Potassium in PDB 8dcl: Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

Enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

All present enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36:
5.1.3.13;

Protein crystallography data

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36, PDB code: 8dcl was solved by J.B.Thoden, M.K.Ghosh, D.F.Xiang, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.75 / 1.55
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	39.84, 44.766, 57.428, 83.25, 79.35, 65.08
*R / R_free (%)*	16.5 / 20

Other elements in 8dcl:

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 (pdb code 8dcl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36, PDB code: 8dcl:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 8dcl

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Potassium Binding Sites List in 8dcl

Potassium binding site 1 out of 2 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K202 b:16.0 occ:1.00	O	A:HOH472	2.6	21.4	1.0
	O	A:LEU48	2.6	11.7	1.0
	O	A:ASP41	2.7	12.2	1.0
	O	A:PRO45	3.0	19.6	1.0
	O	A:HOH468	3.0	28.6	1.0
	O	A:HOH444	3.0	17.7	1.0
	O	A:LEU44	3.2	15.8	1.0
	C	A:PRO45	3.7	22.1	1.0
	C	A:LEU44	3.7	17.4	1.0
	C	A:ASP41	3.7	13.1	1.0
	C	A:LEU48	3.8	13.3	1.0
	CB	A:LEU44	3.8	13.2	1.0
	N	A:LEU48	4.1	16.1	1.0
	N	A:ASN46	4.2	23.7	1.0
	CA	A:LEU44	4.2	14.3	1.0
	CA	A:ASN46	4.2	24.8	1.0
	NA	A:NA204	4.2	30.1	1.0
	N	A:GLY47	4.2	19.0	1.0
	N	A:LEU44	4.4	13.1	1.0
	N	A:PRO45	4.5	18.5	1.0
	CA	A:LEU48	4.5	14.4	1.0
	C	A:ASN46	4.5	22.6	1.0
	N	A:LYS42	4.5	14.2	1.0
	CA	A:LYS42	4.6	16.4	1.0
	CA	A:PRO45	4.6	19.7	1.0
	CA	A:ASP41	4.7	11.8	1.0
	CB	A:ASP41	4.7	13.1	1.0
	C	A:LYS42	4.8	15.8	1.0
	CG	A:LYS49	4.8	14.3	1.0
	N	A:LYS49	4.9	11.9	1.0
	O	A:LYS42	4.9	15.9	1.0
	CB	A:LEU48	4.9	16.0	1.0
	CG	A:LEU44	4.9	13.9	1.0

Potassium binding site 2 out of 2 in 8dcl

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Potassium Binding Sites List in 8dcl

Potassium binding site 2 out of 2 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36

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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:23/36 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:K202 b:19.9 occ:1.00	O	B:HOH446	2.6	30.4	1.0
	O	B:ASP41	2.8	14.3	1.0
	O	B:LEU48	2.8	13.9	1.0
	O	B:PRO45	2.9	14.5	1.0
	O	B:HOH460	3.0	30.2	1.0
	O	B:LEU44	3.0	15.3	1.0
	C	B:LEU44	3.6	17.3	1.0
	CB	B:LEU44	3.7	14.8	1.0
	C	B:ASP41	3.8	13.9	1.0
	C	B:PRO45	3.8	17.3	1.0
	C	B:LEU48	4.0	13.7	1.0
	CA	B:LEU44	4.0	15.0	1.0
	N	B:LEU48	4.2	15.6	1.0
	N	B:LEU44	4.2	14.7	1.0
	N	B:PRO45	4.3	18.0	1.0
	O	B:HOH330	4.3	32.1	1.0
	NA	B:NA203	4.4	30.9	1.0
	CA	B:LYS42	4.4	17.6	1.0
	N	B:LYS42	4.5	14.9	1.0
	C	B:LYS42	4.5	18.5	1.0
	N	B:ASN46	4.5	17.7	1.0
	CA	B:LEU48	4.6	16.2	1.0
	O	B:LYS42	4.6	16.7	1.0
	N	B:GLY47	4.6	16.6	1.0
	CA	B:PRO45	4.7	17.9	1.0
	CA	B:ASN46	4.7	19.5	1.0
	CA	B:ASP41	4.8	12.7	1.0
	CB	B:ASP41	4.8	11.9	1.0
	C	B:ASN46	4.9	18.9	1.0
	CB	B:LEU48	4.9	17.2	1.0
	CG	B:LEU44	4.9	16.5	1.0

Reference:

M.K.Ghosh, D.F.Xiang, J.B.Thoden, H.M.Holden, F.M.Raushel. C3- and C3/C5-Epimerases Required For the Biosynthesis of the Capsular Polysaccharides From Campylobacter Jejuni . Biochemistry V. 61 2036 2022.
ISSN: ISSN 0006-2960
PubMed: 36093987
DOI: 10.1021/ACS.BIOCHEM.2C00364

Page generated: Mon Aug 12 23:30:13 2024

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