Iron in PDB 7dnv: Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Enzymatic activity of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
All present enzymatic activity of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.:
1.17.1.4;
1.17.3.2;
Protein crystallography data
The structure of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol., PDB code: 7dnv
was solved by
K.Okamoto,
T.Nishino,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.48 /
1.99
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
167.704,
123.49,
150.089,
90,
90.9,
90
|
R / Rfree (%)
|
19 /
22.8
|
Other elements in 7dnv:
The structure of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
(pdb code 7dnv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol., PDB code: 7dnv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 1 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1401
b:22.7
occ:1.00
|
FE1
|
A:FES1401
|
0.0
|
22.7
|
1.0
|
S1
|
A:FES1401
|
2.2
|
22.0
|
1.0
|
S2
|
A:FES1401
|
2.3
|
20.8
|
1.0
|
SG
|
A:CYS113
|
2.3
|
21.6
|
1.0
|
SG
|
A:CYS150
|
2.3
|
21.1
|
1.0
|
FE2
|
A:FES1401
|
2.8
|
21.6
|
1.0
|
CB
|
A:CYS150
|
3.3
|
23.0
|
1.0
|
CB
|
A:CYS113
|
3.3
|
21.4
|
1.0
|
O
|
A:HOH1744
|
3.5
|
23.6
|
1.0
|
N
|
A:CYS113
|
3.5
|
21.0
|
1.0
|
CA
|
A:CYS113
|
3.8
|
21.3
|
1.0
|
N
|
A:GLY114
|
3.9
|
20.0
|
1.0
|
N
|
A:CYS150
|
4.1
|
22.9
|
1.0
|
C
|
A:CYS113
|
4.2
|
20.6
|
1.0
|
CA
|
A:CYS150
|
4.3
|
22.8
|
1.0
|
N
|
A:PHE115
|
4.4
|
24.3
|
1.0
|
SG
|
A:CYS148
|
4.5
|
24.0
|
1.0
|
C
|
A:GLN112
|
4.7
|
23.1
|
1.0
|
SG
|
A:CYS116
|
4.7
|
23.0
|
1.0
|
N
|
A:ARG149
|
4.8
|
23.9
|
1.0
|
CB
|
A:GLN112
|
4.9
|
23.0
|
1.0
|
CA
|
A:GLY114
|
4.9
|
22.8
|
1.0
|
N
|
A:CYS116
|
4.9
|
22.9
|
1.0
|
|
Iron binding site 2 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 2 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1401
b:21.6
occ:1.00
|
FE2
|
A:FES1401
|
0.0
|
21.6
|
1.0
|
S1
|
A:FES1401
|
2.2
|
22.0
|
1.0
|
S2
|
A:FES1401
|
2.3
|
20.8
|
1.0
|
SG
|
A:CYS116
|
2.3
|
23.0
|
1.0
|
SG
|
A:CYS148
|
2.3
|
24.0
|
1.0
|
FE1
|
A:FES1401
|
2.8
|
22.7
|
1.0
|
CB
|
A:CYS148
|
3.3
|
21.1
|
1.0
|
CB
|
A:CYS116
|
3.5
|
22.2
|
1.0
|
CA
|
A:CYS148
|
3.6
|
20.8
|
1.0
|
N
|
A:ARG149
|
4.1
|
23.9
|
1.0
|
N
|
A:CYS116
|
4.3
|
22.9
|
1.0
|
C
|
A:CYS148
|
4.3
|
20.4
|
1.0
|
N
|
A:CYS150
|
4.3
|
22.9
|
1.0
|
CB
|
A:CYS150
|
4.4
|
23.0
|
1.0
|
O
|
A:HOH1586
|
4.4
|
19.7
|
1.0
|
CA
|
A:CYS116
|
4.4
|
22.9
|
1.0
|
SG
|
A:CYS150
|
4.5
|
21.1
|
1.0
|
CG2
|
A:THR151
|
4.7
|
20.1
|
1.0
|
SG
|
A:CYS113
|
4.7
|
21.6
|
1.0
|
O
|
A:LEU147
|
4.9
|
22.8
|
1.0
|
CA
|
A:CYS150
|
4.9
|
22.8
|
1.0
|
N
|
A:CYS148
|
4.9
|
22.4
|
1.0
|
|
Iron binding site 3 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 3 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1402
b:24.0
occ:1.00
|
FE1
|
A:FES1402
|
0.0
|
24.0
|
1.0
|
S1
|
A:FES1402
|
2.2
|
25.2
|
1.0
|
S2
|
A:FES1402
|
2.2
|
27.6
|
1.0
|
SG
|
A:CYS73
|
2.3
|
23.4
|
1.0
|
SG
|
A:CYS51
|
2.3
|
23.2
|
1.0
|
FE2
|
A:FES1402
|
2.8
|
23.9
|
1.0
|
CB
|
A:CYS73
|
3.2
|
26.2
|
1.0
|
CB
|
A:CYS51
|
3.4
|
19.9
|
1.0
|
N
|
A:CYS73
|
4.2
|
22.9
|
1.0
|
CB
|
A:ASN71
|
4.2
|
27.1
|
1.0
|
CA
|
A:CYS73
|
4.3
|
25.3
|
1.0
|
N
|
A:GLY46
|
4.3
|
22.7
|
1.0
|
N
|
A:CYS51
|
4.4
|
21.3
|
1.0
|
N
|
A:GLY44
|
4.4
|
24.4
|
1.0
|
SG
|
A:CYS43
|
4.4
|
25.7
|
1.0
|
ND2
|
A:ASN71
|
4.4
|
27.8
|
1.0
|
CA
|
A:CYS51
|
4.5
|
20.4
|
1.0
|
CA
|
A:GLY46
|
4.5
|
24.8
|
1.0
|
CG
|
A:ASN71
|
4.6
|
26.9
|
1.0
|
SG
|
A:CYS48
|
4.7
|
24.1
|
1.0
|
CA
|
A:GLY44
|
4.7
|
22.9
|
1.0
|
N
|
A:GLU45
|
4.8
|
23.0
|
1.0
|
N
|
A:GLY49
|
4.9
|
22.2
|
1.0
|
CA
|
A:ASN71
|
5.0
|
25.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 4 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1402
b:23.9
occ:1.00
|
FE2
|
A:FES1402
|
0.0
|
23.9
|
1.0
|
SG
|
A:CYS48
|
2.2
|
24.1
|
1.0
|
S2
|
A:FES1402
|
2.3
|
27.6
|
1.0
|
S1
|
A:FES1402
|
2.3
|
25.2
|
1.0
|
SG
|
A:CYS43
|
2.4
|
25.7
|
1.0
|
FE1
|
A:FES1402
|
2.8
|
24.0
|
1.0
|
N
|
A:CYS43
|
3.4
|
24.6
|
1.0
|
CB
|
A:CYS48
|
3.4
|
24.2
|
1.0
|
CB
|
A:CYS43
|
3.5
|
28.5
|
1.0
|
N
|
A:CYS48
|
3.6
|
23.9
|
1.0
|
N
|
A:GLY44
|
3.8
|
24.4
|
1.0
|
CA
|
A:CYS43
|
3.9
|
26.8
|
1.0
|
CA
|
A:CYS48
|
3.9
|
23.1
|
1.0
|
N
|
A:GLY49
|
3.9
|
22.2
|
1.0
|
C
|
A:GLY42
|
4.1
|
25.4
|
1.0
|
C
|
A:CYS43
|
4.3
|
27.0
|
1.0
|
C
|
A:CYS48
|
4.3
|
21.6
|
1.0
|
N
|
A:GLY42
|
4.3
|
24.5
|
1.0
|
CA
|
A:GLY42
|
4.3
|
24.2
|
1.0
|
N
|
A:GLY47
|
4.3
|
26.3
|
1.0
|
N
|
A:GLY46
|
4.4
|
22.7
|
1.0
|
N
|
A:ALA50
|
4.4
|
22.9
|
1.0
|
SG
|
A:CYS73
|
4.5
|
23.4
|
1.0
|
N
|
A:GLU45
|
4.7
|
23.0
|
1.0
|
SG
|
A:CYS51
|
4.7
|
23.2
|
1.0
|
C
|
