Chlorine in PDB 5bus: O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp

Enzymatic activity of O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp

All present enzymatic activity of O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp:
6.2.1.26;

Protein crystallography data

The structure of O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp, PDB code: 5bus was solved by Y.Chen, Y.Sun, H.Song, Z.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.52 / 2.60
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 121.811, 121.811, 98.013, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp (pdb code 5bus). 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 Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp, PDB code: 5bus:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5bus

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Chlorine binding site 1 out of 4 in the O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with 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 Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:0.8
occ:1.00
 O B:LEU178 3.7 61.4 1.0
NH2 A:ARG19 3.7 1.0 1.0
NH1 A:ARG19 4.0 0.4 1.0
CA A:GLU184 4.1 74.6 1.0
N A:GLU184 4.2 73.5 1.0
O A:TYR209 4.2 59.4 1.0
CB A:GLU184 4.2 76.8 1.0
O B:ASN179 4.3 73.0 1.0
CZ A:ARG19 4.4 0.6 1.0
O A:THR183 4.4 83.5 1.0
C A:THR183 4.4 75.9 1.0
N B:GLY181 4.5 56.7 1.0
C B:LEU178 4.7 58.9 1.0
CA B:GLY181 4.8 55.3 1.0
C B:ASN179 4.8 68.2 1.0
C B:LEU180 5.0 56.5 1.0

Chlorine binding site 2 out of 4 in 5bus

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Chlorine binding site 2 out of 4 in the O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with 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 Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:0.4
occ:1.00
 O A:LYS345 3.8 58.1 1.0
CG A:PHE358 4.2 53.5 1.0
CD1 A:PHE358 4.2 59.0 1.0
CD2 A:PHE358 4.3 50.4 1.0
CE1 A:PHE358 4.4 59.2 1.0
CE2 A:PHE358 4.5 55.6 1.0
CZ A:PHE358 4.6 54.5 1.0
CB A:PHE358 4.7 50.5 1.0
CB A:SER346 4.8 65.6 1.0
O A:HOH636 4.8 71.3 1.0
C A:LYS345 5.0 69.2 1.0

Chlorine binding site 3 out of 4 in 5bus

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Chlorine binding site 3 out of 4 in the O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with 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 Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:0.5
occ:1.00
 OD2 B:ASP107 3.5 69.1 1.0
CG B:ASP107 3.8 72.8 1.0
NH1 B:ARG63 3.8 74.1 1.0
OD2 B:ASP125 4.0 78.8 1.0
CB B:ASP107 4.2 71.8 1.0
O B:HOH604 4.3 66.7 1.0
OD1 B:ASP107 4.4 79.9 1.0
N B:SER109 4.4 80.6 1.0
N B:SER108 4.5 96.7 1.0
CZ B:ARG63 4.6 76.9 1.0
CB B:SER108 4.6 80.7 1.0
CB B:SER109 4.7 85.4 1.0
CA B:SER108 5.0 89.5 1.0

Chlorine binding site 4 out of 4 in 5bus

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Chlorine binding site 4 out of 4 in the O-Succinylbenzoate Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with 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 Coenzyme A Synthetase (Mene) From Bacillus Subtilis, in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:0.3
occ:1.00
 NH1 B:ARG187 3.2 88.4 1.0
ND1 B:HIS231 3.3 88.7 1.0
NH2 B:ARG187 3.5 75.4 1.0
CZ B:ARG187 3.8 80.8 1.0
CE1 B:HIS231 4.1 89.3 1.0
O B:ARG230 4.2 90.0 1.0
CG B:HIS231 4.3 87.5 1.0
CA B:HIS231 4.3 80.5 1.0
CD1 B:ILE23 4.3 68.9 1.0
CB B:HIS231 4.4 81.8 1.0

Reference:

Y.Chen, Y.Sun, H.Song, Z.Guo. Structural Basis For the Atp-Dependent Configuration of Adenylation Active Site in Bacillus Subtilis O-Succinylbenzoyl-Coa Synthetase J.Biol.Chem. V. 290 23971 2015.
ISSN: ESSN 1083-351X
PubMed: 26276389
DOI: 10.1074/JBC.M115.676304
Page generated: Sat Dec 12 11:33:08 2020

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