Atomistry » Sodium » PDB 5x4b-5xuz » 5x8g
Atomistry »
  Sodium »
    PDB 5x4b-5xuz »
      5x8g »

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 Oct 8 01:10:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy