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Molybdenum in PDB 2w54: Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde, PDB code: 2w54 was solved by J.A.Doebbler, J.J.Truglio, S.Leimkuhler, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.571, 140.695, 157.859, 109.63, 105.83, 101.23
R / Rfree (%) 18.6 / 22.4

Other elements in 2w54:

The structure of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde also contains other interesting chemical elements:

Barium (Ba) 4 atoms
Iron (Fe) 16 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde (pdb code 2w54). 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 Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde, PDB code: 2w54:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 2w54

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Molybdenum binding site 1 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo1778

b:40.4
occ:0.70
 MO B:XAX1778 0.0 40.4 0.7
O2 B:XAX1778 1.7 39.7 0.7
S3 B:XAX1778 2.1 40.6 0.7
O1 B:XAX1778 2.1 39.3 0.7
S2' B:XAX1778 2.3 38.5 0.7
S1' B:XAX1778 2.3 38.2 0.7
C1' B:XAX1778 3.3 36.7 0.7
C2' B:XAX1778 3.3 36.7 0.7
OE2 B:GLU730 3.6 25.7 1.0
CD B:GLU730 4.0 25.4 1.0
CA B:ALA528 4.1 25.0 1.0
CB B:ALA528 4.2 25.0 1.0
N B:ALA529 4.3 25.7 1.0
CG B:GLU730 4.3 24.4 1.0
CA B:GLY229 4.3 22.9 1.0
N B:GLY229 4.4 22.9 1.0
NE2 B:GLN197 4.5 22.5 1.0
N2 B:HHR1780 4.5 83.7 1.0
N B:ARG342 4.5 23.0 1.0
CA B:ARG342 4.5 23.1 1.0
C B:ALA528 4.6 25.3 1.0
C6 B:XAX1778 4.6 35.1 0.7
OE1 B:GLU730 4.6 25.8 1.0
O B:THR527 4.6 24.0 1.0
C3' B:XAX1778 4.7 35.3 0.7
C B:PHE228 4.7 22.9 1.0
O B:PHE228 4.9 23.0 1.0

Molybdenum binding site 2 out of 4 in 2w54

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Molybdenum binding site 2 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mo1778

b:30.9
occ:0.70
 MO D:XAX1778 0.0 30.9 0.7
O1 D:XAX1778 1.7 29.8 0.7
S3 D:XAX1778 2.1 31.3 0.7
O2 D:XAX1778 2.1 29.9 0.7
S2' D:XAX1778 2.3 28.9 0.7
S1' D:XAX1778 2.3 28.8 0.7
C2' D:XAX1778 3.3 27.5 0.7
OE2 D:GLU730 3.3 25.7 1.0
C1' D:XAX1778 3.3 27.4 0.7
CD D:GLU730 3.8 25.5 1.0
CB D:ALA528 4.1 24.8 1.0
CA D:ALA528 4.1 24.6 1.0
CG D:GLU730 4.2 24.5 1.0
N D:ALA529 4.3 25.4 1.0
CA D:GLY229 4.3 22.7 1.0
N2 D:HHR1780 4.4 76.5 1.0
N D:GLY229 4.4 22.6 1.0
NE2 D:GLN197 4.5 22.2 1.0
CA D:ARG342 4.5 23.1 1.0
N D:ARG342 4.6 23.0 1.0
OE1 D:GLU730 4.6 25.8 1.0
C6 D:XAX1778 4.6 25.8 0.7
C D:ALA528 4.7 24.9 1.0
C3' D:XAX1778 4.7 26.7 0.7
C D:PHE228 4.8 22.5 1.0
O D:THR527 4.8 24.0 1.0
O D:PHE228 4.9 22.6 1.0

Molybdenum binding site 3 out of 4 in 2w54

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Molybdenum binding site 3 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mo1778

b:33.0
occ:0.70
 MO F:XAX1778 0.0 33.0 0.7
O2 F:XAX1778 1.7 32.2 0.7
S3 F:XAX1778 2.0 33.1 0.7
O1 F:XAX1778 2.1 32.1 0.7
S2' F:XAX1778 2.3 32.1 0.7
S1' F:XAX1778 2.3 31.5 0.7
C1' F:XAX1778 3.3 30.8 0.7
C2' F:XAX1778 3.3 31.1 0.7
OE2 F:GLU730 3.3 25.7 1.0
CD F:GLU730 3.9 25.7 1.0
CA F:ALA528 4.1 24.8 1.0
CB F:ALA528 4.1 24.9 1.0
CG F:GLU730 4.2 24.5 1.0
CA F:GLY229 4.3 22.8 1.0
N F:ALA529 4.3 25.6 1.0
N F:GLY229 4.4 22.8 1.0
CA F:ARG342 4.5 22.9 1.0
NE2 F:GLN197 4.5 22.3 1.0
N F:ARG342 4.6 22.9 1.0
C6 F:XAX1778 4.6 29.8 0.7
N2 F:HHR1780 4.6 81.9 1.0
C F:ALA528 4.7 25.1 1.0
C F:PHE228 4.7 22.8 1.0
C3' F:XAX1778 4.7 30.7 0.7
OE1 F:GLU730 4.7 26.4 1.0
O F:THR527 4.8 24.0 1.0
O F:PHE228 4.9 22.9 1.0

Molybdenum binding site 4 out of 4 in 2w54

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Molybdenum binding site 4 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde


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 Xanthine Dehydrogenase From Rhodobacter Capsulatus in Complex with Bound Inhibitor Pterin-6-Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mo1778

b:44.8
occ:0.70
 MO H:XAX1778 0.0 44.8 0.7
O2 H:XAX1778 1.7 43.9 0.7
S3 H:XAX1778 2.1 44.2 0.7
O1 H:XAX1778 2.1 43.3 0.7
S2' H:XAX1778 2.3 42.6 0.7
S1' H:XAX1778 2.3 41.6 0.7
C1' H:XAX1778 3.3 40.2 0.7
C2' H:XAX1778 3.3 40.3 0.7
OE2 H:GLU730 3.6 25.5 1.0
CD H:GLU730 3.8 25.5 1.0
CA H:ALA528 4.1 24.9 1.0
CB H:ALA528 4.2 24.9 1.0
OE1 H:GLU730 4.2 25.7 1.0
CA H:GLY229 4.2 23.0 1.0
CG H:GLU730 4.2 24.6 1.0
N H:ALA529 4.3 25.6 1.0
N H:GLY229 4.3 23.0 1.0
NE2 H:GLN197 4.4 22.7 1.0
N2 H:HHR1780 4.5 84.3 1.0
CA H:ARG342 4.6 23.1 1.0
C6 H:XAX1778 4.6 38.7 0.7
N H:ARG342 4.6 22.9 1.0
C H:ALA528 4.7 25.2 1.0
O H:THR527 4.7 24.1 1.0
C3' H:XAX1778 4.7 38.7 0.7
C H:PHE228 4.7 22.9 1.0
O H:PHE228 5.0 22.9 1.0

Reference:

U.Dietzel, J.Kuper, J.A.Doebbler, A.Schulte, J.J.Truglio, S.Leimkuhler, C.Kisker. Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. J.Biol.Chem. V. 284 8768 2009.
ISSN: ISSN 0021-9258
PubMed: 19109249
DOI: 10.1074/JBC.M808114200
Page generated: Sun Oct 6 15:49:03 2024

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