Atomistry » Iron » PDB 1uwm-1vme » 1vdv
Atomistry »
  Iron »
    PDB 1uwm-1vme »
      1vdv »

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:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 4 atoms

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: Sun Dec 13 14:34:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy