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Nickel in PDB 1ox4: Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase

Protein crystallography data

The structure of Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase, PDB code: 1ox4 was solved by B.N.Chaudhuri, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.500, 112.000, 115.300, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26

Nickel Binding Sites:

The binding sites of Nickel atom in the Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase (pdb code 1ox4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase, PDB code: 1ox4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1ox4

Go back to Nickel Binding Sites List in 1ox4
Nickel binding site 1 out of 2 in the Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:33.2
occ:1.00
N A:SER-2 2.0 28.4 1.0
N A:HIS-1 2.0 34.4 1.0
ND1 A:HIS-1 2.0 35.7 1.0
N A:GLY-3 2.0 26.7 1.0
C A:GLY-3 2.8 27.9 1.0
C A:SER-2 2.9 32.4 1.0
CA A:GLY-3 2.9 27.1 1.0
CG A:HIS-1 3.0 35.1 1.0
CA A:SER-2 3.0 31.2 1.0
CE1 A:HIS-1 3.0 36.1 1.0
CA A:HIS-1 3.1 34.9 1.0
CB A:HIS-1 3.3 35.6 1.0
N A:MET1 3.7 37.1 1.0
C A:HIS-1 3.8 36.0 1.0
CD1 B:TYR425 3.9 40.2 1.0
CE1 B:TYR425 3.9 39.9 1.0
OG A:SER-2 4.0 32.9 1.0
O A:GLY-3 4.0 26.9 1.0
O A:SER-2 4.0 31.9 1.0
CB A:SER-2 4.1 30.6 1.0
OE1 A:GLU27 4.1 54.8 1.0
CD2 A:HIS-1 4.1 34.5 1.0
NE2 A:HIS-1 4.1 36.2 1.0
CG B:TYR425 4.1 41.6 1.0
CZ B:TYR425 4.2 40.4 1.0
O A:HOH1025 4.3 23.9 1.0
CD2 B:TYR425 4.4 41.1 1.0
CE2 B:TYR425 4.4 39.9 1.0
O A:MET1 4.7 35.7 1.0
CG A:MET1 4.8 45.6 1.0
OH B:TYR425 4.8 39.4 1.0
CB B:TYR425 4.9 42.4 1.0
CA A:MET1 4.9 37.3 1.0
O A:HIS-1 4.9 36.0 1.0
CD A:GLU27 5.0 52.6 1.0

Nickel binding site 2 out of 2 in 1ox4

Go back to Nickel Binding Sites List in 1ox4
Nickel binding site 2 out of 2 in the Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni901

b:52.7
occ:1.00
N B:SER-2 2.0 48.1 1.0
ND1 B:HIS-1 2.1 42.0 1.0
N B:HIS-1 2.1 49.0 1.0
N B:GLY-3 2.1 48.9 1.0
C B:GLY-3 2.9 49.0 1.0
C B:SER-2 2.9 48.4 1.0
CA B:SER-2 2.9 48.0 1.0
CA B:GLY-3 3.0 49.5 1.0
CE1 B:HIS-1 3.1 40.4 1.0
CG B:HIS-1 3.1 43.9 1.0
CA B:HIS-1 3.2 49.1 1.0
CB B:HIS-1 3.4 46.8 1.0
N B:MET1 3.7 52.0 1.0
C B:HIS-1 3.9 51.0 1.0
O B:GLY-3 4.0 49.1 1.0
O B:SER-2 4.1 48.9 1.0
CB B:SER-2 4.1 46.6 1.0
NE2 B:HIS-1 4.2 41.0 1.0
CD2 B:HIS-1 4.2 41.6 1.0
OG B:SER-2 4.3 45.1 1.0
O B:MET1 4.5 54.5 1.0
CA B:MET1 4.9 52.6 1.0

Reference:

B.N.Chaudhuri, C.Lange, R.S.Myers, V.J.Davisson, J.L.Smith. Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed By Imidazole Glycerophosphate Synthase: Crystal Structures of A Ternary Complex and the Free Enzyme Biochemistry V. 42 7003 2003.
ISSN: ISSN 0006-2960
PubMed: 12795595
DOI: 10.1021/BI034320H
Page generated: Fri Sep 25 07:57:53 2020
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