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

Enzymatic activity of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Amp

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 and Amp:
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 and Amp, PDB code: 5yfw 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) 85.52 / 2.35
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.700, 98.700, 256.551, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 21.3

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

Potassium binding site 1 out of 3 in 5yfw

Go back to Potassium Binding Sites List in 5yfw
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 and Amp


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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:40.2
occ:1.00
 O A:THR196 2.7 23.3 1.0
O A:HOH602 2.8 34.7 1.0
O A:HOH620 2.9 39.8 1.0
O A:LYS194 3.0 29.7 1.0
O A:MET193 3.1 26.1 1.0
CG2 A:VAL230 3.5 25.4 1.0
C A:LYS194 3.5 28.4 1.0
C A:THR196 3.7 24.1 1.0
CA A:LYS194 3.9 31.1 1.0
O A:HOH514 3.9 39.1 1.0
N A:THR196 4.0 24.2 1.0
C A:MET193 4.1 25.7 1.0
O A:HOH631 4.1 38.5 1.0
CA A:THR196 4.4 24.7 1.0
N A:MET195 4.4 26.6 1.0
N A:LYS194 4.4 27.0 1.0
C A:MET195 4.5 26.2 1.0
O A:HOH595 4.6 34.5 1.0
O A:HIS228 4.6 16.6 1.0
N A:ASP197 4.8 24.7 1.0
CA A:MET195 4.8 27.4 1.0
CB A:THR196 5.0 23.3 1.0
CB A:VAL230 5.0 24.2 1.0

Potassium binding site 2 out of 3 in 5yfw

Go back to Potassium Binding Sites List in 5yfw
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 and Amp


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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:39.8
occ:1.00
 O B:HOH632 2.6 39.9 1.0
O B:THR196 2.8 23.6 1.0
O B:LYS194 3.0 27.1 1.0
O B:MET193 3.2 31.2 1.0
C B:LYS194 3.5 27.9 1.0
CG2 B:VAL230 3.6 32.6 1.0
O B:HOH552 3.7 40.1 1.0
C B:THR196 3.9 24.4 1.0
N B:THR196 4.0 23.9 1.0
CA B:LYS194 4.1 33.2 1.0
O B:HOH571 4.2 36.5 1.0
C B:MET193 4.3 26.1 1.0
N B:MET195 4.4 27.1 1.0
CA B:THR196 4.4 23.4 1.0
C B:MET195 4.4 24.2 1.0
O B:HOH574 4.5 40.9 1.0
N B:LYS194 4.6 27.3 1.0
CA B:MET195 4.7 27.5 1.0
O B:HIS228 4.8 25.5 1.0
N B:ASP197 4.9 26.9 1.0

Potassium binding site 3 out of 3 in 5yfw

Go back to Potassium Binding Sites List in 5yfw
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 and Amp


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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:40.2
occ:1.00
 O C:THR196 2.6 25.1 1.0
O C:HOH606 2.7 37.6 1.0
O C:LYS194 3.0 28.7 1.0
O C:MET193 3.1 26.2 1.0
O C:HOH587 3.1 42.3 1.0
C C:LYS194 3.5 25.0 1.0
CG2 C:VAL230 3.6 23.8 1.0
O C:HOH583 3.7 32.6 1.0
C C:THR196 3.7 23.6 1.0
CA C:LYS194 3.9 28.3 1.0
N C:THR196 4.0 24.6 1.0
C C:MET193 4.1 24.5 1.0
N C:MET195 4.3 26.8 1.0
O C:HOH600 4.4 52.5 1.0
CA C:THR196 4.4 24.8 1.0
C C:MET195 4.5 25.4 1.0
N C:LYS194 4.5 24.3 1.0
O C:HOH560 4.6 38.1 1.0
CA C:MET195 4.7 26.9 1.0
N C:ASP197 4.7 23.5 1.0
O C:HIS228 4.8 29.3 1.0
CA C:ASP197 5.0 23.9 1.0
CB C:VAL230 5.0 23.3 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 10:16:26 2025

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