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Potassium in PDB 5yg9: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant C135S From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate, Amp 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, Amp 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, Amp 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, Amp and Gmp, PDB code: 5yg9 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) 85.60 / 2.80
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 98.840, 98.840, 256.281, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 22.7

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, Amp and Gmp (pdb code 5yg9). 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, Amp and Gmp, PDB code: 5yg9:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yg9

Go back to Potassium Binding Sites List in 5yg9
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, Amp 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, Amp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:65.8
occ:1.00
 O A:THR196 2.8 26.8 1.0
O A:LYS194 2.9 34.2 1.0
O A:MET193 3.6 32.6 1.0
C A:LYS194 3.8 34.6 1.0
C A:THR196 3.9 25.4 1.0
CG2 A:VAL230 4.0 28.9 1.0
CA A:LYS194 4.3 37.5 1.0
N A:THR196 4.3 28.6 1.0
O A:HIS228 4.6 22.0 1.0
C A:MET193 4.7 30.4 1.0
CA A:THR196 4.7 27.4 1.0
N A:MET195 4.8 30.8 1.0
N A:ASP197 4.8 23.8 1.0
C A:MET195 4.8 28.9 1.0
CA A:ASP197 5.0 23.3 1.0
N A:LYS194 5.0 35.1 1.0

Potassium binding site 2 out of 3 in 5yg9

Go back to Potassium Binding Sites List in 5yg9
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, Amp 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, Amp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:65.4
occ:1.00
 O B:THR196 2.9 28.4 1.0
O B:LYS194 3.3 30.8 1.0
O B:MET193 3.6 34.3 1.0
C B:LYS194 3.8 33.5 1.0
CG2 B:VAL230 4.0 31.1 1.0
C B:THR196 4.1 26.1 1.0
CA B:LYS194 4.2 34.0 1.0
N B:THR196 4.6 28.3 1.0
C B:MET193 4.6 28.3 1.0
N B:MET195 4.7 31.7 1.0
O B:HIS228 4.8 23.9 1.0
C B:MET195 4.8 30.4 1.0
CA B:THR196 4.9 26.9 1.0
N B:LYS194 4.9 32.7 1.0

Potassium binding site 3 out of 3 in 5yg9

Go back to Potassium Binding Sites List in 5yg9
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, Amp 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, Amp and Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K403

b:62.8
occ:1.00
 O C:THR196 2.8 22.1 1.0
O C:HOH524 3.0 32.9 1.0
O C:LYS194 3.3 30.3 1.0
O C:MET193 3.4 29.1 1.0
CG2 C:VAL230 3.8 24.2 1.0
C C:LYS194 3.9 32.0 1.0
C C:THR196 4.0 21.7 1.0
CA C:LYS194 4.2 35.8 1.0
O C:HIS228 4.4 33.5 1.0
C C:MET193 4.5 28.8 1.0
N C:THR196 4.5 24.9 1.0
N C:MET195 4.7 31.4 1.0
N C:LYS194 4.8 33.4 1.0
CA C:THR196 4.9 22.4 1.0
CB C:HIS228 4.9 31.0 1.0
C C:MET195 4.9 27.6 1.0
N C:ASP197 5.0 20.5 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 15:13:22 2024

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