Iron in PDB 1vdv: Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Enzymatic activity of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
All present enzymatic activity of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form:
1.1.1.204;
Protein crystallography data
The structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv
was solved by
A.Fukunari,
K.Okamoto,
T.Nishino,
B.T.Eger,
E.F.Pai,
M.Kamezawa,
I.Yamada,
N.Kato,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.98
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
166.817,
123.940,
148.888,
90.00,
91.16,
90.00
|
R / Rfree (%)
|
17.8 /
21.5
|
Other elements in 1vdv:
The structure of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
(pdb code 1vdv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 1 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3001
b:11.8
occ:1.00
|
FE1
|
A:FES3001
|
0.0
|
11.8
|
1.0
|
S2
|
A:FES3001
|
2.2
|
11.0
|
1.0
|
S1
|
A:FES3001
|
2.2
|
11.6
|
1.0
|
SG
|
A:CYS113
|
2.4
|
10.6
|
1.0
|
SG
|
A:CYS150
|
2.4
|
13.1
|
1.0
|
FE2
|
A:FES3001
|
2.7
|
10.4
|
1.0
|
CB
|
A:CYS113
|
3.4
|
9.3
|
1.0
|
CB
|
A:CYS150
|
3.4
|
13.6
|
1.0
|
O
|
A:HOH5391
|
3.5
|
12.7
|
1.0
|
N
|
A:CYS113
|
3.6
|
6.7
|
1.0
|
N
|
A:GLY114
|
3.8
|
10.4
|
1.0
|
CA
|
A:CYS113
|
3.9
|
9.7
|
1.0
|
N
|
A:CYS150
|
4.1
|
10.2
|
1.0
|
C
|
A:CYS113
|
4.3
|
10.1
|
1.0
|
CA
|
A:CYS150
|
4.3
|
13.1
|
1.0
|
N
|
A:PHE115
|
4.4
|
12.4
|
1.0
|
SG
|
A:CYS148
|
4.5
|
11.6
|
1.0
|
C
|
A:GLN112
|
4.7
|
9.2
|
1.0
|
SG
|
A:CYS116
|
4.7
|
12.3
|
1.0
|
N
|
A:ARG149
|
4.8
|
10.7
|
1.0
|
CB
|
A:GLN112
|
4.8
|
7.7
|
1.0
|
CA
|
A:GLY114
|
4.8
|
8.9
|
1.0
|
N
|
A:CYS116
|
4.9
|
11.3
|
1.0
|
|
Iron binding site 2 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 2 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3001
b:10.4
occ:1.00
|
FE2
|
A:FES3001
|
0.0
|
10.4
|
1.0
|
S2
|
A:FES3001
|
2.2
|
11.0
|
1.0
|
S1
|
A:FES3001
|
2.2
|
11.6
|
1.0
|
SG
|
A:CYS116
|
2.4
|
12.3
|
1.0
|
SG
|
A:CYS148
|
2.4
|
11.6
|
1.0
|
FE1
|
A:FES3001
|
2.7
|
11.8
|
1.0
|
CB
|
A:CYS116
|
3.4
|
10.9
|
1.0
|
CB
|
A:CYS148
|
3.4
|
12.0
|
1.0
|
CA
|
A:CYS148
|
3.7
|
10.7
|
1.0
|
N
|
A:ARG149
|
4.1
|
10.7
|
1.0
|
N
|
A:CYS116
|
4.2
|
11.3
|
1.0
|
O
|
A:HOH5320
|
4.3
|
7.6
|
1.0
|
C
|
A:CYS148
|
4.3
|
9.7
|
1.0
|
N
|
A:CYS150
|
4.3
|
10.2
|
1.0
|
CA
|
A:CYS116
|
4.4
|
8.7
|
1.0
|
SG
|
A:CYS150
|
4.5
|
13.1
