Calcium in PDB 5d2i: 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate

All present enzymatic activity of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate:
4.1.1.77;

The structure of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate, PDB code: 5d2i 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)	26.68 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.494, 43.750, 79.495, 90.00, 118.21, 90.00
R / Rfree (%)	14.6 / 18.6

The binding sites of Calcium atom in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate (pdb code 5d2i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate, PDB code: 5d2i:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:12.3 occ:1.00 OE2 A:GLU111 2.2 12.9 1.0 OE1 A:GLU142 2.2 9.7 1.0 OE1 A:GLU109 2.3 14.8 1.0 O A:HOH441 2.4 10.3 1.0 O A:ACT308 2.4 12.8 1.0 O A:HOH435 2.4 19.7 1.0 CD A:GLU111 3.3 12.7 1.0 C A:ACT308 3.4 19.3 1.0 CD A:GLU142 3.4 12.2 1.0 CD A:GLU109 3.4 13.2 1.0 OXT A:ACT308 3.6 17.2 1.0 OE1 A:GLU111 3.7 7.8 1.0 NZ A:LYS64 4.0 10.8 1.0 O A:MET65 4.0 11.9 1.0 CB A:GLU142 4.1 11.8 1.0 OE2 A:GLU109 4.1 19.4 1.0 CE A:LYS64 4.1 9.9 1.0 CG2 A:ILE144 4.2 12.0 1.0 N A:GLY236 4.2 11.4 1.0 OE2 A:GLU142 4.3 10.6 1.0 CG A:GLU142 4.3 9.8 1.0 CG A:GLU109 4.5 24.6 1.0 CB A:GLU109 4.5 15.7 1.0 CG A:GLU111 4.5 8.3 1.0 CH3 A:ACT308 4.7 16.4 1.0 C A:GLY235 4.7 12.3 1.0 CA A:GLY235 4.7 12.1 1.0 CA A:GLY236 4.8 11.3 1.0

Calcium binding site 2 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:44.1 occ:1.00 OD2 A:ASP94 2.4 20.6 1.0 O A:SER258 2.4 15.2 1.0 O A:HOH472 2.5 34.5 1.0 OG A:SER258 3.1 24.7 1.0 CG A:ASP94 3.2 17.1 1.0 C A:SER258 3.2 16.7 1.0 OD1 A:ASP94 3.3 12.7 1.0 O A:HOH644 3.8 48.2 1.0 CA A:SER258 3.9 12.6 1.0 N A:SER258 3.9 15.0 1.0 CB A:SER258 4.1 16.8 1.0 N A:VAL259 4.2 13.9 1.0 O A:HOH654 4.2 20.8 1.0 O A:HOH669 4.3 40.7 1.0 N A:GLY172 4.3 19.5 1.0 CA A:VAL259 4.4 12.0 1.0 CB A:ASP94 4.6 15.1 1.0 CA A:GLY172 4.8 16.4 1.0 OG A:SER260 4.8 15.4 1.0 N A:SER260 4.9 11.0 1.0 C A:VAL259 5.0 11.9 1.0

Calcium binding site 3 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Calcium and Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:14.6 occ:1.00 OE2 B:GLU111 2.1 15.1 1.0 OE1 B:GLU142 2.2 12.6 1.0 O B:ACT307 2.3 14.4 1.0 OE1 B:GLU109 2.3 16.9 1.0 O B:HOH450 2.3 12.4 1.0 O B:HOH404 2.4 29.3 1.0 CD B:GLU111 3.2 10.8 1.0 C B:ACT307 3.3 22.3 1.0 CD B:GLU109 3.4 21.4 1.0 CD B:GLU142 3.5 18.3 1.0 OXT B:ACT307 3.5 23.5 1.0 OE1 B:GLU111 3.6 9.4 1.0 OE2 B:GLU109 4.0 34.5 1.0 NZ B:LYS64 4.0 15.4 1.0 N B:GLY236 4.1 10.8 1.0 CE B:LYS64 4.1 12.9 1.0 CG2 B:ILE144 4.1 16.3 1.0 O B:MET65 4.2 12.4 1.0 CB B:GLU142 4.2 9.2 1.0 OE2 B:GLU142 4.3 17.1 1.0 CG B:GLU142 4.4 12.1 1.0 CG B:GLU111 4.5 12.4 1.0 CB B:GLU109 4.5 14.8 1.0 CA B:GLY236 4.6 12.7 1.0 CG B:GLU109 4.6 25.9 1.0 C B:GLY235 4.6 10.8 1.0 CH3 B:ACT307 4.6 25.6 1.0 CA B:GLY235 4.7 8.2 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