Magnesium in PDB 4me6: Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp

Enzymatic activity of Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp

All present enzymatic activity of Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp, PDB code: 4me6 was solved by T.T.N.Doan, J.K.Kim, Y.J.Ahn, B.M.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.32 / 2.10
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	83.236, 83.236, 98.277, 90.00, 90.00, 90.00
*R / R_free (%)*	19.2 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp (pdb code 4me6). 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 D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp, PDB code: 4me6:

Magnesium binding site 1 out of 1 in 4me6

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Magnesium Binding Sites List in 4me6

Magnesium binding site 1 out of 1 in the Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp

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 D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:35.4 occ:1.00	O	A:HOH666	2.5	41.0	1.0
	OD2	A:ASP302	2.6	15.7	1.0
	O2A	A:ADP402	2.7	43.2	1.0
	O	A:HOH552	3.0	33.7	1.0
	OE2	A:GLU315	3.2	27.5	1.0
	O1B	A:ADP402	3.4	46.1	1.0
	ND2	A:ASN314	3.4	25.7	1.0
	CG	A:ASP302	3.6	16.5	1.0
	CD	A:GLU315	3.7	26.7	1.0
	CB	A:GLU315	3.7	19.0	1.0
	CB	A:ASP302	3.8	14.5	1.0
	PA	A:ADP402	3.9	47.1	1.0
	OE1	A:GLU315	4.2	32.5	1.0
	O1A	A:ADP402	4.2	40.8	1.0
	CG	A:GLU315	4.3	22.7	1.0
	CG	A:ASN314	4.3	20.9	1.0
	NH2	A:ARG300	4.5	19.0	1.0
	O	A:HOH544	4.6	24.3	1.0
	O3A	A:ADP402	4.7	45.6	0.5
	PB	A:ADP402	4.7	47.3	1.0
	O3'	A:ADP402	4.7	45.8	1.0
	OD1	A:ASP302	4.7	16.4	1.0
	CB	A:ASN314	4.9	18.5	1.0

Reference:

T.N.N.Doan, J.K.Kim, H.P.T.Ngo, H.T.Tran, S.S.Cha, K.M.Chung, K.H.Huynh, Y.J.Ahn, L.W.Kang. Crystal Structures of D-Alanine-D-Alanine Ligase From Xanthomonas Oryzae Pv. Oryzae Alone and in Complex with Nucleotides Arch.Biochem.Biophys. V.545C 92 2014.
ISSN: ISSN 0003-9861
PubMed: 24440607
DOI: 10.1016/J.ABB.2014.01.009

Page generated: Mon Aug 11 20:21:59 2025

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