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Molybdenum in PDB 3bdj: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor

Enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor, PDB code: 3bdj was solved by B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.517, 124.074, 148.797, 90.00, 91.01, 90.00
R / Rfree (%) 19.1 / 22.4

Other elements in 3bdj:

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Calcium (Ca) 2 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor (pdb code 3bdj). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor, PDB code: 3bdj:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 3bdj

Go back to Molybdenum Binding Sites List in 3bdj
Molybdenum binding site 1 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo3004

b:15.6
occ:1.00
MO1 A:MOW3004 0.0 15.6 1.0
O1 A:MOW3004 1.7 14.4 1.0
N8 A:1415101 2.3 13.8 1.0
S2' A:MTE3003 2.4 14.5 1.0
S1 A:MOW3004 2.4 15.6 1.0
S1' A:MTE3003 2.4 12.1 1.0
C7 A:1415101 3.2 15.1 1.0
N9 A:1415101 3.2 15.6 1.0
C2' A:MTE3003 3.4 12.1 1.0
C1' A:MTE3003 3.4 12.9 1.0
OE2 A:GLU1261 3.8 15.7 1.0
CA A:GLY799 4.0 11.8 1.0
CD A:GLU1261 4.2 15.8 1.0
N A:ALA1079 4.2 14.4 1.0
CB A:ALA1078 4.2 15.9 1.0
N A:GLY799 4.2 10.7 1.0
C5 A:1415101 4.4 14.6 1.0
C4 A:1415101 4.4 15.4 1.0
CA A:ALA1078 4.5 14.2 1.0
C A:PHE798 4.6 12.3 1.0
CG A:GLU1261 4.7 13.7 1.0
CA A:ARG912 4.7 12.7 1.0
NE2 A:GLN767 4.7 13.3 1.0
N A:ARG912 4.7 12.5 1.0
C3' A:MTE3003 4.7 13.9 1.0
OE1 A:GLU1261 4.8 14.4 1.0
O A:PHE798 4.8 12.2 1.0
C6 A:MTE3003 4.8 11.8 1.0
C A:ALA1078 4.9 15.2 1.0
OE2 A:GLU802 4.9 15.7 1.0

Molybdenum binding site 2 out of 2 in 3bdj

Go back to Molybdenum Binding Sites List in 3bdj
Molybdenum binding site 2 out of 2 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo4004

b:16.3
occ:1.00
MO1 B:MOW4004 0.0 16.3 1.0
O1 B:MOW4004 1.7 14.0 1.0
N8 B:1415102 2.3 13.9 1.0
S2' B:MTE4003 2.4 14.2 1.0
S1 B:MOW4004 2.4 14.2 1.0
S1' B:MTE4003 2.4 10.8 1.0
C7 B:1415102 3.2 15.5 1.0
N9 B:1415102 3.2 13.9 1.0
C2' B:MTE4003 3.4 12.8 1.0
C1' B:MTE4003 3.4 13.3 1.0
OE2 B:GLU1261 3.6 15.1 1.0
CB B:ALA1078 4.0 14.2 1.0
CA B:GLY799 4.1 11.2 1.0
CD B:GLU1261 4.1 12.7 1.0
N B:ALA1079 4.2 13.6 1.0
N B:GLY799 4.2 13.7 1.0
C5 B:1415102 4.4 14.9 1.0
C4 B:1415102 4.4 15.2 1.0
CA B:ALA1078 4.4 14.0 1.0
C B:PHE798 4.6 14.8 1.0
CG B:GLU1261 4.6 11.5 1.0
OE1 B:GLU1261 4.6 13.5 1.0
NE2 B:GLN767 4.6 12.5 1.0
CA B:ARG912 4.7 14.2 1.0
O B:PHE798 4.7 14.0 1.0
N B:ARG912 4.8 14.7 1.0
C3' B:MTE4003 4.8 14.7 1.0
OE2 B:GLU802 4.8 11.3 1.0
C6 B:MTE4003 4.9 11.6 1.0
C B:ALA1078 4.9 14.0 1.0

Reference:

K.Okamoto, B.T.Eger, T.Nishino, E.F.Pai, T.Nishino. Mechanism of Inhibition of Xanthine Oxidoreductase By Allopurinol: Crystal Structure of Reduced Bovine Milk Xanthine Oxidoreductase Bound with Oxipurinol. Nucleosides Nucleotides V. 27 888 2008NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 18600558
DOI: 10.1080/15257770802146577
Page generated: Tue Dec 15 05:17:45 2020

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