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Magnesium in PDB 5d2j: 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate

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

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

Protein crystallography data

The structure of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate, PDB code: 5d2j 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) 40.60 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.774, 44.547, 81.253, 90.00, 118.76, 90.00
R / Rfree (%) 15.4 / 19.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate (pdb code 5d2j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate, PDB code: 5d2j:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5d2j

Go back to Magnesium Binding Sites List in 5d2j
Magnesium binding site 1 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate


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 Adipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:15.9
occ:1.00
OE2 A:GLU111 2.1 18.4 1.0
OE1 A:GLU142 2.1 16.2 1.0
O A:HOH416 2.2 28.9 1.0
O A:HOH447 2.2 17.0 1.0
OE1 A:GLU109 2.2 21.2 1.0
O2 A:0L1303 2.2 19.7 1.0
CD A:GLU111 3.2 15.9 1.0
C2 A:0L1303 3.3 25.2 1.0
CD A:GLU109 3.3 27.9 1.0
CD A:GLU142 3.3 20.3 1.0
O1 A:0L1303 3.6 22.8 1.0
OE1 A:GLU111 3.6 13.6 1.0
OE2 A:GLU109 3.8 31.2 1.0
NZ A:LYS64 4.0 18.3 1.0
CE A:LYS64 4.1 20.6 1.0
OE2 A:GLU142 4.1 18.9 1.0
CB A:GLU142 4.2 10.6 1.0
O A:MET65 4.2 20.6 1.0
CG A:GLU142 4.3 13.2 1.0
N A:GLY236 4.3 13.3 1.0
CG2 A:ILE144 4.3 17.6 1.0
CG A:GLU111 4.4 15.4 1.0
CG A:GLU109 4.5 33.2 1.0
C3 A:0L1303 4.6 23.7 1.0
CB A:GLU109 4.7 23.7 1.0
C A:GLY235 4.7 15.1 1.0
CA A:GLY235 4.8 10.2 1.0
CA A:GLY236 4.8 16.8 1.0
O A:HOH403 4.9 37.2 1.0

Magnesium binding site 2 out of 3 in 5d2j

Go back to Magnesium Binding Sites List in 5d2j
Magnesium binding site 2 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate


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 Adipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:28.1
occ:1.00
O A:HOH571 2.0 35.3 1.0
O A:HOH615 2.4 32.5 1.0
O B:HOH425 2.4 21.3 1.0
O A:LEU22 2.5 18.7 1.0
O B:HOH563 2.5 24.2 1.0
O B:HOH608 2.6 29.2 1.0
C A:LEU22 3.5 14.5 1.0
OD1 A:ASN23 4.0 20.4 1.0
O A:HOH612 4.1 38.4 1.0
NZ B:LYS191 4.3 33.0 1.0
CA A:LEU22 4.3 11.6 1.0
CB A:LEU22 4.3 9.8 1.0
N A:ASN23 4.4 12.8 1.0
CG A:ASN23 4.4 18.1 1.0
CA A:ASN23 4.5 13.4 1.0
O A:HOH575 4.5 28.2 1.0
OD2 B:ASP247 4.6 16.5 1.0
O A:HOH646 4.7 45.8 1.0
OD1 B:ASP247 4.7 16.2 1.0
O B:HOH473 4.7 26.9 1.0
ND2 A:ASN23 4.8 16.1 1.0
CB B:ALA244 4.9 17.9 1.0
CE B:LYS191 4.9 25.6 1.0
O A:HOH559 4.9 19.1 1.0
O A:HOH643 5.0 47.4 1.0

Magnesium binding site 3 out of 3 in 5d2j

Go back to Magnesium Binding Sites List in 5d2j
Magnesium binding site 3 out of 3 in the 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 4-Oxalocrotonate Decarboxylase From Pseudomonas Putida G7 - Complexed with Magnesium and Adipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:13.5
occ:1.00
OE1 B:GLU142 2.0 14.0 1.0
OE2 B:GLU111 2.0 15.5 1.0
OE1 B:GLU109 2.0 19.7 1.0
O B:HOH433 2.0 22.6 1.0
O B:HOH450 2.1 14.8 1.0
O B:ACT305 2.2 22.1 1.0
CD B:GLU111 3.1 16.3 1.0
CD B:GLU109 3.1 19.8 1.0
CD B:GLU142 3.3 15.7 1.0
C B:ACT305 3.3 34.4 1.0
OE1 B:GLU111 3.5 12.6 1.0
OXT B:ACT305 3.6 33.6 1.0
OE2 B:GLU109 3.7 19.5 1.0
O B:MET65 3.9 18.5 1.0
NZ B:LYS64 4.0 14.3 1.0
CB B:GLU142 4.0 15.9 1.0
OE2 B:GLU142 4.1 14.8 1.0
CG B:GLU142 4.2 15.5 1.0
CE B:LYS64 4.2 15.0 1.0
CG B:GLU109 4.2 20.3 1.0
CG2 B:ILE144 4.3 14.0 1.0
N B:GLY236 4.3 14.5 1.0
CG B:GLU111 4.4 17.0 1.0
CB B:GLU109 4.5 18.5 1.0
O B:HOH474 4.6 24.8 1.0
CH3 B:ACT305 4.6 34.3 1.0
C B:GLY235 4.8 14.0 1.0
CA B:GLY235 4.8 12.6 1.0
CA B:GLY236 4.9 15.9 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 20:09:50 2020

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