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

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

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

Protein crystallography data

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp, PDB code: 5yfu 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)*	85.72 / 2.35
*Space group*	P 3₁ 1 2
*Cell size a, b, c (Å), α, β, γ (°)*	98.980, 98.980, 256.611, 90.00, 90.00, 120.00
*R / R_free (%)*	18 / 24.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp (pdb code 5yfu). 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 From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp, PDB code: 5yfu:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yfu

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Potassium Binding Sites List in 5yfu

Potassium binding site 1 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-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 From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K402 b:53.5 occ:1.00	O	A:THR196	2.7	36.6	1.0
	O	A:LYS194	2.9	39.5	1.0
	O	A:MET193	3.3	36.2	1.0
	C	A:LYS194	3.6	40.4	1.0
	O	A:HOH504	3.6	39.2	1.0
	CG2	A:VAL230	3.7	38.7	1.0
	O	A:HOH583	3.7	59.8	0.5
	C	A:THR196	3.8	37.2	1.0
	CA	A:LYS194	4.0	42.2	1.0
	N	A:THR196	4.2	36.9	1.0
	C	A:MET193	4.3	36.3	1.0
	O	A:HOH582	4.4	37.8	1.0
	CA	A:THR196	4.5	36.7	1.0
	N	A:MET195	4.5	38.2	1.0
	O	A:HIS228	4.6	27.7	1.0
	C	A:MET195	4.6	39.4	1.0
	N	A:LYS194	4.6	39.9	1.0
	N	A:ASP197	4.7	35.2	1.0
	CA	A:ASP197	4.9	35.6	1.0
	CA	A:MET195	4.9	38.4	1.0

Potassium binding site 2 out of 3 in 5yfu

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Potassium Binding Sites List in 5yfu

Potassium binding site 2 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-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 From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:K402 b:54.7 occ:1.00	O	B:THR196	2.7	39.2	1.0
	O	B:LYS194	3.0	38.1	1.0
	O	B:MET193	3.4	39.2	1.0
	C	B:LYS194	3.6	39.3	1.0
	CG2	B:VAL230	3.7	42.8	1.0
	C	B:THR196	3.8	39.0	1.0
	CA	B:LYS194	4.1	39.0	0.5
	CA	B:LYS194	4.1	38.4	0.5
	N	B:THR196	4.1	36.3	1.0
	C	B:MET193	4.5	35.7	1.0
	N	B:MET195	4.5	37.0	1.0
	C	B:MET195	4.6	35.8	1.0
	CA	B:THR196	4.6	36.7	1.0
	N	B:LYS194	4.8	37.3	1.0
	N	B:ASP197	4.8	38.5	1.0
	O	B:HIS228	4.9	35.4	1.0
	CA	B:MET195	4.9	37.8	1.0
	CA	B:ASP197	5.0	34.9	1.0

Potassium binding site 3 out of 3 in 5yfu

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Potassium Binding Sites List in 5yfu

Potassium binding site 3 out of 3 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Pyrococcus Horikoshii OT3 in Complex with Ribulose-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 From Pyrococcus Horikoshii OT3 in Complex with Ribulose-1,5-Bisphosphate and Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:K402 b:55.9 occ:1.00	O	C:HOH573	2.6	56.1	1.0
	O	C:THR196	2.6	37.8	1.0
	O	C:LYS194	3.1	36.7	1.0
	O	C:MET193	3.2	36.5	1.0
	O	C:HOH541	3.6	43.5	1.0
	CG2	C:VAL230	3.6	35.0	1.0
	C	C:LYS194	3.7	34.6	1.0
	C	C:THR196	3.9	32.5	1.0
	CA	C:LYS194	4.0	39.9	1.0
	N	C:THR196	4.3	33.9	1.0
	C	C:MET193	4.3	34.3	1.0
	O	C:HOH521	4.4	46.6	1.0
	N	C:MET195	4.5	37.6	1.0
	CA	C:THR196	4.6	32.8	1.0
	N	C:LYS194	4.6	35.1	1.0
	O	C:HIS228	4.7	37.8	1.0
	C	C:MET195	4.7	37.5	1.0
	N	C:ASP197	4.8	32.3	1.0
	CB	C:HIS228	5.0	38.4	1.0
	CA	C:ASP197	5.0	34.5	1.0
	CA	C:MET195	5.0	39.1	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 10:15:48 2025

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