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Barium 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:

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

Barium Binding Sites:

The binding sites of Barium 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 Barium atom.
In total 4 binding sites of Barium 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 Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in 2w54

Go back to Barium Binding Sites List in 2w54
Barium 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 Barium with other atoms in the Ba 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:Ba1779

b:0.1
occ:1.00
 O B:GLY267 3.0 22.5 1.0
OG1 B:THR266 3.1 22.2 1.0
ND1 B:HIS173 3.2 22.8 1.0
OE2 B:GLU172 3.4 24.0 1.0
OH B:TYR175 3.5 23.3 1.0
OE1 B:GLU172 3.5 23.9 1.0
CD B:GLU172 3.8 23.6 1.0
CB B:THR266 3.9 22.5 1.0
CE1 B:HIS173 4.0 22.9 1.0
CG B:HIS173 4.1 22.9 1.0
CZ B:TYR175 4.1 23.1 1.0
C B:GLY267 4.2 22.3 1.0
CE2 B:TYR175 4.2 22.9 1.0
CB B:HIS173 4.2 22.8 1.0
N B:HIS173 4.3 22.7 1.0
C B:THR266 4.6 22.4 1.0
N B:GLY267 4.7 22.3 1.0
NZ B:LYS268 4.7 20.4 1.0
OD2 B:ASP262 4.8 23.5 1.0
CG2 B:THR266 4.9 22.7 1.0
O B:THR266 4.9 22.5 1.0
CA B:GLY230 4.9 23.1 1.0
CA B:HIS173 4.9 22.8 1.0
CA B:THR266 4.9 22.5 1.0
CG B:LYS268 4.9 21.8 1.0

Barium binding site 2 out of 4 in 2w54

Go back to Barium Binding Sites List in 2w54
Barium 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 Barium with other atoms in the Ba 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:Ba1779

b:0.4
occ:1.00
 O D:GLY267 2.9 22.4 1.0
OG1 D:THR266 3.0 22.2 1.0
ND1 D:HIS173 3.3 22.6 1.0
OE2 D:GLU172 3.4 23.9 1.0
OH D:TYR175 3.6 23.1 1.0
OE1 D:GLU172 3.8 24.0 1.0
CB D:THR266 3.8 22.3 1.0
CD D:GLU172 3.9 23.6 1.0
CG D:HIS173 4.1 22.7 1.0
CE1 D:HIS173 4.1 22.5 1.0
C D:GLY267 4.2 22.3 1.0
CZ D:TYR175 4.2 22.9 1.0
CE2 D:TYR175 4.2 22.6 1.0
CB D:HIS173 4.2 22.8 1.0
NZ D:LYS268 4.3 20.1 1.0
N D:HIS173 4.4 22.7 1.0
C D:THR266 4.4 22.3 1.0
OD2 D:ASP262 4.5 23.6 1.0
N D:GLY267 4.5 22.3 1.0
O D:THR266 4.7 22.4 1.0
CA D:THR266 4.8 22.3 1.0
CG2 D:THR266 4.9 22.5 1.0
CA D:HIS173 4.9 22.8 1.0
CA D:GLY267 5.0 22.3 1.0

Barium binding site 3 out of 4 in 2w54

Go back to Barium Binding Sites List in 2w54
Barium 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 Barium with other atoms in the Ba 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:Ba1779

b:0.1
occ:1.00
 O F:GLY267 3.0 22.5 1.0
ND1 F:HIS173 3.1 22.8 1.0
OG1 F:THR266 3.2 22.4 1.0
OE2 F:GLU172 3.3 23.8 1.0
OH F:TYR175 3.6 23.4 1.0
OE1 F:GLU172 3.8 24.1 1.0
CD F:GLU172 3.9 23.6 1.0
CB F:THR266 3.9 22.4 1.0
CG F:HIS173 4.0 22.9 1.0
CB F:HIS173 4.1 22.9 1.0
CE1 F:HIS173 4.1 22.5 1.0
N F:HIS173 4.2 22.8 1.0
CZ F:TYR175 4.2 23.4 1.0
C F:GLY267 4.2 22.4 1.0
CE2 F:TYR175 4.3 23.1 1.0
NZ F:LYS268 4.7 20.5 1.0
N F:GLY267 4.7 22.4 1.0
C F:THR266 4.7 22.4 1.0
OD2 F:ASP262 4.7 23.4 1.0
CA F:HIS173 4.8 22.9 1.0
CG F:LYS268 4.9 21.9 1.0
CA F:THR266 5.0 22.4 1.0
O F:THR266 5.0 22.4 1.0
CG2 F:THR266 5.0 22.5 1.0

Barium binding site 4 out of 4 in 2w54

Go back to Barium Binding Sites List in 2w54
Barium 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 Barium with other atoms in the Ba 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:Ba1779

b:0.3
occ:1.00
 O H:GLY267 3.0 22.4 1.0
OG1 H:THR266 3.2 22.3 1.0
ND1 H:HIS173 3.3 22.9 1.0
OE1 H:GLU172 3.5 23.7 1.0
OE2 H:GLU172 3.6 23.9 1.0
OH H:TYR175 3.7 22.9 1.0
CD H:GLU172 3.8 23.6 1.0
CB H:THR266 4.0 22.4 1.0
N H:HIS173 4.1 22.9 1.0
CG H:HIS173 4.1 23.0 1.0
C H:GLY267 4.2 22.3 1.0
CB H:HIS173 4.2 22.9 1.0
CE1 H:HIS173 4.2 22.9 1.0
CZ H:TYR175 4.3 22.9 1.0
CE2 H:TYR175 4.4 22.9 1.0
NZ H:LYS268 4.4 20.5 1.0
CG H:LYS268 4.6 21.7 1.0
C H:THR266 4.7 22.3 1.0
N H:GLY267 4.7 22.3 1.0
CA H:HIS173 4.8 22.9 1.0
O H:THR266 4.8 22.2 1.0
OD2 H:ASP262 4.9 23.6 1.0
CA H:LYS268 4.9 22.2 1.0
CA H:GLU172 4.9 22.7 1.0
CA H:THR266 5.0 22.3 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: Wed Jul 10 15:08:22 2024

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