|
1.0
|
CB
|
A:CYS150
|
4.5
|
13.6
|
1.0
|
CG2
|
A:THR151
|
4.7
|
8.6
|
1.0
|
SG
|
A:CYS113
|
4.7
|
10.6
|
1.0
|
O
|
A:LEU147
|
4.9
|
12.7
|
1.0
|
C
|
A:CYS116
|
5.0
|
9.7
|
1.0
|
CA
|
A:CYS150
|
5.0
|
13.1
|
1.0
|
|
Iron binding site 3 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 3 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3002
b:10.7
occ:1.00
|
FE1
|
A:FES3002
|
0.0
|
10.7
|
1.0
|
S1
|
A:FES3002
|
2.2
|
9.6
|
1.0
|
S2
|
A:FES3002
|
2.2
|
10.5
|
1.0
|
SG
|
A:CYS73
|
2.4
|
10.6
|
1.0
|
SG
|
A:CYS51
|
2.4
|
9.8
|
1.0
|
FE2
|
A:FES3002
|
2.7
|
10.3
|
1.0
|
CB
|
A:CYS73
|
3.3
|
11.0
|
1.0
|
CB
|
A:CYS51
|
3.4
|
5.1
|
1.0
|
N
|
A:CYS51
|
4.2
|
9.5
|
1.0
|
CB
|
A:ASN71
|
4.2
|
11.6
|
1.0
|
N
|
A:GLY46
|
4.3
|
10.2
|
1.0
|
N
|
A:CYS73
|
4.3
|
9.6
|
1.0
|
SG
|
A:CYS43
|
4.4
|
10.6
|
1.0
|
N
|
A:GLY44
|
4.4
|
13.7
|
1.0
|
CA
|
A:GLY46
|
4.4
|
10.7
|
1.0
|
OD1
|
A:ASN71
|
4.4
|
15.9
|
1.0
|
CA
|
A:CYS73
|
4.4
|
13.1
|
1.0
|
CA
|
A:CYS51
|
4.4
|
8.2
|
1.0
|
CG
|
A:ASN71
|
4.5
|
11.6
|
1.0
|
SG
|
A:CYS48
|
4.7
|
9.6
|
1.0
|
CA
|
A:GLY44
|
4.7
|
12.5
|
1.0
|
N
|
A:GLY49
|
4.8
|
11.3
|
1.0
|
N
|
A:ALA50
|
4.9
|
11.7
|
1.0
|
N
|
A:GLU45
|
4.9
|
11.4
|
1.0
|
CA
|
A:ASN71
|
5.0
|
9.8
|
1.0
|
|
Iron binding site 4 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 4 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe3002
b:10.3
occ:1.00
|
FE2
|
A:FES3002
|
0.0
|
10.3
|
1.0
|
S2
|
A:FES3002
|
2.2
|
10.5
|
1.0
|
S1
|
A:FES3002
|
2.2
|
9.6
|
1.0
|
SG
|
A:CYS48
|
2.4
|
9.6
|
1.0
|
SG
|
A:CYS43
|
2.4
|
10.6
|
1.0
|
FE1
|
A:FES3002
|
2.7
|
10.7
|
1.0
|
N
|
A:CYS43
|
3.3
|
7.7
|
1.0
|
CB
|
A:CYS48
|
3.4
|
9.8
|
1.0
|
CB
|
A:CYS43
|
3.4
|
13.0
|
1.0
|
N
|
A:CYS48
|
3.6
|
10.3
|
1.0
|
N
|
A:GLY44
|
3.8
|
13.7
|
1.0
|
CA
|
A:CYS43
|
3.8
|
9.5
|
1.0
|
N
|
A:GLY49
|
3.9
|
11.3
|
1.0
|
CA
|
A:CYS48
|
3.9
|
10.6
|
1.0
|
C
|
A:GLY42
|
4.0
|
8.6
|
1.0
|
N
|
A:GLY42
|
4.2
|
12.2
|
1.0
|
C
|
A:CYS48
|
4.2
|
12.6
|
1.0
|
C
|
A:CYS43
|
4.3
|
12.2
|
1.0
|
CA
|
A:GLY42
|
4.3
|
9.5
|
1.0
|
N
|
A:ALA50
|
4.4
|
11.7
|
1.0
|
N
|
A:GLY47
|
4.4
|
11.8
|
1.0
|
N
|
A:GLY46
|
4.4
|
10.2
|
1.0
|
SG
|
A:CYS73
|
4.5
|
10.6
|
1.0
|
N
|
A:GLU45
|
4.7
|
11.4
|
1.0
|
C
|
A:GLY47
|
4.7
|
13.7
|
1.0
|
SG
|
A:CYS51
|
4.7
|
9.8
|
1.0
|
CA
|
A:GLY46
|
4.8
|
10.7
|
1.0
|
C
|
A:GLY46
|
4.8
|
14.0
|
1.0
|
CA
|
A:GLY44
|
4.8
|
12.5
|
1.0
|
CA
|
A:GLY49
|
4.9
|
11.6
|
1.0
|
O
|
A:GLY42
|
4.9
|
9.2
|
1.0
|
CB
|
A:ALA50
|
4.9
|
12.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 5 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4001
b:10.5
occ:1.00
|
FE1
|
B:FES4001
|
0.0
|
10.5
|
1.0
|
S2
|
B:FES4001
|
2.2
|
9.7
|
1.0
|
S1
|
B:FES4001
|
2.2
|
11.1
|
1.0
|
SG
|
B:CYS113
|
2.4
|
10.3
|
1.0
|
SG
|
B:CYS150
|
2.4
|
11.6
|
1.0
|
FE2
|
B:FES4001
|
2.7
|
10.6
|
1.0
|
CB
|
B:CYS150
|
3.4
|
9.5
|
1.0
|
CB
|
B:CYS113
|
3.4
|
9.3
|
1.0
|
N
|
B:CYS113
|
3.5
|
8.8
|
1.0
|
O
|
B:HOH6323
|
3.6
|
9.6
|
1.0
|
N
|
B:GLY114
|
3.8
|
5.7
|
1.0
|
CA
|
B:CYS113
|
3.9
|
9.0
|
1.0
|
N
|
B:CYS150
|
4.1
|
10.4
|
1.0
|
C
|
B:CYS113
|
4.2
|
8.7
|
1.0
|
CA
|
B:CYS150
|
4.4
|
10.9
|
1.0
|
N
|
B:PHE115
|
4.4
|
9.3
|
1.0
|
SG
|
B:CYS148
|
4.5
|
11.3
|
1.0
|
C
|
B:GLN112
|
4.6
|
9.3
|
1.0
|
SG
|
B:CYS116
|
4.7
|
10.9
|
1.0
|
CA
|
B:GLY114
|
4.7
|
5.3
|
1.0
|
CB
|
B:GLN112
|
4.7
|
12.5
|
1.0
|
N
|
B:ARG149
|
4.8
|
11.6
|
1.0
|
N
|
B:CYS116
|
4.9
|
7.7
|
1.0
|
N
|
B:GLN112
|
5.0
|
10.0
|
1.0
|
C
|
B:GLY114
|
5.0
|
8.8
|
1.0
|
|
Iron binding site 6 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 6 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4001
b:10.6
occ:1.00
|
FE2
|
B:FES4001
|
0.0
|
10.6
|
1.0
|
S2
|
B:FES4001
|
2.2
|
9.7
|
1.0
|
S1
|
B:FES4001
|
2.2
|
11.1
|
1.0
|
SG
|
B:CYS116
|
2.4
|
10.9
|
1.0
|
SG
|
B:CYS148
|
2.4
|
11.3
|
1.0
|
FE1
|
B:FES4001
|
2.7
|
10.5
|
1.0
|
CB
|
B:CYS116
|
3.4
|
9.4
|
1.0
|
CB
|
B:CYS148
|
3.4
|
10.9
|
1.0
|
CA
|
B:CYS148
|
3.7
|
12.4
|
1.0
|
N
|
B:ARG149
|
4.1
|
11.6
|
1.0
|
N
|
B:CYS116
|
4.2
|
7.7
|
1.0
|
C
|
B:CYS148
|
4.3
|
12.0
|
1.0
|
O
|
B:HOH5370
|
4.3
|
9.8
|
1.0
|
N
|
B:CYS150
|
4.3
|
10.4
|
1.0
|
CA
|
B:CYS116
|
4.4
|
8.1
|
1.0
|
CB
|
B:CYS150
|
4.5
|
9.5
|
1.0
|
SG
|
B:CYS150
|
4.5
|
11.6
|
1.0
|
SG
|
B:CYS113
|
4.7
|
10.3
|
1.0
|
CG2
|
B:THR151
|
4.8
|
7.8
|
1.0
|
O
|
B:LEU147
|
4.9
|
11.4
|
1.0
|
C
|
B:CYS116
|
5.0
|
9.2
|
1.0
|
N
|
B:CYS148
|
5.0
|
13.1
|
1.0
|
CA
|
B:CYS150
|
5.0
|
10.9
|
1.0
|
N
|
B:THR151
|
5.0
|
11.1
|
1.0
|
|
Iron binding site 7 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 7 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4002
b:11.3
occ:1.00
|
FE1
|
B:FES4002
|
0.0
|
11.3
|
1.0
|
S2
|
B:FES4002
|
2.2
|
10.5
|
1.0
|
S1
|
B:FES4002
|
2.2
|
11.8
|
1.0
|
SG
|
B:CYS73
|
2.4
|
10.8
|
1.0
|
SG
|
B:CYS51
|
2.4
|
9.5
|
1.0
|
FE2
