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Potassium in PDB 5yg5: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp

All present enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp:
5.3.1.29;

Protein crystallography data

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp, PDB code: 5yg5 was solved by P.Gogoi, S.P.Kanaujia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.73 / 2.75
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.990, 98.990, 257.091, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 23.2

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp (pdb code 5yg5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp, PDB code: 5yg5:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yg5

Go back to Potassium Binding Sites List in 5yg5
Potassium binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:46.1
occ:1.00
 O A:THR196 2.7 32.8 1.0
O A:LYS194 2.8 33.9 1.0
O A:MET193 3.2 39.6 1.0
C A:LYS194 3.5 35.9 1.0
O A:HOH540 3.6 20.2 0.5
CG2 A:VAL230 3.7 27.5 1.0
C A:THR196 3.8 30.8 1.0
CA A:LYS194 4.0 40.6 1.0
N A:THR196 4.1 30.5 1.0
C A:MET193 4.3 34.0 1.0
N A:MET195 4.5 32.8 1.0
CA A:THR196 4.5 30.6 1.0
C A:MET195 4.6 30.9 1.0
N A:LYS194 4.6 39.9 1.0
O A:HIS228 4.7 22.0 1.0
N A:ASP197 4.8 29.9 1.0
CA A:MET195 4.9 30.8 1.0
CA A:ASP197 5.0 28.6 1.0

Potassium binding site 2 out of 3 in 5yg5

Go back to Potassium Binding Sites List in 5yg5
Potassium binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:46.7
occ:1.00
 O B:THR196 2.8 27.7 1.0
O B:LYS194 3.1 31.3 1.0
O B:MET193 3.2 30.1 1.0
C B:LYS194 3.6 34.9 1.0
CG2 B:VAL230 3.9 32.9 1.0
CA B:LYS194 3.9 37.1 1.0
C B:THR196 4.0 26.1 1.0
C B:MET193 4.3 28.4 1.0
N B:THR196 4.3 25.4 1.0
N B:MET195 4.4 32.8 1.0
N B:LYS194 4.6 33.4 1.0
O B:HIS228 4.6 29.5 1.0
C B:MET195 4.7 27.5 1.0
CA B:THR196 4.7 25.5 1.0
CA B:MET195 4.9 29.6 1.0

Potassium binding site 3 out of 3 in 5yg5

Go back to Potassium Binding Sites List in 5yg5
Potassium binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:41.2
occ:1.00
 O C:THR196 2.7 26.6 1.0
O C:LYS194 2.8 31.3 1.0
O C:HOH516 3.1 32.2 1.0
O C:MET193 3.3 31.8 1.0
C C:LYS194 3.5 32.6 1.0
CG2 C:VAL230 3.8 28.6 1.0
C C:THR196 3.9 26.7 1.0
CA C:LYS194 3.9 35.1 1.0
N C:THR196 4.2 27.8 1.0
C C:MET193 4.3 30.5 1.0
N C:MET195 4.5 32.0 1.0
O C:HIS228 4.6 32.8 1.0
N C:LYS194 4.6 33.5 1.0
CA C:THR196 4.7 27.6 1.0
C C:MET195 4.7 30.1 1.0
N C:ASP197 4.9 27.1 1.0
CA C:MET195 4.9 31.4 1.0
CB C:HIS228 5.0 31.1 1.0

Reference:

P.Gogoi, S.P.Kanaujia. A Presumed Homologue of the Regulatory Subunits of EIF2B Functions As Ribose-1,5-Bisphosphate Isomerase in Pyrococcus Horikoshii OT3. Sci Rep V. 8 1891 2018.
ISSN: ESSN 2045-2322
PubMed: 29382938
DOI: 10.1038/S41598-018-20418-W
Page generated: Mon Aug 12 15:12:09 2024

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