Magnesium in PDB 5d2k: 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate

All present enzymatic activity of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate:
4.1.1.77;

The structure of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate, PDB code: 5d2k 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)	40.78 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.328, 44.411, 81.623, 90.00, 118.68, 90.00
R / Rfree (%)	15.1 / 17.5

The binding sites of Magnesium atom in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate (pdb code 5d2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate, PDB code: 5d2k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate


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 2-Oxoadipate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:12.6 occ:1.00 OE2 A:GLU111 2.0 13.4 1.0 OE1 A:GLU142 2.0 13.6 1.0 O A:HOH441 2.1 12.8 1.0 O4 A:OOG302 2.1 16.6 1.0 OE1 A:GLU109 2.1 15.4 1.0 O5 A:OOG302 2.2 13.7 1.0 C6 A:OOG302 2.8 17.5 1.0 C5 A:OOG302 2.9 17.0 1.0 CD A:GLU111 3.1 12.3 1.0 CD A:GLU109 3.3 22.6 1.0 CD A:GLU142 3.3 14.9 1.0 OE1 A:GLU111 3.5 10.2 1.0 OE2 A:GLU109 3.8 32.9 1.0 NZ A:LYS64 3.9 13.8 1.0 CB A:GLU142 4.0 9.5 1.0 O3 A:OOG302 4.0 20.4 1.0 N A:GLY236 4.1 13.0 1.0 CE A:LYS64 4.1 14.1 1.0 OE2 A:GLU142 4.1 15.1 1.0 CG A:GLU142 4.2 11.1 1.0 O A:MET65 4.3 14.0 1.0 C4 A:OOG302 4.3 22.4 1.0 CG A:GLU111 4.3 9.3 1.0 CG2 A:ILE144 4.4 13.8 1.0 CG A:GLU109 4.4 24.1 1.0 CB A:GLU109 4.5 20.6 1.0 C A:GLY235 4.7 10.8 1.0 CA A:GLY236 4.7 11.6 1.0 CA A:GLY235 4.7 8.6 1.0 C3 A:OOG302 4.9 26.4 1.0 CE A:MET233 4.9 12.8 1.0

Magnesium binding site 2 out of 2 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and 2-Oxoadipate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:11.3 occ:1.00 OE1 B:GLU142 2.0 12.6 1.0 OE2 B:GLU111 2.0 12.3 1.0 O3 B:OOG302 2.1 10.7 0.6 OE1 B:GLU109 2.1 15.9 1.0 O B:HOH430 2.1 10.3 1.0 O3 B:OOG302 2.2 16.1 0.4 O5 B:OOG302 2.3 15.5 0.6 C6 B:OOG302 2.8 23.4 0.6 C5 B:OOG302 2.8 21.9 0.6 CD B:GLU111 3.1 10.9 1.0 CD B:GLU109 3.2 16.7 1.0 CD B:GLU142 3.2 12.7 1.0 C6 B:OOG302 3.2 20.1 0.4 OE1 B:GLU111 3.5 10.1 1.0 O4 B:OOG302 3.6 22.1 0.4 OE2 B:GLU109 3.7 20.8 1.0 O B:MET65 3.9 15.9 1.0 CB B:GLU142 3.9 11.0 1.0 NZ B:LYS64 4.0 12.4 1.0 O4 B:OOG302 4.0 25.8 0.6 OE2 B:GLU142 4.1 11.9 1.0 CG B:GLU142 4.1 11.2 1.0 CE B:LYS64 4.2 10.8 1.0 CG B:GLU109 4.3 16.2 1.0 CG2 B:ILE144 4.3 13.5 1.0 C4 B:OOG302 4.3 23.8 0.6 N B:GLY236 4.3 12.6 1.0 CG B:GLU111 4.4 10.2 1.0 CB B:GLU109 4.4 14.2 1.0 C5 B:OOG302 4.5 20.6 0.4 CA B:GLY235 4.8 10.1 1.0 C B:GLY235 4.8 11.6 1.0 C3 B:OOG302 4.9 24.0 0.6 CA B:GLY236 5.0 12.7 1.0 O B:HOH401 5.0 24.5 1.0

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