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Calcium in PDB 1jrp: Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus

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

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus, PDB code: 1jrp 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) 30.00 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.617, 140.728, 157.665, 109.59, 105.84, 101.25
R / Rfree (%) 19.3 / 24.3

Other elements in 1jrp:

The structure of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Iron (Fe) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus (pdb code 1jrp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus, PDB code: 1jrp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1jrp

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Calcium binding site 1 out of 4 in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3006

b:36.5
occ:1.00
 OG1 B:THR266 2.5 17.2 1.0
ND1 B:HIS173 3.0 22.0 1.0
O B:GLY267 3.0 19.4 1.0
OE2 B:GLU172 3.1 28.8 1.0
OH B:TYR175 3.1 18.1 1.0
OE1 B:GLU172 3.2 27.2 1.0
CB B:THR266 3.5 19.4 1.0
CD B:GLU172 3.5 27.8 1.0
CZ B:TYR175 3.7 17.7 1.0
CE2 B:TYR175 3.8 16.3 1.0
CE1 B:HIS173 3.9 22.9 1.0
CG B:HIS173 3.9 22.3 1.0
CB B:HIS173 4.1 21.6 1.0
CG2 B:THR266 4.2 20.7 1.0
C B:GLY267 4.2 19.6 1.0
OD2 B:ASP262 4.2 23.9 1.0
N B:HIS173 4.3 19.9 1.0
N B:GLY267 4.5 18.5 1.0
NZ B:LYS268 4.6 9.6 1.0
C B:THR266 4.6 18.8 1.0
CA B:THR266 4.7 19.1 1.0
CE1 B:TYR175 4.8 18.5 1.0
CA B:HIS173 4.9 19.6 1.0
CA B:GLY230 4.9 19.4 1.0
CD2 B:TYR175 4.9 17.6 1.0
O B:THR266 4.9 19.0 1.0
NE2 B:HIS173 5.0 21.5 1.0
CA B:GLY267 5.0 19.2 1.0
CD2 B:HIS173 5.0 21.0 1.0

Calcium binding site 2 out of 4 in 1jrp

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Calcium binding site 2 out of 4 in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca3006

b:27.2
occ:1.00
 ND1 D:HIS173 2.7 18.0 1.0
OG1 D:THR266 2.7 16.4 1.0
O D:GLY267 3.0 13.3 1.0
OH D:TYR175 3.0 14.9 1.0
OE1 D:GLU172 3.2 23.1 1.0
OE2 D:GLU172 3.2 30.4 1.0
CD D:GLU172 3.6 25.5 1.0
CE1 D:HIS173 3.6 18.3 1.0
CE2 D:TYR175 3.6 9.8 1.0
CG D:HIS173 3.7 19.9 1.0
CZ D:TYR175 3.7 14.2 1.0
CB D:THR266 3.7 16.5 1.0
CB D:HIS173 3.9 18.0 1.0
C D:GLY267 4.2 13.3 1.0
N D:HIS173 4.3 17.1 1.0
N D:GLY267 4.4 14.0 1.0
OD2 D:ASP262 4.4 22.3 1.0
CG2 D:THR266 4.6 16.5 1.0
C D:THR266 4.6 15.5 1.0
CD2 D:TYR175 4.8 15.3 1.0
NE2 D:HIS173 4.8 16.3 1.0
CD2 D:HIS173 4.8 16.6 1.0
CA D:THR266 4.8 16.1 1.0
CA D:HIS173 4.8 16.8 1.0
CE1 D:TYR175 4.9 13.2 1.0
CA D:GLY230 4.9 18.0 1.0
NZ D:LYS268 4.9 10.6 1.0
CA D:GLY267 4.9 13.3 1.0
O D:THR266 5.0 17.0 1.0

Calcium binding site 3 out of 4 in 1jrp

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Calcium binding site 3 out of 4 in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca3006

b:32.0
occ:1.00
 O F:GLY267 2.8 17.3 1.0
OG1 F:THR266 2.8 20.8 1.0
ND1 F:HIS173 2.9 26.8 1.0
OH F:TYR175 3.1 23.0 1.0
OE2 F:GLU172 3.1 28.4 1.0
OE1 F:GLU172 3.3 27.8 1.0
CD F:GLU172 3.6 27.3 1.0
CB F:THR266 3.6 22.1 1.0
CZ F:TYR175 3.7 25.1 1.0
CE1 F:HIS173 3.8 23.5 1.0
CE2 F:TYR175 3.8 22.1 1.0
CG F:HIS173 3.8 23.4 1.0
C F:GLY267 4.0 19.0 1.0
CB F:HIS173 4.0 20.9 1.0
N F:HIS173 4.2 20.6 1.0
N F:GLY267 4.4 21.2 1.0
OD2 F:ASP262 4.4 25.7 1.0
CG2 F:THR266 4.4 23.4 1.0
C F:THR266 4.5 22.7 1.0
NZ F:LYS268 4.6 17.0 1.0
CA F:THR266 4.7 22.1 1.0
CE1 F:TYR175 4.8 26.0 1.0
CA F:GLY267 4.8 19.9 1.0
CA F:HIS173 4.8 21.0 1.0
O F:THR266 4.9 23.9 1.0
CA F:GLY230 4.9 20.9 1.0
NE2 F:HIS173 4.9 22.1 1.0
N F:LYS268 4.9 18.2 1.0
CD2 F:HIS173 5.0 23.1 1.0
CG F:LYS268 5.0 19.3 1.0

Calcium binding site 4 out of 4 in 1jrp

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Calcium binding site 4 out of 4 in the Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Xanthine Dehydrogenase Inhibited By Alloxanthine From Rhodobacter Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca3006

b:41.1
occ:1.00
 OG1 H:THR266 2.5 19.8 1.0
OH H:TYR175 2.9 15.0 1.0
ND1 H:HIS173 3.0 22.7 1.0
O H:GLY267 3.1 22.9 1.0
OE2 H:GLU172 3.2 30.6 1.0
OE1 H:GLU172 3.2 33.6 1.0
CB H:THR266 3.5 22.4 1.0
CZ H:TYR175 3.6 16.1 1.0
CD H:GLU172 3.6 33.3 1.0
CE2 H:TYR175 3.7 15.7 1.0
CE1 H:HIS173 3.9 24.0 1.0
CG H:HIS173 3.9 26.3 1.0
OD2 H:ASP262 4.1 28.1 1.0
CB H:HIS173 4.1 25.3 1.0
C H:GLY267 4.3 23.3 1.0
CG2 H:THR266 4.3 21.4 1.0
N H:GLY267 4.4 21.7 1.0
C H:THR266 4.5 21.4 1.0
N H:HIS173 4.5 25.6 1.0
CA H:THR266 4.6 21.6 1.0
CE1 H:TYR175 4.7 16.5 1.0
O H:THR266 4.8 22.3 1.0
NZ H:LYS268 4.8 13.2 1.0
CD2 H:TYR175 4.8 15.9 1.0
NE2 H:GLN179 4.9 33.0 1.0
CA H:GLY267 4.9 23.6 1.0
O H:ASP262 4.9 28.0 1.0
NE2 H:HIS173 5.0 25.4 1.0
CA H:GLY230 5.0 22.5 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: Thu Jul 11 10:52:35 2024

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