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Nickel in PDB 1qy4: Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate

Enzymatic activity of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate

All present enzymatic activity of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate:
5.3.1.9;

Protein crystallography data

The structure of Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate, PDB code: 1qy4 was solved by M.K.Swan, J.T.G.Solomons, C.C.Beeson, T.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 / 1.80
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 (%) 21.8 / 26.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate (pdb code 1qy4). 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 Gluconate 6-Phosphate, PDB code: 1qy4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1qy4

Go back to Nickel Binding Sites List in 1qy4
Nickel binding site 1 out of 2 in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate


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 Gluconate 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni210

b:42.9
occ:1.00
OE2 A:GLU97 1.6 40.5 1.0
NE2 A:HIS88 2.2 38.8 1.0
O1A A:6PG300 2.2 31.5 0.8
NE2 A:HIS136 2.3 35.4 1.0
CD A:GLU97 2.4 34.5 1.0
O2 A:6PG300 2.4 27.9 0.8
OE1 A:GLU97 2.6 36.6 1.0
CE1 A:HIS88 2.9 37.7 1.0
CE1 A:HIS136 3.0 33.1 1.0
C1 A:6PG300 3.1 31.7 0.8
C2 A:6PG300 3.2 27.2 0.8
NE2 A:HIS90 3.2 38.0 1.0
CD2 A:HIS88 3.4 36.5 1.0
CD2 A:HIS136 3.5 30.2 1.0
CD2 A:HIS90 3.8 37.6 1.0
CG A:GLU97 3.8 29.6 1.0
ND1 A:HIS88 4.1 39.3 1.0
ND1 A:HIS136 4.2 30.7 1.0
OH A:TYR99 4.3 35.5 1.0
CE1 A:HIS90 4.3 38.1 1.0
O1 A:6PG300 4.3 29.3 0.8
CD2 A:HIS158 4.3 41.1 1.0
CG A:HIS88 4.4 36.6 1.0
CG A:HIS136 4.5 29.6 1.0
C3 A:6PG300 4.6 29.7 0.8
NE2 A:HIS158 4.7 42.9 1.0
O4 A:6PG300 4.8 32.9 0.8
C4 A:6PG300 4.8 30.9 0.8
CB A:GLU97 4.8 25.1 1.0

Nickel binding site 2 out of 2 in 1qy4

Go back to Nickel Binding Sites List in 1qy4
Nickel binding site 2 out of 2 in the Crystal Structure of Phosphoglucose Isomerase From Pyrococcus Furiosus in Complex with Gluconate 6-Phosphate


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 Gluconate 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni211

b:36.8
occ:1.00
OE1 B:GLU97 1.4 34.3 1.0
O1A B:6PG301 2.1 30.4 0.8
NE2 B:HIS88 2.2 29.8 1.0
NE2 B:HIS136 2.2 30.7 1.0
O2 B:6PG301 2.4 20.2 0.8
CD B:GLU97 2.5 28.0 1.0
NE2 B:HIS90 2.8 35.5 1.0
OE2 B:GLU97 2.9 33.4 1.0
CE1 B:HIS88 3.0 28.5 1.0
C1 B:6PG301 3.0 28.8 0.8
CE1 B:HIS136 3.1 26.0 1.0
C2 B:6PG301 3.2 27.4 0.8
CD2 B:HIS88 3.2 25.1 1.0
CD2 B:HIS136 3.3 23.6 1.0
CD2 B:HIS90 3.5 35.8 1.0
CG B:GLU97 3.8 26.7 1.0
CE1 B:HIS90 3.8 37.7 1.0
ND1 B:HIS88 4.1 31.6 1.0
O B:HOH314 4.2 38.2 1.0
O1 B:6PG301 4.2 30.2 0.8
ND1 B:HIS136 4.2 25.4 1.0
CG B:HIS88 4.3 29.2 1.0
OH B:TYR99 4.3 27.3 1.0
CD2 B:HIS158 4.4 40.0 1.0
CG B:HIS136 4.4 24.6 1.0
NE2 B:HIS158 4.4 44.2 1.0
C3 B:6PG301 4.6 27.8 0.8
CG B:HIS90 4.8 36.2 1.0
O4 B:6PG301 4.8 32.1 0.8
ND1 B:HIS90 4.8 37.8 1.0
CB B:GLU97 4.9 22.1 1.0
C4 B:6PG301 4.9 28.1 0.8

Reference:

M.K.Swan, J.T.G.Solomons, C.C.Beeson, T.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 08:00:28 2020
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