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

Go back to

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

Go back to

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

Go back to

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: Mon Aug 12 15:11:27 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy