Magnesium in PDB 2vhx: Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate

Enzymatic activity of Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate

All present enzymatic activity of Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate:
1.4.1.1;

Protein crystallography data

The structure of Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate, PDB code: 2vhx was solved by D.Agren, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.00 / 2.0
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	176.247, 171.767, 98.254, 90.00, 90.00, 90.00
*R / R_free (%)*	17.2 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate (pdb code 2vhx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate, PDB code: 2vhx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2vhx

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Magnesium Binding Sites List in 2vhx

Magnesium binding site 1 out of 3 in the Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate

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 the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1372 b:32.6 occ:1.00	NE2	A:HIS327	2.2	16.8	1.0
	CE1	A:HIS327	3.1	14.4	1.0
	CD2	A:HIS327	3.2	16.7	1.0
	OE2	A:GLU323	3.5	30.3	1.0
	OD2	A:ASP326	4.0	19.0	1.0
	OE1	A:GLU323	4.0	32.0	1.0
	CD	A:GLU323	4.2	27.7	1.0
	ND1	A:HIS327	4.3	15.1	1.0
	CG	A:HIS327	4.4	14.7	1.0
	CB	A:ASP326	4.4	16.4	1.0
	CG	A:ASP326	4.7	19.6	1.0

Magnesium binding site 2 out of 3 in 2vhx

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Magnesium Binding Sites List in 2vhx

Magnesium binding site 2 out of 3 in the Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1372 b:28.8 occ:1.00	NE2	B:HIS327	2.3	12.5	1.0
	CE1	B:HIS327	3.1	11.4	1.0
	CD2	B:HIS327	3.4	10.6	1.0
	OD2	B:ASP326	3.9	18.4	1.0
	O	B:HOH2212	4.1	32.7	1.0
	O	B:HOH2009	4.3	32.1	1.0
	ND1	B:HIS327	4.3	12.3	1.0
	CB	B:ASP326	4.4	11.1	1.0
	O	B:HOH2026	4.4	24.6	1.0
	CG	B:HIS327	4.5	11.1	1.0
	CG	B:ASP326	4.6	14.3	1.0
	OE1	B:GLU323	4.7	32.8	1.0

Magnesium binding site 3 out of 3 in 2vhx

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Magnesium Binding Sites List in 2vhx

Magnesium binding site 3 out of 3 in the Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Ternary Complex of L-Alanine Dehydrogenase From Mycobacterium Tuberculosis with Nad+ and Pyruvate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
F:Mg1374 b:53.5 occ:1.00	NE2	F:HIS327	2.4	20.2	1.0
	CD2	F:HIS327	3.3	19.7	1.0
	OE2	F:GLU323	3.3	31.2	1.0
	CE1	F:HIS327	3.4	21.4	1.0
	OE1	F:GLU323	3.7	30.1	1.0
	CD	F:GLU323	3.9	29.3	1.0
	OD2	F:ASP326	4.1	19.9	1.0
	CB	F:ASP326	4.4	13.5	1.0
	CG	F:HIS327	4.5	17.4	1.0
	ND1	F:HIS327	4.5	19.7	1.0
	CG	F:ASP326	4.8	16.8	1.0

Reference:

D.Agren, M.Stehr, C.L.Berthold, S.Kapoor, W.Oehlmann, M.Singh, G.Schneider. Three-Dimensional Structures of Apo- and Holo-L- Alanine Dehydrogenase From Mycobacterium Tuberculosis Reveal Conformational Changes Upon Coenzyme Binding. J.Mol.Biol. V. 377 1161 2008.
ISSN: ISSN 0022-2836
PubMed: 18304579
DOI: 10.1016/J.JMB.2008.01.091

Page generated: Wed Aug 14 05:13:51 2024

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