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Calcium in PDB 5x8f: Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom

Enzymatic activity of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom

All present enzymatic activity of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom:
6.2.1.26;

Protein crystallography data

The structure of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom, PDB code: 5x8f 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) 29.96 / 1.76
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.870, 96.360, 98.070, 80.44, 77.96, 81.11
R / Rfree (%) 16.3 / 19.4

Other elements in 5x8f:

The structure of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 27 atoms
Sodium (Na) 33 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom (pdb code 5x8f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom, PDB code: 5x8f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5x8f

Go back to Calcium Binding Sites List in 5x8f
Calcium binding site 1 out of 3 in the Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca518

b:34.4
occ:1.00
 O A:HOH761 2.7 12.4 1.0
ND1 A:HIS169 2.8 13.4 1.0
O A:CYS292 2.9 13.5 1.0
CB A:SER201 3.5 10.7 1.0
CD1 A:ILE197 3.6 15.7 1.0
CE1 A:HIS169 3.7 13.9 1.0
CG A:HIS169 3.7 9.5 1.0
CA A:HIS169 3.8 11.7 1.0
OG A:SER172 3.8 13.4 1.0
CB A:SER172 3.8 11.9 1.0
CB A:CYS292 3.9 13.9 1.0
CB A:HIS169 3.9 10.4 1.0
CG1 A:ILE197 3.9 15.3 1.0
C A:CYS292 4.0 13.6 1.0
CA A:SER201 4.0 12.6 1.0
CD2 A:PHE204 4.0 13.1 1.0
O A:HOH775 4.1 15.9 1.0
O A:HIS169 4.4 12.7 1.0
CA A:CYS292 4.4 12.7 1.0
OG A:SER293 4.5 13.8 1.0
CE2 A:PHE204 4.5 14.2 1.0
C A:HIS169 4.6 11.5 1.0
N A:HIS169 4.8 10.5 1.0
OG A:SER201 4.8 13.7 1.0
NE2 A:HIS169 4.8 12.5 1.0
N A:SER201 4.9 13.2 1.0
CD2 A:HIS169 4.9 12.8 1.0
O A:ASN168 4.9 14.1 1.0
CB A:SER293 5.0 14.3 1.0

Calcium binding site 2 out of 3 in 5x8f

Go back to Calcium Binding Sites List in 5x8f
Calcium binding site 2 out of 3 in the Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca521

b:64.9
occ:1.00
 OE1 B:GLU25 2.6 44.5 1.0
OE2 B:GLU25 2.9 42.0 1.0
CD B:GLU25 3.0 39.6 1.0
O B:HOH1061 4.1 55.0 1.0
O B:HOH785 4.4 34.3 1.0
CG B:GLU25 4.5 27.4 1.0
OD2 B:ASP223 4.7 52.6 1.0
CA B:GLU25 4.9 20.3 1.0
O B:HOH850 4.9 32.1 1.0
CB B:GLU25 4.9 23.0 1.0
O B:HOH650 5.0 45.3 1.0
MG B:MG509 5.0 42.6 1.0

Calcium binding site 3 out of 3 in 5x8f

Go back to Calcium Binding Sites List in 5x8f
Calcium binding site 3 out of 3 in the Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Amp and Its Product Analogue Osb-Ncoa at 1.76 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca517

b:62.1
occ:1.00
 O C:HOH891 2.4 30.4 1.0
OE2 C:GLU318 2.6 26.5 1.0
O C:SER316 3.0 18.4 1.0
CD C:GLU318 3.5 21.1 1.0
CD A:PRO6 3.6 22.2 1.0
CA C:GLY340 3.7 14.8 1.0
CG C:GLU318 3.7 21.9 1.0
CG C:LYS339 3.8 24.3 1.0
NZ C:LYS339 3.8 35.8 1.0
O C:LYS339 3.9 18.1 1.0
N C:GLY340 3.9 15.5 1.0
C C:LYS339 4.0 20.0 1.0
CG A:PRO6 4.0 23.8 1.0
C C:SER316 4.1 16.2 1.0
O C:HOH987 4.3 43.5 1.0
CE C:LYS339 4.3 33.6 1.0
CB C:LYS339 4.5 17.9 1.0
CA C:CYS317 4.5 13.4 1.0
O A:GLU4 4.5 25.0 1.0
CD C:PRO341 4.5 14.1 1.0
CB C:GLU318 4.6 15.7 1.0
N C:GLU318 4.6 12.1 1.0
C C:CYS317 4.6 14.6 1.0
OE1 C:GLU318 4.7 24.4 1.0
CD C:LYS339 4.7 32.3 1.0
C C:GLY340 4.7 15.1 1.0
N C:CYS317 4.7 16.5 1.0
N A:PRO6 4.7 19.8 1.0
CE1 A:TYR140 4.8 22.2 1.0
CA C:LYS339 4.9 15.8 1.0
CA A:GLN5 4.9 13.8 1.0
O A:HOH801 4.9 29.1 1.0
N C:PRO341 5.0 13.3 1.0

Reference:

Y.Chen, T.L.Li, X.Lin, X.Li, X.D.Li, Z.Guo. Crystal Structure of the Thioesterification Conformation of Bacillus Subtilis O-Succinylbenzoyl-Coa Synthetase Reveals A Distinct Substrate-Binding Mode J. Biol. Chem. V. 292 12296 2017.
ISSN: ESSN 1083-351X
PubMed: 28559280
DOI: 10.1074/JBC.M117.790410
Page generated: Mon Jul 15 14:48:00 2024

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