Calcium in PDB 6ph9: Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

Enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

All present enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex:
3.6.1.54;

Protein crystallography data

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9 was solved by J.Cho, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	45.90 / 1.92
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	105.990, 105.990, 52.570, 90.00, 90.00, 120.00
*R / R_free (%)*	17.8 / 19.9

Other elements in 6ph9:

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex (pdb code 6ph9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9:

Calcium binding site 1 out of 1 in 6ph9

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Calcium Binding Sites List in 6ph9

Calcium binding site 1 out of 1 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca308 b:60.0 occ:1.00	O	A:GLU170	2.4	65.3	1.0
	O	A:HOH559	2.4	60.4	1.0
	O	A:HOH403	2.5	52.3	1.0
	O	A:HOH448	2.6	66.4	1.0
	OD1	A:ASP173	2.6	58.4	1.0
	O	A:HOH500	2.7	69.6	1.0
	C	A:GLU170	3.4	68.3	1.0
	CG	A:ASP173	3.5	59.4	1.0
	OD2	A:ASP173	3.7	60.4	1.0
	CA	A:GLU170	3.9	67.0	1.0
	OD2	A:ASP121	4.0	53.1	1.0
	CB	A:GLU170	4.4	71.6	1.0
	N	A:ILE171	4.5	63.6	1.0
	O	A:VAL174	4.6	39.8	1.0
	O	A:ASP173	4.8	43.6	1.0
	O	A:MET169	4.9	65.9	1.0
	CA	A:ILE171	4.9	61.2	1.0
	CB	A:ASP173	5.0	49.8	1.0

Reference:

J.Cho, M.Lee, C.Cochrane, C.Webster, B.Fenton, J.Zhao, J.Hong, P.Zhao. Structural Basis of the Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh Inhibition By Sulfonyl Piperazine Antibiotics Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1912876117

Page generated: Wed Jul 9 16:47:34 2025

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