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Potassium in PDB 5yfs: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate

All present enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate:
5.3.1.29;

Protein crystallography data

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yfs 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) 85.58 / 2.30
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.650, 98.650, 256.731, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 19.8

Other elements in 5yfs:

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate (pdb code 5yfs). 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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yfs:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yfs

Go back to Potassium Binding Sites List in 5yfs
Potassium binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:30.5
occ:1.00
 O A:HOH641 2.6 27.9 1.0
O A:THR196 2.7 17.1 1.0
O A:LYS194 2.9 21.1 1.0
O A:MET193 3.0 19.9 1.0
C A:LYS194 3.4 24.2 1.0
CG2 A:VAL230 3.5 22.3 1.0
C A:THR196 3.8 18.5 1.0
O A:HOH567 3.8 36.4 1.0
CA A:LYS194 3.9 25.1 1.0
N A:THR196 3.9 20.9 1.0
C A:MET193 4.1 19.7 1.0
O A:HOH596 4.1 29.4 1.0
N A:MET195 4.3 25.3 1.0
CA A:THR196 4.3 20.6 1.0
C A:MET195 4.4 22.4 1.0
N A:LYS194 4.5 21.6 1.0
O A:HIS228 4.7 14.2 1.0
CA A:MET195 4.7 24.9 1.0
N A:ASP197 4.8 19.7 1.0
CB A:THR196 4.8 19.5 1.0
O A:MET195 4.9 22.3 1.0
CB A:VAL230 4.9 20.6 1.0

Potassium binding site 2 out of 3 in 5yfs

Go back to Potassium Binding Sites List in 5yfs
Potassium binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:28.0
occ:1.00
 O B:HOH630 2.6 22.8 1.0
O B:THR196 2.7 24.4 1.0
O B:LYS194 2.8 21.3 1.0
O B:MET193 3.0 19.8 1.0
O B:HOH620 3.0 41.0 1.0
C B:LYS194 3.4 21.5 1.0
CG2 B:VAL230 3.5 22.9 1.0
C B:THR196 3.8 20.4 1.0
O B:HOH649 3.8 40.3 1.0
N B:THR196 3.9 20.7 1.0
CA B:LYS194 4.0 23.2 1.0
O B:HOH581 4.0 32.2 1.0
C B:MET193 4.1 19.4 1.0
N B:MET195 4.3 23.1 1.0
O B:HOH518 4.3 37.7 1.0
C B:MET195 4.3 21.6 1.0
CA B:THR196 4.4 20.6 1.0
N B:LYS194 4.5 19.1 1.0
CA B:MET195 4.6 23.4 1.0
O B:HIS228 4.6 18.1 1.0
N B:ASP197 4.8 21.1 1.0
CB B:VAL230 4.9 21.1 1.0
CA B:ASP197 5.0 21.2 1.0
O B:MET195 5.0 22.2 1.0
CB B:THR196 5.0 20.3 1.0

Potassium binding site 3 out of 3 in 5yfs

Go back to Potassium Binding Sites List in 5yfs
Potassium binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:29.2
occ:1.00
 O C:THR196 2.6 17.2 1.0
O C:LYS194 2.7 21.3 1.0
O C:HOH607 2.7 22.1 1.0
O C:MET193 2.9 18.5 1.0
O C:HOH648 3.1 31.1 1.0
C C:LYS194 3.3 23.8 1.0
CG2 C:VAL230 3.5 20.3 1.0
C C:THR196 3.7 17.7 1.0
CA C:LYS194 3.8 25.7 1.0
N C:THR196 3.9 19.2 1.0
C C:MET193 4.0 19.5 1.0
O C:HOH560 4.2 24.6 1.0
N C:MET195 4.2 23.8 1.0
O C:HOH658 4.3 44.5 1.0
CA C:THR196 4.3 18.8 1.0
C C:MET195 4.3 21.4 1.0
N C:LYS194 4.3 21.1 1.0
O C:HOH601 4.4 32.7 1.0
CA C:MET195 4.6 21.8 1.0
O C:HIS228 4.7 14.3 1.0
N C:ASP197 4.7 18.6 1.0
CB C:THR196 4.8 18.4 1.0
O C:MET195 4.9 21.1 1.0
O C:HOH649 4.9 38.7 1.0
CB C:VAL230 4.9 19.7 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 10:15:30 2025

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