Atomistry » Barium » PDB 1djh-2x6b » 2w54
Atomistry »
  Barium »
    PDB 1djh-2x6b »
      2w54 »

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: Sat Dec 12 01:55:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy