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Nickel in PDB 1jvn: Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites

Protein crystallography data

The structure of Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites, PDB code: 1jvn was solved by B.N.Chaudhuri, J.L.Smith, V.J.Davisson, R.S.Myers, S.C.Lange, S.V.Chittur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.21 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.370, 112.173, 116.680, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites (pdb code 1jvn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites, PDB code: 1jvn:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1jvn

Go back to Nickel Binding Sites List in 1jvn
Nickel binding site 1 out of 2 in the Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:26.6
occ:1.00
N A:SER-2 1.8 22.2 1.0
ND1 A:HIS-1 1.9 25.9 1.0
N A:HIS-1 2.0 24.1 1.0
N A:GLY-3 2.1 22.1 1.0
C A:GLY-3 2.7 23.4 1.0
C A:SER-2 2.8 23.3 1.0
CA A:SER-2 2.8 22.9 1.0
CA A:GLY-3 2.9 23.7 1.0
CE1 A:HIS-1 2.9 26.9 1.0
CG A:HIS-1 2.9 26.1 1.0
CA A:HIS-1 3.1 25.0 1.0
CB A:HIS-1 3.3 25.7 1.0
CD1 B:TYR425 3.6 29.5 1.0
N A:MET1 3.6 26.9 1.0
CE1 B:TYR425 3.6 28.6 1.0
C A:HIS-1 3.8 25.8 1.0
O A:GLY-3 3.9 23.7 1.0
OE1 A:GLU27 3.9 33.1 1.0
OG A:SER-2 3.9 26.2 1.0
CB A:SER-2 3.9 23.1 1.0
O A:SER-2 4.0 24.4 1.0
NE2 A:HIS-1 4.0 27.3 1.0
CD2 A:HIS-1 4.1 26.4 1.0
CG B:TYR425 4.2 28.9 1.0
CZ B:TYR425 4.2 29.7 1.0
O B:HOH1028 4.3 22.8 1.0
O A:MET1 4.5 26.1 1.0
CD2 B:TYR425 4.6 28.7 1.0
CE2 B:TYR425 4.7 29.2 1.0
CG A:MET1 4.7 29.6 1.0
OH B:TYR425 4.8 29.9 1.0
CA A:MET1 4.8 27.9 1.0
CD A:GLU27 4.9 31.8 1.0
CB B:TYR425 4.9 30.1 1.0

Nickel binding site 2 out of 2 in 1jvn

Go back to Nickel Binding Sites List in 1jvn
Nickel binding site 2 out of 2 in the Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni901

b:27.8
occ:1.00
N B:SER-2 1.9 26.8 1.0
ND1 B:HIS-1 1.9 28.6 1.0
N B:GLY-3 2.1 26.4 1.0
N B:HIS-1 2.1 28.8 1.0
C B:GLY-3 2.7 27.9 1.0
CA B:GLY-3 2.9 27.5 1.0
CA B:SER-2 2.9 26.1 1.0
C B:SER-2 2.9 27.8 1.0
CG B:HIS-1 2.9 28.2 1.0
CE1 B:HIS-1 2.9 27.8 1.0
CA B:HIS-1 3.1 29.9 1.0
CB B:HIS-1 3.3 27.7 1.0
N B:MET1 3.5 32.8 1.0
C B:HIS-1 3.8 30.9 1.0
O B:GLY-3 3.9 28.7 1.0
CB B:SER-2 4.0 25.2 1.0
NE2 B:HIS-1 4.0 28.2 1.0
CD2 B:HIS-1 4.0 26.9 1.0
OG B:SER-2 4.1 27.1 1.0
O B:SER-2 4.1 28.3 1.0
O B:MET1 4.8 33.3 1.0
CA B:MET1 4.8 34.0 1.0

Reference:

B.N.Chaudhuri, S.C.Lange, R.S.Myers, S.V.Chittur, V.J.Davisson, J.L.Smith. Crystal Structure of Imidazole Glycerol Phosphate Synthase: A Tunnel Through A (Beta/Alpha)8 Barrel Joins Two Active Sites. Structure V. 9 987 2001.
ISSN: ISSN 0969-2126
PubMed: 11591353
DOI: 10.1016/S0969-2126(01)00661-X
Page generated: Fri Sep 25 07:56:14 2020
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