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Chlorine 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:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the O-Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis in Complex with the Acyl-Adenylate Intermediate Osb-Amp, PDB code: 5gtd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5gtd

Go back to Chlorine Binding Sites List in 5gtd
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl501

b:1.0
occ:1.00
 O B:LEU178 3.7 79.2 1.0
NH1 A:ARG19 3.7 91.5 1.0
O A:TYR209 3.8 64.6 1.0
NH2 A:ARG19 3.9 91.6 1.0
CZ A:ARG19 4.3 91.5 1.0
CA A:GLU184 4.5 95.9 1.0
O B:ASN179 4.6 90.5 1.0
O A:THR183 4.7 87.1 1.0
C B:LEU178 4.7 74.5 1.0
CB A:GLU184 4.8 98.9 1.0
CG2 A:ILE182 4.9 83.8 1.0
N A:GLU184 4.9 91.9 1.0
C A:THR183 5.0 87.2 1.0
C B:ASN179 5.0 80.9 1.0

Chlorine binding site 2 out of 4 in 5gtd

Go back to Chlorine Binding Sites List in 5gtd
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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
A:Cl502

b:0.8
occ:1.00
 ND1 A:HIS90 4.2 90.4 1.0
CE1 A:HIS90 4.2 92.1 1.0
CG A:PHE94 4.3 63.8 1.0
CB A:PHE94 4.4 64.2 1.0
CD2 A:PHE94 4.6 68.1 1.0
CD1 A:PHE94 4.7 61.5 1.0
CG A:GLU91 4.7 62.3 1.0
CA A:GLU91 4.9 69.7 1.0

Chlorine binding site 3 out of 4 in 5gtd

Go back to Chlorine Binding Sites List in 5gtd
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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
A:Cl503

b:30.0
occ:1.00
 ND2 A:ASN393 4.5 0.0 1.0
CD A:ARG323 4.5 86.5 1.0
CG A:ARG323 4.8 82.2 1.0
CD1 A:LEU368 4.9 62.8 1.0
CD2 A:LEU386 4.9 80.9 1.0
CD2 A:LEU368 4.9 58.8 1.0
O A:HIS333 5.0 80.7 1.0

Chlorine binding site 4 out of 4 in 5gtd

Go back to Chlorine Binding Sites List in 5gtd
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl501

b:96.1
occ:1.00
 OG B:SER172 2.7 59.8 1.0
O B:GLN294 2.9 71.8 1.0
O B:THR291 2.9 64.2 1.0
O B:CYS292 3.1 70.5 1.0
CB B:SER172 3.2 52.6 1.0
ND2 B:ASN342 3.3 61.9 1.0
C B:CYS292 3.5 69.1 1.0
C B:SER293 3.5 73.0 1.0
CB B:SER293 3.6 76.5 1.0
O B:SER293 3.7 69.6 1.0
CA B:SER172 3.7 58.3 1.0
N B:GLN294 3.8 75.2 1.0
CA B:SER293 3.8 73.4 1.0
N B:SER293 3.8 72.5 1.0
C B:GLN294 3.9 71.8 1.0
CB B:ASN342 4.0 59.4 1.0
C B:THR291 4.1 70.7 1.0
CG B:ASN342 4.1 62.7 1.0
OG B:SER293 4.2 89.5 1.0
CA B:GLN294 4.4 73.5 1.0
CA B:CYS292 4.4 65.1 1.0
CB B:CYS292 4.4 57.7 1.0
C B:SER172 4.6 59.5 1.0
O B:SER172 4.6 60.4 1.0
CG B:GLN294 4.6 83.7 1.0
N B:CYS292 4.7 71.2 1.0
N B:SER172 4.9 58.6 1.0
N B:ILE295 4.9 71.9 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: Fri Jul 26 08:32:08 2024

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