A:GLY47
|
4.7
|
28.0
|
1.0
|
C
|
A:GLY46
|
4.8
|
26.5
|
1.0
|
CA
|
A:GLY44
|
4.9
|
22.9
|
1.0
|
CA
|
A:GLY46
|
4.9
|
24.8
|
1.0
|
CA
|
A:GLY49
|
4.9
|
23.3
|
1.0
|
|
Iron binding site 5 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 5 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1401
b:22.1
occ:1.00
|
FE1
|
B:FES1401
|
0.0
|
22.1
|
1.0
|
S2
|
B:FES1401
|
2.2
|
20.5
|
1.0
|
S1
|
B:FES1401
|
2.3
|
24.0
|
1.0
|
SG
|
B:CYS113
|
2.3
|
22.1
|
1.0
|
SG
|
B:CYS150
|
2.3
|
22.6
|
1.0
|
FE2
|
B:FES1401
|
2.7
|
22.1
|
1.0
|
CB
|
B:CYS150
|
3.2
|
20.5
|
1.0
|
CB
|
B:CYS113
|
3.3
|
18.7
|
1.0
|
O
|
B:HOH1722
|
3.5
|
21.4
|
1.0
|
N
|
B:CYS113
|
3.6
|
21.1
|
1.0
|
CA
|
B:CYS113
|
3.9
|
19.4
|
1.0
|
N
|
B:GLY114
|
3.9
|
21.5
|
1.0
|
N
|
B:CYS150
|
4.1
|
21.4
|
1.0
|
CA
|
B:CYS150
|
4.3
|
20.5
|
1.0
|
C
|
B:CYS113
|
4.3
|
19.9
|
1.0
|
SG
|
B:CYS148
|
4.3
|
21.9
|
1.0
|
N
|
B:PHE115
|
4.4
|
24.8
|
1.0
|
SG
|
B:CYS116
|
4.6
|
23.4
|
1.0
|
C
|
B:GLN112
|
4.7
|
21.6
|
1.0
|
CB
|
B:GLN112
|
4.8
|
20.0
|
1.0
|
N
|
B:ARG149
|
4.8
|
23.2
|
1.0
|
CA
|
B:GLY114
|
4.9
|
21.4
|
1.0
|
N
|
B:GLN112
|
5.0
|
21.1
|
1.0
|
N
|
B:CYS116
|
5.0
|
21.9
|
1.0
|
|
Iron binding site 6 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 6 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1401
b:22.1
occ:1.00
|
FE2
|
B:FES1401
|
0.0
|
22.1
|
1.0
|
S1
|
B:FES1401
|
2.2
|
24.0
|
1.0
|
SG
|
B:CYS148
|
2.2
|
21.9
|
1.0
|
S2
|
B:FES1401
|
2.3
|
20.5
|
1.0
|
SG
|
B:CYS116
|
2.3
|
23.4
|
1.0
|
FE1
|
B:FES1401
|
2.7
|
22.1
|
1.0
|
CB
|
B:CYS148
|
3.2
|
21.0
|
1.0
|
CB
|
B:CYS116
|
3.4
|
23.3
|
1.0
|
CA
|
B:CYS148
|
3.6
|
20.9
|
1.0
|
N
|
B:ARG149
|
4.1
|
23.2
|
1.0
|
C
|
B:CYS148
|
4.3
|
19.6
|
1.0
|
N
|
B:CYS116
|
4.3
|
21.9
|
1.0
|
N
|
B:CYS150
|
4.3
|
21.4
|
1.0
|
CB
|
B:CYS150
|
4.3
|
20.5
|
1.0
|
O
|
B:HOH1652
|
4.4
|
19.8
|
1.0
|
SG
|
B:CYS150
|
4.4
|
22.6
|
1.0
|
CA
|
B:CYS116
|
4.4
|
20.5
|
1.0
|
SG
|
B:CYS113
|
4.7
|
22.1
|
1.0
|
CG2
|
B:THR151
|
4.8
|
25.2
|
1.0
|
N
|
B:CYS148
|
4.9
|
22.6
|
1.0
|
CA
|
B:CYS150
|
4.9
|
20.5
|
1.0
|
O
|
B:LEU147
|
4.9
|
20.7
|
1.0
|
|
Iron binding site 7 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 7 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1402
b:22.7
occ:1.00
|
FE1
|
B:FES1402
|
0.0
|
22.7
|
1.0
|
S1
|
B:FES1402
|
2.2
|
