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Potassium in PDB 5yg6: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Gmp

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

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 and Gmp:
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 and Gmp, PDB code: 5yg6 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) 85.54 / 2.35
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.570, 98.570, 256.621, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 20.9

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 and Gmp (pdb code 5yg6). 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 and Gmp, PDB code: 5yg6:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yg6

Go back to Potassium Binding Sites List in 5yg6
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 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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:30.7
occ:1.00
 O A:THR196 2.7 19.6 1.0
O A:HOH627 2.7 26.1 1.0
O A:LYS194 3.0 25.6 1.0
O A:MET193 3.1 22.2 1.0
CG2 A:VAL230 3.5 24.5 1.0
C A:LYS194 3.5 23.9 1.0
O A:HOH584 3.7 47.4 1.0
C A:THR196 3.8 20.9 1.0
O A:HOH525 3.8 37.5 1.0
CA A:LYS194 3.9 29.0 1.0
N A:THR196 4.0 21.6 1.0
C A:MET193 4.1 22.5 1.0
N A:MET195 4.4 23.3 1.0
CA A:THR196 4.4 21.7 1.0
C A:MET195 4.4 21.9 1.0
N A:LYS194 4.5 24.9 1.0
O A:HIS228 4.6 21.1 1.0
CA A:MET195 4.8 24.3 1.0
N A:ASP197 4.8 21.6 1.0
CB A:VAL230 4.9 23.4 1.0
CB A:THR196 4.9 21.0 1.0

Potassium binding site 2 out of 3 in 5yg6

Go back to Potassium Binding Sites List in 5yg6
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 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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:35.4
occ:1.00
 O B:THR196 2.6 25.5 1.0
O B:HOH607 2.6 29.1 1.0
O B:LYS194 2.9 24.8 1.0
O B:MET193 3.0 23.7 1.0
O B:HOH585 3.1 37.8 1.0
C B:LYS194 3.4 23.3 1.0
O B:HOH573 3.5 33.5 1.0
CG2 B:VAL230 3.6 22.7 1.0
C B:THR196 3.8 21.6 1.0
O B:HOH615 3.8 38.0 1.0
CA B:LYS194 3.9 26.2 1.0
N B:THR196 4.0 22.6 1.0
C B:MET193 4.1 22.9 1.0
O B:HOH572 4.2 34.8 1.0
N B:MET195 4.3 25.1 1.0
N B:LYS194 4.5 23.4 1.0
O B:HOH612 4.5 51.1 1.0
CA B:THR196 4.5 22.4 1.0
C B:MET195 4.5 23.0 1.0
O B:HIS228 4.6 23.6 1.0
CA B:MET195 4.7 25.5 1.0
N B:ASP197 4.8 21.7 1.0
O B:HOH588 4.9 48.4 1.0
CB B:HIS228 4.9 21.9 1.0
CB B:VAL230 5.0 21.4 1.0
CA B:ASP197 5.0 22.4 1.0

Potassium binding site 3 out of 3 in 5yg6

Go back to Potassium Binding Sites List in 5yg6
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 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 Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:31.0
occ:1.00
 O C:THR196 2.6 21.4 1.0
O C:HOH587 2.8 28.9 1.0
O C:LYS194 2.8 23.0 1.0
O C:HOH622 2.9 37.4 1.0
O C:MET193 3.0 22.4 1.0
C C:LYS194 3.4 24.2 1.0
CG2 C:VAL230 3.5 22.5 1.0
C C:THR196 3.7 20.1 1.0
CA C:LYS194 3.8 26.4 1.0
O C:HOH573 3.9 34.5 1.0
N C:THR196 4.0 21.0 1.0
C C:MET193 4.0 21.7 1.0
CA C:THR196 4.3 20.4 1.0
N C:MET195 4.4 23.4 1.0
N C:LYS194 4.4 23.1 1.0
C C:MET195 4.4 21.8 1.0
O C:HOH578 4.4 31.7 1.0
O C:HIS228 4.6 14.1 1.0
N C:ASP197 4.7 20.2 1.0
CA C:MET195 4.8 23.7 1.0
CB C:THR196 4.9 19.9 1.0
O C:MET195 4.9 22.0 1.0
O C:HOH620 4.9 41.1 1.0
CB C:VAL230 5.0 22.4 1.0
CA C:ASP197 5.0 22.0 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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