Potassium in PDB 5yg7: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase Mutant D204N 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 D204N 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 D204N 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 D204N From Pyrococcus Horikoshii OT3 in Complex with Ribose-1,5- Bisphosphate and Gmp, PDB code: 5yg7 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)*	85.87 / 2.50
*Space group*	P 3₁ 1 2
*Cell size a, b, c (Å), α, β, γ (°)*	99.160, 99.160, 257.041, 90.00, 90.00, 120.00
*R / R_free (%)*	17.3 / 22.6

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 Gmp (pdb code 5yg7). 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 Gmp, PDB code: 5yg7:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5yg7

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Potassium Binding Sites List in 5yg7

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 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 D204N 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:47.1 occ:1.00	O	A:THR196	2.7	38.2	1.0
	O	A:LYS194	2.9	37.6	1.0
	O	A:MET193	3.1	35.5	1.0
	C	A:LYS194	3.6	40.9	1.0
	CG2	A:VAL230	3.6	33.0	1.0
	C	A:THR196	3.8	36.8	1.0
	CA	A:LYS194	3.9	42.7	1.0
	O	A:HOH544	4.1	38.1	1.0
	N	A:THR196	4.1	33.7	1.0
	C	A:MET193	4.2	35.4	1.0
	CA	A:THR196	4.4	36.3	1.0
	N	A:MET195	4.5	39.6	1.0
	N	A:LYS194	4.6	40.7	1.0
	C	A:MET195	4.6	35.0	1.0
	O	A:HIS228	4.6	19.3	1.0
	N	A:ASP197	4.8	35.0	1.0
	CA	A:MET195	4.9	36.0	1.0
	CB	A:THR196	5.0	33.6	1.0
	CB	A:HIS228	5.0	29.9	1.0

Potassium binding site 2 out of 3 in 5yg7

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Potassium Binding Sites List in 5yg7

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 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 D204N 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:47.8 occ:1.00	O	B:THR196	2.8	36.0	1.0
	O	B:LYS194	3.0	42.1	1.0
	O	B:MET193	3.2	36.7	1.0
	C	B:LYS194	3.6	40.7	1.0
	CG2	B:VAL230	3.8	37.0	1.0
	O	B:HOH553	3.8	33.0	1.0
	C	B:THR196	3.9	35.5	1.0
	CA	B:LYS194	4.0	44.1	1.0
	N	B:THR196	4.2	35.1	1.0
	C	B:MET193	4.3	35.1	1.0
	N	B:MET195	4.4	37.4	1.0
	C	B:MET195	4.6	33.3	1.0
	CA	B:THR196	4.6	34.2	1.0
	N	B:LYS194	4.7	38.2	1.0
	O	B:HIS228	4.8	26.7	1.0
	CA	B:MET195	4.8	37.9	1.0
	N	B:ASP197	4.9	39.8	1.0

Potassium binding site 3 out of 3 in 5yg7

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Potassium Binding Sites List in 5yg7

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 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 D204N 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:46.1 occ:1.00	O	C:THR196	2.7	30.7	1.0
	O	C:LYS194	2.9	37.4	1.0
	O	C:MET193	3.2	40.2	1.0
	C	C:LYS194	3.6	35.4	1.0
	CG2	C:VAL230	3.7	32.4	1.0
	C	C:THR196	3.9	31.7	1.0
	CA	C:LYS194	4.0	38.4	1.0
	N	C:THR196	4.1	34.4	1.0
	C	C:MET193	4.3	31.7	1.0
	N	C:MET195	4.5	35.9	1.0
	O	C:HIS228	4.5	34.9	1.0
	C	C:MET195	4.6	37.0	1.0
	CA	C:THR196	4.6	33.9	1.0
	N	C:LYS194	4.6	34.1	1.0
	CA	C:MET195	4.9	38.2	1.0
	N	C:ASP197	4.9	32.4	1.0
	CB	C:HIS228	4.9	35.2	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 10:16:59 2025

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