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Molybdenum 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 (Fe) 8 atoms
Calcium (Ca) 4 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum 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 Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form, PDB code: 1vdv:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 1vdv

Go back to Molybdenum Binding Sites List in 1vdv
Molybdenum binding site 1 out of 2 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo 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:Mo3004

b:19.9
occ:1.00
MO A:MOS3004 0.0 19.9 1.0
O2 A:MOS3004 1.7 18.9 1.0
O1 A:MOS3004 2.0 20.3 1.0
S A:MOS3004 2.2 21.7 1.0
S2' A:MTE3003 2.4 17.9 1.0
S1' A:MTE3003 2.4 12.9 1.0
C1' A:MTE3003 3.2 16.4 1.0
C2' A:MTE3003 3.3 14.0 1.0
O A:HOH5555 3.9 23.2 1.0
CA A:GLY799 4.1 11.4 1.0
OE2 A:GLU1261 4.2 14.9 1.0
N A:GLY799 4.2 8.2 1.0
CB A:ALA1078 4.2 13.9 1.0
N A:ALA1079 4.3 14.0 1.0
CD A:GLU1261 4.3 15.1 1.0
CA A:ALA1078 4.4 14.0 1.0
C A:PHE798 4.5 11.7 1.0
C6 A:MTE3003 4.5 15.2 1.0
NE2 A:GLN767 4.6 11.2 1.0
O A:PHE798 4.6 13.3 1.0
N A:ARG912 4.6 12.7 1.0
CA A:ARG912 4.7 13.9 1.0
CG A:GLU1261 4.7 9.8 1.0
OE2 A:GLU802 4.7 14.9 1.0
OE1 A:GLU1261 4.8 13.5 1.0
C3' A:MTE3003 4.8 17.0 1.0
C A:ALA1078 4.9 13.5 1.0

Molybdenum binding site 2 out of 2 in 1vdv

Go back to Molybdenum Binding Sites List in 1vdv
Molybdenum binding site 2 out of 2 in the Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Bovine Milk Xanthine Dehydrogenase Y-700 Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo4004

b:21.6
occ:1.00
MO B:MOS4004 0.0 21.6 1.0
O2 B:MOS4004 1.7 18.7 1.0
O1 B:MOS4004 2.0 18.0 1.0
S B:MOS4004 2.2 21.4 1.0
S2' B:MTE4003 2.4 18.7 1.0
S1' B:MTE4003 2.4 15.0 1.0
C1' B:MTE4003 3.2 17.4 1.0
C2' B:MTE4003 3.3 17.4 1.0
O B:HOH6314 3.9 19.6 1.0
OE2 B:GLU1261 4.0 14.2 1.0
CA B:GLY799 4.0 13.5 1.0
CB B:ALA1078 4.0 12.0 1.0
N B:GLY799 4.1 14.2 1.0
N B:ALA1079 4.2 12.4 1.0
CA B:ALA1078 4.3 13.7 1.0
CD B:GLU1261 4.3 13.6 1.0
C B:PHE798 4.4 14.3 1.0
C6 B:MTE4003 4.6 16.3 1.0
NE2 B:GLN767 4.6 11.1 1.0
O B:PHE798 4.6 13.8 1.0
CG B:GLU1261 4.6 9.2 1.0
N B:ARG912 4.7 14.1 1.0
OE2 B:GLU802 4.7 11.3 1.0
CA B:ARG912 4.7 15.8 1.0
C B:ALA1078 4.8 12.7 1.0
OE1 B:GLU1261 4.8 11.9 1.0
C3' B:MTE4003 4.9 18.5 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: Tue Dec 15 05:16:39 2020

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