|
B:FES4002
|
2.7
|
9.8
|
1.0
|
CB
|
B:CYS73
|
3.3
|
8.0
|
1.0
|
CB
|
B:CYS51
|
3.4
|
5.5
|
1.0
|
N
|
B:GLY46
|
4.2
|
14.6
|
1.0
|
CB
|
B:ASN71
|
4.2
|
8.1
|
1.0
|
N
|
B:CYS73
|
4.3
|
9.4
|
1.0
|
N
|
B:CYS51
|
4.3
|
9.3
|
1.0
|
CA
|
B:GLY46
|
4.4
|
12.4
|
1.0
|
CA
|
B:CYS73
|
4.4
|
10.8
|
1.0
|
SG
|
B:CYS43
|
4.4
|
11.5
|
1.0
|
N
|
B:GLY44
|
4.4
|
7.8
|
1.0
|
OD1
|
B:ASN71
|
4.4
|
15.0
|
1.0
|
CG
|
B:ASN71
|
4.5
|
11.6
|
1.0
|
CA
|
B:CYS51
|
4.5
|
10.0
|
1.0
|
CA
|
B:GLY44
|
4.7
|
10.0
|
1.0
|
SG
|
B:CYS48
|
4.7
|
10.4
|
1.0
|
N
|
B:GLY49
|
4.8
|
10.6
|
1.0
|
N
|
B:GLU45
|
4.9
|
13.6
|
1.0
|
CA
|
B:ASN71
|
5.0
|
8.6
|
1.0
|
N
|
B:ALA50
|
5.0
|
10.5
|
1.0
|
|
Iron binding site 8 out
of 8 in 1vdv
Go back to
Iron Binding Sites List in 1vdv
Iron binding site 8 out
of 8 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe4002
b:9.8
occ:1.00
|
FE2
|
B:FES4002
|
0.0
|
9.8
|
1.0
|
S2
|
B:FES4002
|
2.2
|
10.5
|
1.0
|
S1
|
B:FES4002
|
2.2
|
11.8
|
1.0
|
SG
|
B:CYS48
|
2.4
|
10.4
|
1.0
|
SG
|
B:CYS43
|
2.4
|
11.5
|
1.0
|
FE1
|
B:FES4002
|
2.7
|
11.3
|
1.0
|
N
|
B:CYS43
|
3.4
|
9.7
|
1.0
|
CB
|
B:CYS48
|
3.4
|
10.7
|
1.0
|
CB
|
B:CYS43
|
3.5
|
10.1
|
1.0
|
N
|
B:CYS48
|
3.6
|
11.3
|
1.0
|
N
|
B:GLY44
|
3.8
|
7.8
|
1.0
|
CA
|
B:CYS43
|
3.9
|
9.2
|
1.0
|
N
|
B:GLY49
|
3.9
|
10.6
|
1.0
|
CA
|
B:CYS48
|
3.9
|
10.5
|
1.0
|
C
|
B:GLY42
|
4.0
|
10.7
|
1.0
|
N
|
B:GLY42
|
4.2
|
9.0
|
1.0
|
C
|
B:CYS48
|
4.3
|
11.2
|
1.0
|
CA
|
B:GLY42
|
4.3
|
9.9
|
1.0
|
N
|
B:GLY46
|
4.3
|
14.6
|
1.0
|
C
|
B:CYS43
|
4.3
|
10.8
|
1.0
|
N
|
B:GLY47
|
4.4
|
12.6
|
1.0
|
N
|
B:ALA50
|
4.4
|
10.5
|
1.0
|
SG
|
B:CYS73
|
4.5
|
10.8
|
1.0
|
N
|
B:GLU45
|
4.6
|
13.6
|
1.0
|
C
|
B:GLY47
|
4.7
|
14.7
|
1.0
|
SG
|
B:CYS51
|
4.7
|
9.5
|
1.0
|
CA
|
B:GLY46
|
4.7
|
12.4
|
1.0
|
C
|
B:GLY46
|
4.8
|
13.8
|
1.0
|
CA
|
B:GLY44
|
4.8
|
10.0
|
1.0
|
CA
|
B:GLY49
|
4.9
|
8.9
|
1.0
|
O
|
B:GLY42
|
4.9
|
10.2
|
1.0
|
CB
|
B:ALA50
|
5.0
|
10.0
|
1.0
|
|
Reference:
A.Fukunari,
K.Okamoto,
T.Nishino,
B.T.Eger,
E.F.Pai,
M.Kamezawa,
I.Yamada,
N.Kato.
Y-700 [1-[3-Cyano-4-(2,2-Dimethylpropoxy)Phenyl]-1H- Pyrazole-4-Carboxylic Acid]: A Potent Xanthine Oxidoreductase Inhibitor with Hepatic Excretion J.Pharmacol.Exp.Ther. V. 311 519 2004.
ISSN: ISSN 0022-3565
PubMed: 15190124
DOI: 10.1124/JPET.104.070433
Page generated: Sat Aug 3 16:12:46 2024
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