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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

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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

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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

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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

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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

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