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Molybdenum in PDB 3eub: Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

Enzymatic activity of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

All present enzymatic activity of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine, PDB code: 3eub was solved by J.M.Pauff, H.Cao, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.08 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.298, 133.176, 142.633, 96.88, 93.11, 90.02
R / Rfree (%) 21.4 / 26.8

Other elements in 3eub:

The structure of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine (pdb code 3eub). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine, PDB code: 3eub:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 3eub

Go back to Molybdenum Binding Sites List in 3eub
Molybdenum binding site 1 out of 4 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo1334

b:16.6
occ:1.00
MO1 C:MOM1334 0.0 16.6 1.0
OM2 C:MOM1334 1.7 16.9 1.0
OM1 C:MOM1334 2.0 17.7 1.0
OM3 C:MOM1334 2.2 20.2 1.0
S1' C:MTE1333 2.3 11.6 1.0
S2' C:MTE1333 2.6 7.7 1.0
C1' C:MTE1333 3.4 9.8 1.0
C2' C:MTE1333 3.5 9.8 1.0
OE2 C:GLU1261 3.8 12.8 1.0
CD C:GLU1261 4.1 11.3 1.0
CA C:GLY799 4.1 5.8 1.0
N C:ALA1079 4.1 8.2 1.0
N C:GLY799 4.3 5.3 1.0
CA C:ALA1078 4.3 7.2 1.0
N C:ARG912 4.3 4.6 1.0
CA C:ARG912 4.3 6.0 1.0
CB C:ALA1078 4.4 7.0 1.0
CG C:GLU1261 4.4 10.4 1.0
C C:PHE798 4.4 4.5 1.0
NE2 C:GLN767 4.5 5.9 1.0
O C:PHE798 4.5 4.6 1.0
C8 C:XAN7319 4.6 27.7 1.0
OE1 C:GLU1261 4.7 12.8 1.0
OE2 C:GLU802 4.7 13.5 1.0
C C:ALA1078 4.7 7.7 1.0
C6 C:MTE1333 4.8 10.7 1.0
C3' C:MTE1333 4.9 11.1 1.0

Molybdenum binding site 2 out of 4 in 3eub

Go back to Molybdenum Binding Sites List in 3eub
Molybdenum binding site 2 out of 4 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mo1334

b:15.8
occ:1.00
MO1 L:MOM1334 0.0 15.8 1.0
OM2 L:MOM1334 1.7 15.3 1.0
OM1 L:MOM1334 2.0 12.4 1.0
OM3 L:MOM1334 2.2 16.2 1.0
S1' L:MTE1333 2.4 13.8 1.0
S2' L:MTE1333 2.5 12.0 1.0
C1' L:MTE1333 3.4 11.7 1.0
C2' L:MTE1333 3.4 11.4 1.0
OE2 L:GLU1261 4.0 12.6 1.0
CD L:GLU1261 4.0 11.2 1.0
CA L:GLY799 4.1 5.8 1.0
N L:ALA1079 4.2 8.2 1.0
N L:GLY799 4.2 5.2 1.0
CA L:ARG912 4.2 5.4 1.0
N L:ARG912 4.2 4.6 1.0
CA L:ALA1078 4.3 7.1 1.0
OE1 L:GLU1261 4.3 12.4 1.0
C L:PHE798 4.4 4.6 1.0
CB L:ALA1078 4.4 6.7 1.0
CG L:GLU1261 4.4 10.3 1.0
NE2 L:GLN767 4.5 5.7 1.0
O L:PHE798 4.5 4.5 1.0
C8 L:XAN7319 4.6 33.1 1.0
OE2 L:GLU802 4.6 13.9 1.0
C L:ALA1078 4.7 7.6 1.0
C6 L:MTE1333 4.8 8.8 1.0
C3' L:MTE1333 4.9 9.6 1.0
CB L:ARG912 5.0 5.5 1.0

