
|
C
|
J:GLN112
|
4.7
|
13.3
|
1.0
|
N
|
J:ARG149
|
4.7
|
16.0
|
1.0
|
CB
|
J:GLN112
|
4.8
|
13.1
|
1.0
|
N
|
J:CYS116
|
4.9
|
15.0
|
1.0
|
C
|
J:ARG149
|
5.0
|
16.0
|
1.0
|
CA
|
J:GLY114
|
5.0
|
12.8
|
1.0
|
|
Iron binding site 6 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 6 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe601
b:14.6
occ:1.00
|
FE2
|
J:FES601
|
0.0
|
14.6
|
1.0
|
S1
|
J:FES601
|
2.2
|
16.2
|
1.0
|
S2
|
J:FES601
|
2.2
|
16.5
|
1.0
|
SG
|
J:CYS116
|
2.2
|
14.7
|
1.0
|
SG
|
J:CYS148
|
2.4
|
17.4
|
1.0
|
FE1
|
J:FES601
|
2.6
|
14.6
|
1.0
|
CB
|
J:CYS148
|
3.3
|
16.4
|
1.0
|
CB
|
J:CYS116
|
3.4
|
15.3
|
1.0
|
CA
|
J:CYS148
|
3.6
|
16.1
|
1.0
|
N
|
J:ARG149
|
4.1
|
16.0
|
1.0
|
N
|
J:CYS116
|
4.2
|
15.0
|
1.0
|
C
|
J:CYS148
|
4.3
|
16.0
|
1.0
|
N
|
J:CYS150
|
4.3
|
16.0
|
1.0
|
O
|
J:HOH584
|
4.3
|
14.9
|
1.0
|
CA
|
J:CYS116
|
4.4
|
15.0
|
1.0
|
SG
|
J:CYS150
|
4.4
|
14.4
|
1.0
|
CB
|
J:CYS150
|
4.5
|
14.8
|
1.0
|
SG
|
J:CYS113
|
4.6
|
15.7
|
1.0
|
CG2
|
J:THR151
|
4.8
|
14.2
|
1.0
|
N
|
J:CYS148
|
4.9
|
16.1
|
1.0
|
O
|
J:LEU147
|
5.0
|
16.4
|
1.0
|
CA
|
J:CYS150
|
5.0
|
14.7
|
1.0
|
C
|
J:CYS116
|
5.0
|
15.2
|
1.0
|
|
Iron binding site 7 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 7 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe602
b:16.5
occ:1.00
|
FE1
|
J:FES602
|
0.0
|
16.5
|
1.0
|
S1
|
J:FES602
|
2.2
|
15.7
|
1.0
|
S2
|
J:FES602
|
2.2
|
15.3
|
1.0
|
SG
|
J:CYS73
|
2.2
|
16.7
|
1.0
|
SG
|
J:CYS51
|
2.2
|
17.6
|
1.0
|
FE2
|
J:FES602
|
2.8
|
16.2
|
1.0
|
CB
|
J:CYS73
|
3.1
|
17.6
|
1.0
|
CB
|
J:CYS51
|
3.4
|
16.5
|
1.0
|
CB
|
J:ASN71
|
4.1
|
16.4
|
1.0
|
N
|
J:CYS73
|
4.2
|
16.7
|
1.0
|
CA
|
J:CYS73
|
4.2
|
17.6
|
1.0
|
N
|
J:CYS51
|
4.3
|
15.3
|
1.0
|
N
|
J:GLY46
|
4.3
|
20.1
|
1.0
|
SG
|
J:CYS43
|
4.4
|
16.9
|
1.0
|
CG
|
J:ASN71
|
4.4
|
18.2
|
1.0
|
CA
|
J:CYS51
|
4.5
|
15.8
|
1.0
|
OD1
|
J:ASN71
|
4.5
|
20.7
|
1.0
|
N
|
J:GLY44
|
4.5
|
18.1
|
1.0
|
CA
|
J:GLY46
|
4.5
|
20.0
|
1.0
|
SG
|
J:CYS48
|
4.7
|
16.9
|
1.0
|
CA
|
J:GLY44
|
4.7
|
17.9
|
1.0
|
N
|
J:GLY49
|
4.8
|
15.8
|
1.0
|
CA
|
J:ASN71
|
4.8
|
17.1
|
1.0
|
N
|
J:GLU45
|
4.9
|
19.2
|
1.0
|
|
Iron binding site 8 out
of 8 in 3nvv
Go back to
Iron Binding Sites List in 3nvv
Iron binding site 8 out
of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Fe602
b:16.2
occ:1.00
|
FE2
|
J:FES602
|
0.0
|
16.2
|
1.0
|
S2
|
J:FES602
|
2.2
|
15.3
|
1.0
|
S1
|
J:FES602
|
2.2
|
15.7
|
1.0
|
SG
|
J:CYS43
|
2.3
|
16.9
|
1.0
|
SG
|
J:CYS48
|
2.3
|
16.9
|
1.0
|
FE1
|
J:FES602
|
2.8
|
16.5
|
1.0
|
N
|
J:CYS43
|
3.4
|
18.0
|
1.0
|
CB
|
J:CYS48
|
3.4
|
17.0
|
1.0
|
CB
|
J:CYS43
|
3.5
|
16.0
|
1.0
|
N
|
J:CYS48
|
3.5
|
17.4
|
1.0
|
N
|
J:GLY49
|
3.8
|
15.8
|
1.0
|
CA
|
J:CYS43
|
3.9
|
16.9
|
1.0
|
CA
|
J:CYS48
|
3.9
|
17.3
|
1.0
|
N
|
J:GLY44
|
3.9
|
18.1
|
1.0
|
C
|
J:GLY42
|
4.0
|
17.2
|
1.0
|
C
|
J:CYS48
|
4.2
|
16.1
|
1.0
|
N
|
J:GLY47
|
4.3
|
20.2
|
1.0
|
N
|
J:GLY42
|
4.3
|
16.5
|
1.0
|
C
|
J:CYS43
|
4.3
|
18.4
|
1.0
|
CA
|
J:GLY42
|
4.3
|
16.9
|
1.0
|
SG
|
J:CYS73
|
4.4
|
16.7
|
1.0
|
N
|
J:GLY46
|
4.5
|
20.1
|
1.0
|
N
|
J:ALA50
|
4.5
|
15.8
|
1.0
|
SG
|
J:CYS51
|
4.6
|
17.6
|
1.0
|
C
|
J:GLY47
|
4.6
|
19.9
|
1.0
|
N
|
J:GLU45
|
4.7
|
19.2
|
1.0
|
C
|
J:GLY46
|
4.8
|
20.0
|
1.0
|
O
|
J:GLY42
|
4.8
|
17.2
|
1.0
|
CA
|
J:GLY49
|
4.8
|
15.9
|
1.0
|
CA
|
J:GLY46
|
4.9
|
20.0
|
1.0
|
CA
|
J:GLY44
|
4.9
|
17.9
|
1.0
|
CA
|
J:GLY47
|
5.0
|
19.7
|
1.0
|
|
Reference:
H.Cao,
J.Hall,
R.Hille.
X-Ray Crystal Structure of Arsenite-Inhibited Xanthine Oxidase: Mu-Sulfido,Mu-Oxo Double Bridge Between Molybdenum and Arsenic in the Active Site. J.Am.Chem.Soc. V. 133 12414 2011.
ISSN: ISSN 0002-7863
PubMed: 21761899
DOI: 10.1021/JA2050265
Page generated: Sun Aug 4 16:44:30 2024
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