Magnesium in PDB 5nri: Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala

Enzymatic activity of Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala

All present enzymatic activity of Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala, PDB code: 5nri was solved by L.Diaz-Saez, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	69.97 / 1.50
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	69.642, 61.133, 69.972, 90.00, 90.31, 90.00
*R / R_free (%)*	13.3 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala (pdb code 5nri). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala, PDB code: 5nri:

Magnesium binding site 1 out of 1 in 5nri

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Magnesium Binding Sites List in 5nri

Magnesium binding site 1 out of 1 in the Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase in Complex with Amp and D-Ala-D-Ala within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg404 b:23.4 occ:1.00	O	A:HOH712	1.7	47.2	1.0
	O	A:HOH850	1.9	54.8	1.0
	O	A:HOH642	1.9	41.9	1.0
	O	A:HOH501	2.0	58.2	1.0
	NE2	A:HIS70	2.1	18.6	0.5
	O	A:HOH683	2.5	75.5	1.0
	O	A:HOH505	2.8	40.4	1.0
	CD2	A:HIS70	3.0	18.1	0.5
	CE1	A:HIS70	3.1	20.6	0.5
	N	A:DAL403	3.6	33.1	0.0
	OE1	A:GLU75	3.9	27.6	1.0
	OE2	A:GLU75	4.0	29.7	1.0
	CG	A:HIS70	4.2	21.8	0.5
	ND1	A:HIS70	4.2	20.8	0.5
	CD	A:GLU75	4.4	22.2	1.0
	OE2	A:GLU22	4.5	63.4	1.0
	CD	A:GLU22	4.8	47.1	1.0
	O	A:DAL403	4.8	42.8	1.0

Reference:

L.Diaz-Saez, L.S.Torrie, S.P.Mcelroy, D.Gray, W.N.Hunter. Burkholderia Pseudomallei D-Alanine-D-Alanine Ligase; Detailed Characterisation and Assessment of A Potential Antibiotic Drug Target. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31260169
DOI: 10.1111/FEBS.14976

Page generated: Sun Sep 29 23:39:13 2024

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