Atomistry » Barium » PDB 1djh-2x6b » 2w55
Atomistry »
  Barium »
    PDB 1djh-2x6b »
      2w55 »

Barium in PDB 2w55: Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine, PDB code: 2w55 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 / 3.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.741, 140.568, 157.606, 109.45, 106.10, 101.09
R / Rfree (%) 22.1 / 27

Other elements in 2w55:

The structure of Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine 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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine (pdb code 2w55). 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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine, PDB code: 2w55:
Jump to Barium binding site number: 1; 2; 3; 4;

Barium binding site 1 out of 4 in 2w55

Go back to Barium Binding Sites List in 2w55
Barium binding site 1 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba1779

b:0.6
occ:1.00
 O B:GLY267 3.2 42.4 1.0
OE2 B:GLU172 3.4 43.7 1.0
OG1 B:THR266 3.4 43.1 1.0
ND1 B:HIS173 3.4 42.8 1.0
OE1 B:GLU172 3.5 43.4 1.0
OH B:TYR175 3.6 43.7 1.0
CD B:GLU172 3.8 43.9 1.0
O B:THR266 4.0 42.6 1.0
C B:GLY267 4.0 42.3 1.0
CG2 B:THR266 4.1 42.1 1.0
C B:THR266 4.2 42.4 1.0
CG B:HIS173 4.2 43.0 1.0
CE1 B:HIS173 4.2 43.0 1.0
CB B:THR266 4.3 42.4 1.0
CB B:HIS173 4.3 43.2 1.0
CZ B:TYR175 4.3 43.4 1.0
N B:GLY267 4.4 42.2 1.0
N B:HIS173 4.4 43.3 1.0
OD2 B:ASP262 4.5 43.5 1.0
NZ B:LYS268 4.5 41.1 1.0
CE2 B:TYR175 4.5 43.2 1.0
CG B:LYS268 4.7 41.8 1.0
O B:ASP262 4.7 43.8 1.0
CA B:GLY267 4.8 42.2 1.0
N B:LYS268 4.8 42.3 1.0
CA B:THR266 4.8 42.4 1.0
CA B:LYS268 4.8 42.2 1.0

Barium binding site 2 out of 4 in 2w55

Go back to Barium Binding Sites List in 2w55
Barium binding site 2 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba1779

b:0.5
occ:1.00
 O D:GLY267 3.0 42.1 1.0
OG1 D:THR266 3.2 42.5 1.0
OE2 D:GLU172 3.4 43.9 1.0
ND1 D:HIS173 3.5 42.5 1.0
OH D:TYR175 3.6 43.0 1.0
CG2 D:THR266 3.8 42.1 1.0
OE1 D:GLU172 3.8 43.3 1.0
CD D:GLU172 4.0 43.8 1.0
O D:THR266 4.0 42.5 1.0
C D:GLY267 4.0 42.2 1.0
CB D:THR266 4.0 42.4 1.0
C D:THR266 4.1 42.4 1.0
N D:GLY267 4.3 42.3 1.0
CZ D:TYR175 4.3 43.2 1.0
CG D:HIS173 4.3 42.9 1.0
CB D:HIS173 4.4 43.3 1.0
CE1 D:HIS173 4.4 42.4 1.0
OD2 D:ASP262 4.4 43.9 1.0
O D:ASP262 4.4 44.2 1.0
CE2 D:TYR175 4.5 42.8 1.0
N D:HIS173 4.5 43.4 1.0
CA D:THR266 4.6 42.4 1.0
NZ D:LYS268 4.7 40.7 1.0
CA D:GLY267 4.7 42.3 1.0
N D:LYS268 5.0 42.2 1.0

Barium binding site 3 out of 4 in 2w55

Go back to Barium Binding Sites List in 2w55
Barium binding site 3 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ba1779

b:99.0
occ:1.00
 O F:GLY267 3.1 42.2 1.0
OE2 F:GLU172 3.3 43.5 1.0
OG1 F:THR266 3.4 42.9 1.0
ND1 F:HIS173 3.5 42.6 1.0
OH F:TYR175 3.6 43.8 1.0
CG2 F:THR266 3.8 42.6 1.0
O F:THR266 3.9 42.9 1.0
O F:ASP262 3.9 43.8 1.0
CD F:GLU172 4.0 43.6 1.0
C F:THR266 4.0 42.7 1.0
OE1 F:GLU172 4.0 43.2 1.0
C F:GLY267 4.0 42.2 1.0
CB F:THR266 4.1 42.8 1.0
OD2 F:ASP262 4.2 43.6 1.0
N F:GLY267 4.3 42.5 1.0
CB F:HIS173 4.3 43.3 1.0
CG F:HIS173 4.3 43.0 1.0
CZ F:TYR175 4.3 43.7 1.0
CE1 F:HIS173 4.4 42.5 1.0
N F:HIS173 4.5 43.5 1.0
NZ F:LYS268 4.5 40.5 1.0
CA F:THR266 4.6 42.7 1.0
CA F:GLY267 4.7 42.4 1.0
CE2 F:TYR175 4.8 43.3 1.0
N F:LYS268 4.9 42.2 1.0
C F:ASP262 5.0 43.8 1.0
CG F:LYS268 5.0 42.2 1.0

Barium binding site 4 out of 4 in 2w55

Go back to Barium Binding Sites List in 2w55
Barium binding site 4 out of 4 in the Crystal Structure of Xanthine Dehydrogenase (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine


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 (E232Q Variant) From Rhodobacter Capsulatus in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ba1779

b:0.9
occ:1.00
 O H:GLY267 3.2 42.4 1.0
OG1 H:THR266 3.3 43.4 1.0
OE2 H:GLU172 3.4 43.3 1.0
ND1 H:HIS173 3.4 42.5 1.0
OH H:TYR175 3.6 44.0 1.0
CG2 H:THR266 3.9 42.8 1.0
CD H:GLU172 4.0 43.4 1.0
OE1 H:GLU172 4.1 42.7 1.0
C H:GLY267 4.1 42.5 1.0
CB H:THR266 4.1 43.0 1.0
CG H:HIS173 4.2 42.8 1.0
CB H:HIS173 4.2 43.1 1.0
O H:THR266 4.2 42.7 1.0
CZ H:TYR175 4.2 43.2 1.0
OD2 H:ASP262 4.2 43.7 1.0
C H:THR266 4.3 42.7 1.0
N H:HIS173 4.3 43.3 1.0
CE1 H:HIS173 4.3 42.4 1.0
N H:GLY267 4.5 42.6 1.0
O H:ASP262 4.5 44.0 1.0
CE2 H:TYR175 4.6 43.1 1.0
CG H:LYS268 4.8 42.0 1.0
CA H:GLY267 4.8 42.6 1.0
CA H:THR266 4.8 42.7 1.0
N H:LYS268 4.9 42.4 1.0
CA H:HIS173 4.9 43.1 1.0
NZ H:LYS268 4.9 40.4 1.0
CA H:LYS268 4.9 42.3 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 15:08:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy