Magnesium in PDB 5d2h: 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate

Enzymatic activity of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate

All present enzymatic activity of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate:
4.1.1.77;

Protein crystallography data

The structure of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate, PDB code: 5d2h was solved by S.L.Guimaraes, R.A.P.Nagem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	42.27 / 1.94
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	43.741, 44.904, 125.318, 90.00, 90.00, 90.00
*R / R_free (%)*	16.3 / 23.1

Other elements in 5d2h:

The structure of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate (pdb code 5d2h). 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 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate, PDB code: 5d2h:

Magnesium binding site 1 out of 1 in 5d2h

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Magnesium Binding Sites List in 5d2h

Magnesium binding site 1 out of 1 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Alpha-Ketoglutarate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg301 b:19.4 occ:1.00	OE2	A:GLU109	1.9	23.7	1.0
	OE1	A:GLU142	2.0	16.7	1.0
	OE1	A:GLU111	2.0	18.9	1.0
	O	A:HOH470	2.0	16.1	1.0
	O	A:HOH421	2.1	20.2	1.0
	O2	A:AKG302	2.4	21.0	1.0
	CD	A:GLU109	2.9	23.4	1.0
	CD	A:GLU111	3.0	23.4	1.0
	CD	A:GLU142	3.2	20.1	1.0
	C1	A:AKG302	3.3	29.9	1.0
	OE2	A:GLU111	3.4	17.9	1.0
	O1	A:AKG302	3.5	35.8	1.0
	OE1	A:GLU109	3.6	22.4	1.0
	CG	A:GLU109	3.8	22.2	1.0
	O	A:MET65	3.8	19.5	1.0
	NZ	A:LYS64	3.9	14.1	1.0
	CE	A:LYS64	4.0	14.6	1.0
	CB	A:GLU142	4.0	19.8	1.0
	OE2	A:GLU142	4.1	16.8	1.0
	CG	A:GLU142	4.2	16.7	1.0
	CG2	A:ILE144	4.2	17.1	1.0
	CG	A:GLU111	4.3	17.2	1.0
	N	A:GLY236	4.4	18.6	1.0
	C2	A:AKG302	4.6	29.4	1.0
	C	A:GLY235	4.8	20.6	1.0
	CA	A:GLY235	4.8	16.9	1.0
	O	A:HOH426	4.8	25.3	1.0
	O5	A:AKG302	4.9	37.0	1.0
	C	A:MET65	4.9	18.2	1.0
	CA	A:GLY236	4.9	22.9	1.0

Reference:

S.L.Guimaraes, J.B.Coitinho, D.M.Costa, S.S.Araujo, C.P.Whitman, R.A.Nagem. Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover A Structural Basis For the Metal-Assisted Decarboxylation of A Vinylogous Beta-Keto Acid. Biochemistry V. 55 2632 2016.
ISSN: ISSN 0006-2960
PubMed: 27082660
DOI: 10.1021/ACS.BIOCHEM.6B00050

Page generated: Sun Sep 29 02:28:33 2024

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