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Magnesium in PDB 5gtd: O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp

Enzymatic activity of O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp

All present enzymatic activity of O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp:
6.2.1.26;

Protein crystallography data

The structure of O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp, PDB code: 5gtd was solved by Y.Chen, Z.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.96 / 2.69
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 121.814, 121.814, 98.563, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.7

Other elements in 5gtd:

The structure of O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp (pdb code 5gtd). 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 O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp, PDB code: 5gtd:

Magnesium binding site 1 out of 1 in 5gtd

Go back to Magnesium Binding Sites List in 5gtd
Magnesium binding site 1 out of 1 in the O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:78.0
occ:1.00
 OE1 B:GLN11 2.9 61.2 1.0
O B:PRO6 2.9 62.7 1.0
CE2 A:PHE315 3.3 62.8 1.0
CA A:SER316 3.5 55.5 1.0
CD1 B:TRP8 3.6 51.8 1.0
N A:SER316 3.6 51.4 1.0
CD2 A:PHE315 3.7 63.8 1.0
CG B:PRO6 3.7 54.7 1.0
CB B:GLN5 3.7 53.9 1.0
CD B:PRO6 3.8 53.4 1.0
CZ A:PHE315 3.9 60.8 1.0
C B:PRO6 3.9 62.0 1.0
N B:PRO6 4.0 56.0 1.0
CD B:GLN11 4.1 54.1 1.0
OG A:SER316 4.1 58.3 1.0
OE1 B:GLN5 4.1 65.8 1.0
NE1 B:TRP8 4.2 53.7 1.0
CB A:SER316 4.3 54.6 1.0
CA B:PRO6 4.4 62.1 1.0
C B:GLN5 4.4 60.4 1.0
CB B:PRO6 4.5 58.8 1.0
CG A:PHE315 4.5 62.6 1.0
CA B:TRP8 4.5 61.3 1.0
CD B:GLN5 4.6 58.1 1.0
CA B:GLN5 4.6 57.3 1.0
CG B:GLN5 4.6 53.8 1.0
N B:TRP8 4.6 62.3 1.0
CE1 A:PHE315 4.7 62.8 1.0
C A:SER316 4.7 56.9 1.0
CG B:TRP8 4.7 55.5 1.0
CB B:GLN11 4.7 51.4 1.0
C A:PHE315 4.8 53.5 1.0
C B:ASN7 4.8 60.2 1.0
CG B:GLN11 4.9 48.8 1.0
CD1 A:PHE315 4.9 63.7 1.0
O B:ASN7 5.0 60.5 1.0

Reference:

Y.Chen, Y.Jiang, Z.Guo. Mechanistic Insights From the Crystal Structure of Bacillus Subtilis O-Succinylbenzoyl-Coa Synthetase Complexed with the Adenylate Intermediate Biochemistry V. 55 6685 2016.
ISSN: ISSN 1520-4995
PubMed: 27933791
DOI: 10.1021/ACS.BIOCHEM.6B00889
Page generated: Sun Sep 29 15:25:25 2024

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