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Potassium in PDB 5yft: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N 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 D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yft 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 / 2.21
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.810, 98.810, 257.081, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 19.3

Other elements in 5yft:

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate (pdb code 5yft). 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 D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, PDB code: 5yft:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yft

Go back to Potassium Binding Sites List in 5yft
Potassium binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N 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:27.9
occ:1.00
 O A:THR196 2.7 20.4 1.0
O A:HOH602 2.7 25.2 1.0
O A:LYS194 2.8 20.2 1.0
O A:MET193 2.9 19.7 1.0
O A:HOH672 3.1 41.4 1.0
C A:LYS194 3.3 21.5 1.0
CG2 A:VAL230 3.4 21.5 1.0
CA A:LYS194 3.7 24.8 1.0
C A:THR196 3.7 21.3 1.0
O A:HOH691 3.9 39.7 1.0
N A:THR196 4.0 18.1 1.0
C A:MET193 4.0 21.3 1.0
O A:HOH573 4.0 26.6 1.0
O A:HOH613 4.2 32.2 1.0
N A:MET195 4.3 20.0 1.0
N A:LYS194 4.3 21.5 1.0
C A:MET195 4.4 18.3 1.0
CA A:THR196 4.4 19.6 1.0
O A:HIS228 4.6 14.6 1.0
CA A:MET195 4.7 20.2 1.0
N A:ASP197 4.8 22.3 1.0
CB A:VAL230 4.9 19.6 1.0
CB A:THR196 4.9 17.3 1.0
O A:MET195 5.0 18.8 1.0

Potassium binding site 2 out of 3 in 5yft

Go back to Potassium Binding Sites List in 5yft
Potassium binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N 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:28.9
occ:1.00
 O B:HOH662 2.6 21.8 1.0
O B:THR196 2.7 21.3 1.0
O B:LYS194 2.9 19.5 1.0
O B:MET193 3.0 20.1 1.0
C B:LYS194 3.4 22.6 1.0
CG2 B:VAL230 3.5 21.5 1.0
C B:THR196 3.7 20.8 1.0
CA B:LYS194 3.8 25.9 1.0
N B:THR196 3.9 20.8 1.0
O B:HOH566 4.0 26.3 1.0
C B:MET193 4.1 20.1 1.0
O B:HOH543 4.1 40.5 1.0
N B:MET195 4.2 24.1 1.0
CA B:THR196 4.3 20.1 1.0
C B:MET195 4.4 21.8 1.0
N B:LYS194 4.4 22.2 1.0
O B:HIS228 4.6 17.7 1.0
CA B:MET195 4.7 25.3 1.0
N B:ASP197 4.8 20.2 1.0
O B:HOH602 4.9 46.6 1.0
CB B:THR196 4.9 18.9 1.0
CB B:VAL230 4.9 20.4 1.0

Potassium binding site 3 out of 3 in 5yft

Go back to Potassium Binding Sites List in 5yft
Potassium binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N 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:28.7
occ:1.00
 O C:THR196 2.5 24.6 1.0
O C:HOH642 2.7 23.8 1.0
O C:LYS194 2.9 21.4 1.0
O C:HOH661 2.9 42.3 1.0
O C:MET193 3.1 20.3 1.0
O C:HOH619 3.2 40.8 1.0
C C:LYS194 3.4 20.0 1.0
CG2 C:VAL230 3.5 19.0 1.0
C C:THR196 3.7 20.1 1.0
CA C:LYS194 3.8 23.7 1.0
O C:HOH601 3.9 29.0 1.0
N C:THR196 3.9 20.6 1.0
C C:MET193 4.1 21.2 1.0
N C:MET195 4.3 21.3 1.0
O C:HOH542 4.3 36.7 1.0
CA C:THR196 4.4 18.7 1.0
C C:MET195 4.4 22.4 1.0
N C:LYS194 4.5 20.9 1.0
O C:HOH656 4.6 53.8 1.0
N C:ASP197 4.7 20.7 1.0
CA C:MET195 4.7 24.3 1.0
O C:HIS228 4.7 22.1 1.0
O C:HOH594 4.9 41.2 1.0
CB C:VAL230 4.9 17.4 1.0
CA C:ASP197 4.9 20.2 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 10:15:45 2025

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