Molybdenum binding site 3 out of 4 in 3eub

Go back to Molybdenum Binding Sites List in 3eub
Molybdenum binding site 3 out of 4 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mo1334

b:15.9
occ:1.00
MO1 U:MOM1334 0.0 15.9 1.0
OM2 U:MOM1334 1.7 12.7 1.0
OM1 U:MOM1334 2.0 15.0 1.0
OM3 U:MOM1334 2.2 15.8 1.0
S1' U:MTE1333 2.4 15.1 1.0
S2' U:MTE1333 2.6 14.8 1.0
C1' U:MTE1333 3.4 13.6 1.0
C2' U:MTE1333 3.5 13.2 1.0
OE2 U:GLU1261 4.0 12.4 1.0
CA U:GLY799 4.1 5.9 1.0
CD U:GLU1261 4.1 12.6 1.0
N U:GLY799 4.1 6.1 1.0
N U:ALA1079 4.3 5.7 1.0
C8 U:XAN7319 4.3 41.6 1.0
CB U:ALA1078 4.3 4.1 1.0
CG U:GLU1261 4.4 11.4 1.0
N U:ARG912 4.4 4.4 1.0
CA U:ALA1078 4.4 4.2 1.0
CA U:ARG912 4.4 5.1 1.0
C U:PHE798 4.4 5.6 1.0
OE1 U:GLU1261 4.6 15.4 1.0
O U:PHE798 4.7 5.8 1.0
N9 U:XAN7319 4.7 42.0 1.0
NE2 U:GLN767 4.8 8.6 1.0
C6 U:MTE1333 4.8 12.3 1.0
OE2 U:GLU802 4.8 9.3 1.0
C U:ALA1078 4.9 5.0 1.0
C3' U:MTE1333 4.9 10.7 1.0

Molybdenum binding site 4 out of 4 in 3eub

Go back to Molybdenum Binding Sites List in 3eub
Molybdenum binding site 4 out of 4 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mo1334

b:14.9
occ:1.00
MO1 4:MOM1334 0.0 14.9 1.0
OM2 4:MOM1334 1.7 12.8 1.0
OM1 4:MOM1334 2.0 12.4 1.0
OM3 4:MOM1334 2.1 18.6 1.0
S1' 4:MTE1333 2.2 12.8 1.0
S2' 4:MTE1333 2.6 12.2 1.0
C1' 4:MTE1333 3.2 14.8 1.0
C2' 4:MTE1333 3.3 13.4 1.0
CA 4:GLY799 4.1 6.0 1.0
N 4:GLY799 4.2 6.3 1.0
OE2 4:GLU1261 4.2 13.2 1.0
N 4:ALA1079 4.2 5.2 1.0
CB 4:ALA1078 4.3 4.1 1.0
CA 4:ALA1078 4.3 4.2 1.0
CD 4:GLU1261 4.3 12.9 1.0
C 4:PHE798 4.4 5.7 1.0
CA 4:ARG912 4.5 5.3 1.0
C8 4:XAN7319 4.5 34.4 1.0
O 4:PHE798 4.5 5.7 1.0
N 4:ARG912 4.5 4.2 1.0
CG 4:GLU1261 4.6 11.4 1.0
C6 4:MTE1333 4.6 13.8 1.0
NE2 4:GLN767 4.7 8.5 1.0
OE2 4:GLU802 4.7 9.0 1.0
C3' 4:MTE1333 4.8 14.7 1.0
OE1 4:GLU1261 4.8 15.1 1.0
C 4:ALA1078 4.8 4.9 1.0

Reference:

J.M.Pauff, H.Cao, R.Hille. Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: Crystal Structures in Complex with Xanthine and Lumazine. J.Biol.Chem. V. 284 8760 2009.
ISSN: ISSN 0021-9258
PubMed: 19109252
DOI: 10.1074/JBC.M804517200
Page generated: Tue Dec 15 05:17:52 2020

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