Magnesium in PDB 8grd: Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg

Enzymatic activity of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg

All present enzymatic activity of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg:
1.1.1.41;

Protein crystallography data

The structure of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg, PDB code: 8grd was solved by X.Chen, P.Sun, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	23.31 / 2.70
*Space group*	I 4 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	165.897, 165.897, 129.583, 90, 90, 90
*R / R_free (%)*	19.4 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg (pdb code 8grd). 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 A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg, PDB code: 8grd:

Magnesium binding site 1 out of 1 in 8grd

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Magnesium Binding Sites List in 8grd

Magnesium binding site 1 out of 1 in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg

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 A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Adp and Mg within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:32.8 occ:1.00	OD2	B:ASP217	2.1	45.4	1.0
	OD1	A:ASP230	2.1	59.6	1.0
	O	B:HOH522	2.3	42.4	1.0
	OD1	A:ASP234	2.4	55.1	1.0
	O	A:ASP230	3.1	46.7	1.0
	CG	A:ASP230	3.1	49.8	1.0
	CG	B:ASP217	3.3	50.0	1.0
	CG	A:ASP234	3.4	50.2	1.0
	OD2	A:ASP230	3.6	45.6	1.0
	OD2	A:ASP234	3.9	51.7	1.0
	C	A:ASP230	4.0	44.0	1.0
	CB	B:ASP217	4.1	47.2	1.0
	CA	A:ASP230	4.2	46.0	1.0
	OD1	B:ASP217	4.2	53.8	1.0
	CB	A:ASP230	4.2	46.2	1.0
	NH1	A:ARG98	4.5	37.5	1.0
	OG	A:SER233	4.6	38.4	1.0
	CB	A:ASP234	4.6	44.5	1.0

Reference:

X.Chen, P.Sun, Y.Liu, S.Shen, T.Ma, J.Ding. Structures of A Constitutively Active Mutant of Human IDH3 Reveal New Insights Into the Mechanisms of Allosteric Activation and the Catalytic Reaction. J.Biol.Chem. V. 298 02695 2022.
ISSN: ESSN 1083-351X
PubMed: 36375638
DOI: 10.1016/J.JBC.2022.102695

Page generated: Fri Oct 4 03:55:04 2024

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