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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

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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

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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

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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

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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

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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

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