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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 / Rfree (%) 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

Go back to 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: Mon Dec 14 20:09:49 2020

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