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Molybdenum in PDB 1jro: Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus, PDB code: 1jro was solved by J.J.Truglio, K.Theis, S.Leimkuhler, R.Rappa, K.V.Rajagopalan, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.875, 141.053, 158.113, 109.53, 105.83, 101.33
R / Rfree (%) 21.3 / 25.2

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus (pdb code 1jro). 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, PDB code: 1jro:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 1jro

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Molybdenum binding site 1 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mo3004

b:31.5
occ:0.70
MO B:MOS3004 0.0 31.5 0.7
O2 B:MOS3004 1.7 33.0 0.7
O1 B:MOS3004 2.0 31.6 0.7
S B:MOS3004 2.1 36.6 0.7
S2' B:MTE3003 2.2 32.0 0.7
S1' B:MTE3003 2.3 15.8 0.7
OE2 B:GLU730 2.7 27.4 1.0
C1' B:MTE3003 3.2 24.3 0.7
C2' B:MTE3003 3.4 24.3 0.7
CD B:GLU730 3.6 31.6 1.0
N B:ALA529 3.9 34.2 1.0
CB B:ALA528 4.0 29.9 1.0
CA B:ALA528 4.2 29.9 1.0
CG B:GLU730 4.2 25.1 1.0
CA B:GLY229 4.4 17.1 1.0
CA B:ARG342 4.4 22.9 1.0
N B:ARG342 4.4 22.0 1.0
C B:ALA528 4.6 32.5 1.0
OE1 B:GLU730 4.6 35.6 1.0
N B:GLY229 4.6 17.9 1.0
C6 B:MTE3003 4.6 21.7 0.7
NE2 B:GLN197 4.7 11.6 1.0
C B:PHE228 4.8 18.8 1.0
C3' B:MTE3003 4.9 27.9 0.7
CA B:ALA529 5.0 35.1 1.0

Molybdenum binding site 2 out of 4 in 1jro

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Molybdenum binding site 2 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mo3004

b:25.2
occ:0.70
MO D:MOS3004 0.0 25.2 0.7
O2 D:MOS3004 1.7 31.1 0.7
S D:MOS3004 2.0 30.2 0.7
O1 D:MOS3004 2.0 26.0 0.7
S2' D:MTE3003 2.2 25.5 0.7
S1' D:MTE3003 2.4 17.6 0.7
OE2 D:GLU730 2.8 25.8 1.0
C1' D:MTE3003 3.4 22.2 0.7
C2' D:MTE3003 3.5 22.6 0.7
CD D:GLU730 3.8 28.0 1.0
N D:ALA529 3.8 28.2 1.0
CB D:ALA528 4.0 27.1 1.0
CA D:ALA528 4.1 26.4 1.0
N D:ARG342 4.3 20.1 1.0
CA D:GLY229 4.4 13.1 1.0
CA D:ARG342 4.4 20.4 1.0
CG D:GLU730 4.4 26.4 1.0
C D:ALA528 4.5 27.6 1.0
N D:GLY229 4.6 13.0 1.0
NE2 D:GLN197 4.7 16.9 1.0
C6 D:MTE3003 4.7 18.9 0.7
OE1 D:GLU730 4.8 28.6 1.0
C D:PHE228 4.8 13.3 1.0
O D:PHE228 4.8 16.0 1.0
CA D:ALA529 4.9 30.6 1.0
C D:PHE341 5.0 20.7 1.0

Molybdenum binding site 3 out of 4 in 1jro

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Molybdenum binding site 3 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mo3004

b:27.1
occ:0.70
MO F:MOS3004 0.0 27.1 0.7
O2 F:MOS3004 1.7 26.9 0.7
S F:MOS3004 2.0 32.8 0.7
O1 F:MOS3004 2.0 18.0 0.7
S1' F:MTE3003 2.2 14.6 0.7
S2' F:MTE3003 2.4 34.5 0.7
OE2 F:GLU730 2.6 36.4 1.0
C1' F:MTE3003 3.2 24.0 0.7
C2' F:MTE3003 3.5 26.2 0.7
CD F:GLU730 3.5 37.8 1.0
N F:ALA529 4.0 32.1 1.0
CG F:GLU730 4.1 30.9 1.0
CA F:ARG342 4.3 22.7 1.0
CA F:GLY229 4.3 18.3 1.0
N F:ARG342 4.4 23.0 1.0
CA F:ALA528 4.4 28.9 1.0
OE1 F:GLU730 4.4 43.5 1.0
N F:GLY229 4.4 18.3 1.0
CB F:ALA528 4.4 28.1 1.0
C6 F:MTE3003 4.6 24.7 0.7
C F:ALA528 4.7 30.5 1.0
C F:PHE228 4.7 19.1 1.0
NE2 F:GLN197 4.8 16.1 1.0
N F:GLY343 4.9 22.9 1.0
CA F:ALA529 4.9 34.4 1.0
O F:PHE228 4.9 20.5 1.0
C F:PHE341 5.0 24.3 1.0

Molybdenum binding site 4 out of 4 in 1jro

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Molybdenum binding site 4 out of 4 in the Crystal Structure of Xanthine Dehydrogenase From Rhodobacter Capsulatus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mo3004

b:43.0
occ:0.70
MO H:MOS3004 0.0 43.0 0.7
O2 H:MOS3004 1.7 45.7 0.7
O1 H:MOS3004 2.0 40.5 0.7
S H:MOS3004 2.1 39.4 0.7
S2' H:MTE3003 2.4 36.1 0.7
S1' H:MTE3003 2.5 24.8 0.7
OE2 H:GLU730 2.7 42.7 1.0
C1' H:MTE3003 3.4 28.2 0.7
C2' H:MTE3003 3.5 27.4 0.7
CD H:GLU730 3.7 40.9 1.0
N H:ALA529 4.0 34.1 1.0
CB H:ALA528 4.2 29.9 1.0
CA H:ALA528 4.3 30.1 1.0
CA H:ARG342 4.3 28.3 1.0
CG H:GLU730 4.3 33.6 1.0
N H:ARG342 4.3 28.9 1.0
CA H:GLY229 4.4 22.6 1.0
C H:ALA528 4.6 32.5 1.0
OE1 H:GLU730 4.7 42.7 1.0
N H:GLY229 4.7 22.0 1.0
C6 H:MTE3003 4.7 26.6 0.7
O H:PHE228 4.7 23.6 1.0
C H:PHE228 4.8 23.3 1.0
N H:GLY343 4.9 28.8 1.0
NE2 H:GLN197 4.9 21.3 1.0
N H:SER530 4.9 37.4 1.0
CA H:ALA529 5.0 35.6 1.0
C H:PHE341 5.0 28.7 1.0

Reference:

J.J.Truglio, K.Theis, S.Leimkuhler, R.Rappa, K.V.Rajagopalan, C.Kisker. Crystal Structures of the Active and Alloxanthine-Inhibited Forms of Xanthine Dehydrogenase From Rhodobacter Capsulatus Structure V. 10 115 2002.
ISSN: ISSN 0969-2126
PubMed: 11796116
DOI: 10.1016/S0969-2126(01)00697-9
Page generated: Wed Sep 23 13:27:32 2020
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