23.2
|
1.0
|
S2
|
B:FES1402
|
2.2
|
23.3
|
1.0
|
SG
|
B:CYS73
|
2.3
|
21.8
|
1.0
|
SG
|
B:CYS51
|
2.3
|
22.2
|
1.0
|
FE2
|
B:FES1402
|
2.8
|
22.7
|
1.0
|
CB
|
B:CYS73
|
3.0
|
25.9
|
1.0
|
CB
|
B:CYS51
|
3.4
|
20.6
|
1.0
|
CA
|
B:CYS73
|
4.2
|
24.4
|
1.0
|
N
|
B:CYS73
|
4.2
|
24.3
|
1.0
|
CB
|
B:ASN71
|
4.3
|
22.1
|
1.0
|
N
|
B:GLY46
|
4.3
|
23.3
|
1.0
|
SG
|
B:CYS43
|
4.4
|
22.3
|
1.0
|
N
|
B:CYS51
|
4.4
|
20.9
|
1.0
|
N
|
B:GLY44
|
4.4
|
22.2
|
1.0
|
OD1
|
B:ASN71
|
4.5
|
26.1
|
1.0
|
CA
|
B:CYS51
|
4.5
|
21.3
|
1.0
|
CA
|
B:GLY46
|
4.6
|
23.3
|
1.0
|
CG
|
B:ASN71
|
4.6
|
23.0
|
1.0
|
SG
|
B:CYS48
|
4.7
|
20.7
|
1.0
|
CA
|
B:GLY44
|
4.7
|
23.8
|
1.0
|
N
|
B:GLY49
|
4.9
|
22.5
|
1.0
|
N
|
B:GLU45
|
4.9
|
23.5
|
1.0
|
CA
|
B:ASN71
|
4.9
|
22.0
|
1.0
|
|
Iron binding site 8 out
of 8 in 7dnv
Go back to
Iron Binding Sites List in 7dnv
Iron binding site 8 out
of 8 in the Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Oxidized Structure of Bovine Xanthine Oxidoreductase Bound with Oxypurinol. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1402
b:22.7
occ:1.00
|
FE2
|
B:FES1402
|
0.0
|
22.7
|
1.0
|
SG
|
B:CYS48
|
2.2
|
20.7
|
1.0
|
S1
|
B:FES1402
|
2.2
|
23.2
|
1.0
|
S2
|
B:FES1402
|
2.3
|
23.3
|
1.0
|
SG
|
B:CYS43
|
2.3
|
22.3
|
1.0
|
FE1
|
B:FES1402
|
2.8
|
22.7
|
1.0
|
N
|
B:CYS43
|
3.4
|
23.4
|
1.0
|
CB
|
B:CYS48
|
3.4
|
21.3
|
1.0
|
CB
|
B:CYS43
|
3.5
|
24.7
|
1.0
|
N
|
B:CYS48
|
3.5
|
22.3
|
1.0
|
N
|
B:GLY44
|
3.9
|
22.2
|
1.0
|
N
|
B:GLY49
|
3.9
|
22.5
|
1.0
|
CA
|
B:CYS48
|
3.9
|
21.8
|
1.0
|
CA
|
B:CYS43
|
3.9
|
25.4
|
1.0
|
C
|
B:GLY42
|
4.0
|
24.0
|
1.0
|
C
|
B:CYS48
|
4.2
|
23.1
|
1.0
|
CA
|
B:GLY42
|
4.3
|
22.8
|
1.0
|
N
|
B:GLY42
|
4.3
|
22.8
|
1.0
|
C
|
B:CYS43
|
4.3
|
25.6
|
1.0
|
N
|
B:GLY47
|
4.4
|
23.5
|
1.0
|
N
|
B:GLY46
|
4.5
|
23.3
|
1.0
|
N
|
B:ALA50
|
4.5
|
21.9
|
1.0
|
SG
|
B:CYS73
|
4.5
|
21.8
|
1.0
|
SG
|
B:CYS51
|
4.7
|
22.2
|
1.0
|
N
|
B:GLU45
|
4.7
|
23.5
|
1.0
|
C
|
B:GLY47
|
4.7
|
25.0
|
1.0
|
C
|
B:GLY46
|
4.8
|
22.6
|
1.0
|
CA
|
B:GLY49
|
4.9
|
21.5
|
1.0
|
CA
|
B:GLY44
|
4.9
|
23.8
|
1.0
|
CA
|
B:GLY46
|
4.9
|
23.3
|
1.0
|
O
|
B:GLY42
|
5.0
|
24.2
|
1.0
|
|
Reference:
K.Okamoto,
T.Nishino.
Bovine Xanthine Oxidoreductase Bounf with Oxypurinol (Oxidized Form) To Be Published.
Page generated: Fri Dec 17 09:31:45 2021
|