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Sodium in PDB 5x8g: Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom

Enzymatic activity of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom

All present enzymatic activity of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom:
6.2.1.26;

Protein crystallography data

The structure of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom, PDB code: 5x8g 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) 31.03 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.950, 96.480, 97.660, 80.14, 77.81, 81.17
R / Rfree (%) 16.4 / 20.6

Other elements in 5x8g:

The structure of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms
Calcium (Ca) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom (pdb code 5x8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom, PDB code: 5x8g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5x8g

Go back to Sodium Binding Sites List in 5x8g
Sodium binding site 1 out of 5 in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:48.9
occ:1.00
 O A:HOH751 2.9 23.6 1.0
O A:HOH839 3.1 40.4 1.0
O A:HOH1011 3.7 56.5 1.0
CG A:PRO330 3.8 34.5 1.0
CD A:PRO330 3.9 33.1 1.0
O A:CYS328 4.0 26.5 1.0
N A:PRO330 4.0 29.7 1.0
O A:HOH830 4.1 25.1 1.0
CD1 A:LEU371 4.3 26.6 1.0
CA A:PRO330 4.3 32.3 1.0
C A:GLU329 4.3 27.4 1.0
CB A:LEU371 4.5 27.1 1.0
CB A:PRO330 4.5 37.2 1.0
CA A:GLU329 4.8 31.5 1.0
O A:GLU329 4.8 26.7 1.0

Sodium binding site 2 out of 5 in 5x8g

Go back to Sodium Binding Sites List in 5x8g
Sodium binding site 2 out of 5 in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:51.7
occ:1.00
 OE1 B:GLU4 2.7 36.3 1.0
O B:HOH992 2.8 64.9 1.0
CD B:GLU4 3.6 28.8 1.0
O B:HOH764 3.7 50.1 1.0
OE2 B:GLU4 3.7 29.7 1.0
CD2 B:TYR140 3.7 22.1 1.0
NE2 B:GLN142 3.7 38.2 1.0
CG B:TYR140 4.1 20.2 1.0
CB B:TYR140 4.2 21.9 1.0
O B:HOH1021 4.2 57.5 1.0
O B:HOH749 4.3 26.1 1.0
CE2 B:TYR140 4.4 28.9 1.0
CD B:GLN142 4.9 33.4 1.0
CG B:GLU4 5.0 23.6 1.0

Sodium binding site 3 out of 5 in 5x8g

Go back to Sodium Binding Sites List in 5x8g
Sodium binding site 3 out of 5 in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:55.3
occ:1.00
 O D:HOH744 3.6 39.7 1.0
OH B:TYR140 4.0 28.9 1.0
O B:HOH906 4.1 50.7 1.0
O B:HOH1017 4.2 52.2 1.0
OE1 D:GLU318 4.5 23.5 1.0
O D:HOH908 4.5 30.1 1.0
O B:HOH673 4.6 43.2 1.0
CZ B:TYR140 4.8 26.0 1.0
CZ2 D:TRP362 4.9 31.0 1.0
CE2 B:TYR140 5.0 28.9 1.0

Sodium binding site 4 out of 5 in 5x8g

Go back to Sodium Binding Sites List in 5x8g
Sodium binding site 4 out of 5 in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na505

b:58.2
occ:1.00
 O D:PHE358 2.6 41.8 1.0
O D:GLU355 2.7 40.5 1.0
C D:PHE358 3.8 42.8 1.0
C D:GLU355 4.0 41.9 1.0
CA D:GLN359 4.1 47.3 1.0
CB D:GLN359 4.1 42.3 1.0
N D:GLN359 4.4 47.0 1.0
O D:ALA356 4.8 33.0 1.0
CA D:ALA356 4.8 40.9 1.0
C D:ALA356 4.8 36.1 1.0
N D:ALA356 4.9 40.1 1.0
CA D:GLU355 4.9 42.4 1.0
N D:PHE358 4.9 38.7 1.0
CA D:PHE358 5.0 31.6 1.0

Sodium binding site 5 out of 5 in 5x8g

Go back to Sodium Binding Sites List in 5x8g
Sodium binding site 5 out of 5 in the Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Binary Complex Structure of A Double Mutant I454RA456K of O- Succinylbenzoate Coa Synthetase (Mene) From Bacillus Subtilis Bound with Its Product Analogue Osb-Ncoa at 1.90 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na505

b:52.9
occ:1.00
 O C:HOH974 2.9 58.4 1.0
O C:ASN179 3.4 16.2 1.0
O C:HOH827 3.5 66.7 1.0
CE2 C:PHE283 3.6 28.1 1.0
CZ C:PHE283 3.9 27.2 1.0
O C:HOH948 4.1 36.5 1.0
OG C:SER299 4.2 53.2 1.0
CA C:LEU180 4.3 17.4 1.0
C C:ASN179 4.4 18.3 1.0
O C:LEU180 4.6 18.6 1.0
CD2 C:LEU180 4.6 16.4 1.0
O C:HOH905 4.7 51.5 1.0
C C:LEU180 4.7 22.4 1.0
CD2 C:PHE283 4.8 20.2 1.0
N C:LEU180 4.9 17.9 1.0
O C:HOH929 4.9 51.1 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: Tue Dec 15 11:49:19 2020

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