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

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

All present enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate:
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, PDB code: 5yfj 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) 85.69 / 2.20
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.630, 98.630, 257.061, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 19

Other elements in 5yfj:

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

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 (pdb code 5yfj). 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, PDB code: 5yfj:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yfj

Go back to Potassium Binding Sites List in 5yfj
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:35.5
occ:1.00
 O A:HOH591 2.6 32.8 1.0
O A:THR196 2.7 22.9 1.0
O A:LYS194 2.7 28.3 1.0
O A:MET193 2.9 26.7 1.0
O A:HOH646 3.1 58.7 1.0
C A:LYS194 3.4 28.8 1.0
CG2 A:VAL230 3.4 24.3 1.0
C A:THR196 3.8 23.1 1.0
CA A:LYS194 3.8 32.0 1.0
N A:THR196 3.9 23.8 1.0
C A:MET193 4.0 27.2 1.0
O A:HOH565 4.1 35.3 1.0
O A:HOH547 4.2 42.2 1.0
C A:MET195 4.3 24.6 1.0
N A:MET195 4.3 26.1 1.0
N A:LYS194 4.3 29.2 1.0
CA A:THR196 4.4 22.2 1.0
O A:HIS228 4.7 20.7 1.0
CA A:MET195 4.7 27.6 1.0
N A:ASP197 4.8 24.9 1.0
CB A:VAL230 4.9 20.9 1.0
O A:HOH630 4.9 47.7 1.0
O A:MET195 4.9 25.8 1.0
CB A:THR196 5.0 21.0 1.0
CA A:ASP197 5.0 24.6 1.0

Potassium binding site 2 out of 3 in 5yfj

Go back to Potassium Binding Sites List in 5yfj
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:34.4
occ:1.00
 O B:HOH631 2.6 33.6 1.0
O B:THR196 2.7 26.3 1.0
O B:LYS194 2.9 28.0 1.0
O B:MET193 3.0 23.1 1.0
O B:HOH636 3.0 43.0 1.0
O B:HOH633 3.1 56.2 1.0
C B:LYS194 3.4 27.6 1.0
CG2 B:VAL230 3.5 24.5 1.0
C B:THR196 3.8 25.6 1.0
O B:HOH608 3.8 42.8 1.0
N B:THR196 3.9 23.2 1.0
CA B:LYS194 3.9 30.4 1.0
C B:MET193 4.0 25.5 1.0
N B:MET195 4.3 27.7 1.0
CA B:THR196 4.4 22.5 1.0
C B:MET195 4.4 24.2 1.0
N B:LYS194 4.4 26.7 1.0
O B:HOH514 4.4 40.9 1.0
CA B:MET195 4.7 32.4 1.0
O B:HIS228 4.7 23.6 1.0
N B:ASP197 4.8 26.0 1.0
CB B:THR196 4.9 22.7 1.0
CB B:VAL230 4.9 22.2 1.0

Potassium binding site 3 out of 3 in 5yfj

Go back to Potassium Binding Sites List in 5yfj
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:34.2
occ:1.00
 O C:HOH605 2.6 30.1 1.0
O C:THR196 2.6 29.9 1.0
O C:LYS194 2.8 26.4 1.0
O C:MET193 3.0 25.4 1.0
O C:HOH586 3.0 45.5 1.0
C C:LYS194 3.4 26.8 1.0
CG2 C:VAL230 3.4 22.2 1.0
C C:THR196 3.7 25.6 1.0
CA C:LYS194 3.8 31.4 1.0
N C:THR196 4.0 26.7 1.0
C C:MET193 4.0 28.2 1.0
O C:HOH575 4.1 36.9 1.0
N C:MET195 4.3 29.1 1.0
CA C:THR196 4.4 24.4 1.0
N C:LYS194 4.4 27.9 1.0
C C:MET195 4.4 27.9 1.0
O C:HOH513 4.5 43.9 1.0
O C:HIS228 4.7 29.4 1.0
CA C:MET195 4.7 31.5 1.0
N C:ASP197 4.7 25.9 1.0
CB C:VAL230 4.9 22.1 1.0
CB C:THR196 4.9 24.9 1.0
CA C:ASP197 5.0 27.4 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: Sat Aug 9 10:15:00 2025

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