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Calcium in PDB 2w3s: Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine, PDB code: 2w3s was solved by U.Dietzel, J.Kuper, S.Leimkuhler, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.12 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.830, 140.560, 158.170, 109.60, 105.89, 101.18
R / Rfree (%) 23.2 / 28.4

Other elements in 2w3s:

The structure of Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine 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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine (pdb code 2w3s). 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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine, PDB code: 2w3s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2w3s

Go back to Calcium Binding Sites List in 2w3s
Calcium binding site 1 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1779

b:48.5
occ:1.00
 OG1 B:THR266 2.7 31.0 1.0
ND1 B:HIS173 2.8 29.4 1.0
O B:GLY267 2.9 30.6 1.0
OE2 B:GLU172 3.0 35.2 1.0
CB B:THR266 3.3 30.4 1.0
OH B:TYR175 3.4 25.3 1.0
CE1 B:HIS173 3.5 31.1 1.0
OE1 B:GLU172 3.6 32.1 1.0
CD B:GLU172 3.7 33.6 1.0
CG B:HIS173 3.8 31.6 1.0
CZ B:TYR175 4.0 27.3 1.0
CE2 B:TYR175 4.1 26.3 1.0
C B:GLY267 4.2 31.1 1.0
CB B:HIS173 4.2 31.4 1.0
CG2 B:THR266 4.2 29.3 1.0
C B:THR266 4.4 30.5 1.0
CA B:THR266 4.5 30.6 1.0
NZ B:LYS268 4.6 26.4 1.0
N B:GLY267 4.6 30.7 1.0
O B:THR266 4.6 30.6 1.0
NE2 B:HIS173 4.6 32.3 1.0
N B:HIS173 4.7 31.8 1.0
OD2 B:ASP262 4.7 32.7 1.0
CA B:GLY230 4.7 25.8 1.0
CD2 B:HIS173 4.8 31.4 1.0
CG B:LYS268 4.9 31.2 1.0
O B:ASP262 4.9 33.4 1.0

Calcium binding site 2 out of 4 in 2w3s

Go back to Calcium Binding Sites List in 2w3s
Calcium binding site 2 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1779

b:49.1
occ:1.00
 O D:GLY267 2.6 29.2 1.0
ND1 D:HIS173 2.7 30.3 1.0
OG1 D:THR266 2.9 28.6 1.0
OE2 D:GLU172 3.0 34.5 1.0
OE1 D:GLU172 3.1 32.5 1.0
CD D:GLU172 3.4 33.6 1.0
CE1 D:HIS173 3.5 29.8 1.0
CB D:THR266 3.7 29.1 1.0
C D:GLY267 3.8 29.9 1.0
CG D:HIS173 3.8 31.0 1.0
OH D:TYR175 3.9 26.2 1.0
N D:HIS173 4.2 30.2 1.0
N D:GLY267 4.2 29.6 1.0
CB D:HIS173 4.2 30.2 1.0
C D:THR266 4.4 29.6 1.0
CZ D:TYR175 4.5 26.5 1.0
CE2 D:TYR175 4.5 25.6 1.0
OD2 D:ASP262 4.6 31.6 1.0
CA D:GLY267 4.6 29.7 1.0
NZ D:LYS268 4.7 26.1 1.0
CA D:THR266 4.7 29.3 1.0
NE2 D:HIS173 4.7 30.9 1.0
N D:LYS268 4.8 30.0 1.0
CG2 D:THR266 4.8 28.2 1.0
CG D:LYS268 4.8 30.0 1.0
O D:THR266 4.8 29.5 1.0
CA D:HIS173 4.8 30.6 1.0
CA D:LYS268 4.8 30.1 1.0
CG D:GLU172 4.8 31.6 1.0
CD2 D:HIS173 4.9 30.4 1.0
CE D:LYS268 4.9 28.2 1.0

Calcium binding site 3 out of 4 in 2w3s

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Calcium binding site 3 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1779

b:56.3
occ:1.00
 O F:GLY267 2.6 29.2 1.0
OE2 F:GLU172 2.7 35.0 1.0
OG1 F:THR266 2.9 30.3 1.0
ND1 F:HIS173 3.2 29.8 1.0
CD F:GLU172 3.4 33.8 1.0
OE1 F:GLU172 3.5 34.1 1.0
OH F:TYR175 3.6 26.4 1.0
CB F:THR266 3.6 29.8 1.0
C F:GLY267 3.8 30.2 1.0
CE1 F:HIS173 4.0 30.3 1.0
NZ F:LYS268 4.1 27.4 1.0
C F:THR266 4.1 30.2 1.0
CG F:HIS173 4.2 30.3 1.0
N F:GLY267 4.3 29.9 1.0
O F:THR266 4.3 30.1 1.0
N F:HIS173 4.3 30.9 1.0
CZ F:TYR175 4.4 28.1 1.0
CB F:HIS173 4.4 30.8 1.0
CE2 F:TYR175 4.5 28.3 1.0
CG F:LYS268 4.5 29.7 1.0
CA F:THR266 4.5 30.1 1.0
OD2 F:ASP262 4.6 31.3 1.0
CA F:GLY267 4.6 29.7 1.0
CG2 F:THR266 4.7 29.4 1.0
N F:LYS268 4.8 30.4 1.0
O F:ASP262 4.8 32.0 1.0
CG F:GLU172 4.8 31.4 1.0
CA F:LYS268 4.9 30.4 1.0

Calcium binding site 4 out of 4 in 2w3s

Go back to Calcium Binding Sites List in 2w3s
Calcium binding site 4 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine


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 (Desulfo Form) From Rhodobacter Capsulatus in Complex with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1779

b:58.5
occ:1.00
 OG1 H:THR266 2.6 30.6 1.0
O H:GLY267 2.7 31.4 1.0
OE2 H:GLU172 2.7 34.5 1.0
ND1 H:HIS173 2.9 30.8 1.0
OE1 H:GLU172 3.0 33.2 1.0
CD H:GLU172 3.2 33.4 1.0
CB H:THR266 3.4 30.4 1.0
OH H:TYR175 3.5 26.6 1.0
CE1 H:HIS173 3.6 31.8 1.0
CG H:HIS173 3.9 32.2 1.0
C H:GLY267 3.9 31.4 1.0
CE2 H:TYR175 4.1 25.8 1.0
CZ H:TYR175 4.2 27.5 1.0
C H:THR266 4.2 30.1 1.0
N H:GLY267 4.2 30.5 1.0
NZ H:LYS268 4.3 25.7 1.0
CB H:HIS173 4.3 31.8 1.0
N H:HIS173 4.4 31.5 1.0
CA H:THR266 4.5 30.4 1.0
CG2 H:THR266 4.5 28.7 1.0
O H:THR266 4.5 30.4 1.0
CA H:GLY267 4.7 30.9 1.0
OD2 H:ASP262 4.7 31.8 1.0
NE2 H:HIS173 4.7 33.0 1.0
CG H:GLU172 4.8 32.0 1.0
CD2 H:HIS173 4.9 32.6 1.0
N H:LYS268 4.9 31.8 1.0
CG H:LYS268 4.9 30.5 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: Fri Jul 12 18:29:21 2024

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