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Nickel in PDB 1qxr: Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate

Enzymatic activity of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate

All present enzymatic activity of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate:
5.3.1.9;

Protein crystallography data

The structure of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate, PDB code: 1qxr was solved by M.K.Swan, J.T.G.Solomons, C.C.Beeson, P.Hansen, P.Schonheit, C.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.000, 39.700, 74.700, 73.70, 78.50, 72.60
R / Rfree (%) 22.1 / 26.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate (pdb code 1qxr). 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 Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate, PDB code: 1qxr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1qxr

Go back to Nickel Binding Sites List in 1qxr
Nickel binding site 1 out of 2 in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate


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 Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni200

b:43.3
occ:1.00
OE2 A:GLU97 2.2 29.4 1.0
O A:HOH343 2.3 32.7 1.0
NE2 A:HIS88 2.3 33.0 1.0
NE2 A:HIS136 2.4 30.4 1.0
O1A A:PA5300 2.4 25.8 1.0
CE1 A:HIS88 2.9 34.4 1.0
NE2 A:HIS90 3.0 35.3 1.0
CE1 A:HIS136 3.0 31.3 1.0
CD A:GLU97 3.2 27.2 1.0
C1 A:PA5300 3.4 29.9 1.0
OE1 A:GLU97 3.5 28.0 1.0
CD2 A:HIS88 3.5 32.9 1.0
CD2 A:HIS90 3.5 35.6 1.0
CD2 A:HIS136 3.6 26.7 1.0
O1 A:PA5300 3.6 32.9 1.0
CE1 A:HIS90 4.1 36.8 1.0
ND1 A:HIS88 4.1 34.8 1.0
ND1 A:HIS136 4.2 29.2 1.0
CG A:HIS88 4.4 31.4 1.0
CG A:GLU97 4.5 27.6 1.0
CG A:HIS136 4.6 26.9 1.0
OH A:TYR99 4.6 28.1 1.0
C2 A:PA5300 4.7 29.9 1.0
CG A:HIS90 4.7 35.6 1.0
NE2 A:HIS158 4.8 39.9 1.0
CB A:GLU97 4.8 22.8 1.0
CD2 A:HIS158 4.8 39.1 1.0
O3 A:PA5300 5.0 32.0 1.0
ND1 A:HIS90 5.0 34.5 1.0

Nickel binding site 2 out of 2 in 1qxr

Go back to Nickel Binding Sites List in 1qxr
Nickel binding site 2 out of 2 in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate


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 Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with 5-Phosphoarabinonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:37.1
occ:1.00
OE2 B:GLU97 2.1 25.0 1.0
O B:HOH378 2.2 31.4 1.0
NE2 B:HIS88 2.4 27.0 1.0
NE2 B:HIS136 2.4 26.8 1.0
O1A B:PA5301 2.5 24.8 1.0
NE2 B:HIS90 2.6 25.0 1.0
CE1 B:HIS136 2.9 28.1 1.0
CD B:GLU97 3.1 21.3 1.0
CD2 B:HIS88 3.3 29.3 1.0
CE1 B:HIS88 3.3 26.1 1.0
CD2 B:HIS90 3.3 27.1 1.0
C1 B:PA5301 3.4 27.2 1.0
OE1 B:GLU97 3.5 28.1 1.0
O1 B:PA5301 3.5 30.5 1.0
CE1 B:HIS90 3.6 26.5 1.0
CD2 B:HIS136 3.7 25.7 1.0
ND1 B:HIS136 4.1 27.4 1.0
O B:HOH313 4.3 22.6 1.0
ND1 B:HIS88 4.4 28.6 1.0
CG B:HIS88 4.4 26.7 1.0
CG B:HIS90 4.5 27.4 1.0
CG B:GLU97 4.5 21.2 1.0
CG B:HIS136 4.5 22.3 1.0
ND1 B:HIS90 4.6 27.6 1.0
OH B:TYR99 4.7 28.9 1.0
CB B:GLU97 4.7 18.7 1.0
C2 B:PA5301 4.8 27.8 1.0
CD2 B:HIS158 5.0 35.0 1.0

Reference:

M.K.Swan, J.T.G.Solomons, C.C.Beeson, P.Hansen, P.Schonheit, C.Davies. Structural Evidence For A Hydride Transfer Mechanism of Catalysis in Phosphoglucose Isomerase From Pyrococcus Furiosus J.Biol.Chem. V. 278 47261 2003.
ISSN: ISSN 0021-9258
PubMed: 12970347
DOI: 10.1074/JBC.M308603200
Page generated: Fri Sep 25 08:00:25 2020
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