Sodium 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

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;

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

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
Calcium	(Ca)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 33 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 33 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 Sodium with other atoms in the Na 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:Na511 b:52.3 occ:1.00 O A:HOH890 2.6 37.9 1.0 O A:HOH641 2.7 35.6 1.0 O A:ALA412 2.8 29.9 1.0 O A:HOH926 3.0 41.2 1.0 OE1 A:GLU400 3.8 27.6 1.0 C A:ALA412 4.0 28.5 1.0 CD1 A:LEU404 4.1 47.2 1.0 CD2 A:LEU472 4.2 33.2 1.0 CD A:GLU400 4.2 28.8 1.0 CB A:GLU400 4.4 24.9 1.0 N A:ALA412 4.5 29.2 1.0 CG A:GLU400 4.5 26.4 1.0 O A:HOH871 4.6 42.8 1.0 CA A:ALA412 4.7 28.1 1.0 OE2 A:GLU400 4.9 29.5 1.0 CB A:LEU472 4.9 40.0 1.0 NH2 A:ARG466 4.9 36.0 1.0 CG A:LEU404 5.0 40.3 1.0

Sodium binding site 2 out of 33 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 Sodium with other atoms in the Na 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 A:Na512 b:46.1 occ:1.00 OD1 B:ASN349 2.4 34.1 1.0 OE2 A:GLU351 2.5 24.6 1.0 O A:HOH845 3.0 27.6 1.0 MG A:MG504 3.2 39.2 1.0 N B:ASN349 3.3 15.3 1.0 CB A:GLU351 3.5 19.4 1.0 CA B:ASN349 3.6 19.9 1.0 CG B:ASN349 3.6 30.5 1.0 CD A:GLU351 3.6 26.4 1.0 O A:HOH829 3.8 22.9 1.0 O B:HOH891 3.8 27.0 1.0 CA A:GLU351 3.8 17.0 1.0 O A:HOH955 3.9 39.7 1.0 N A:GLU351 4.0 19.0 1.0 CG A:GLU351 4.1 21.0 1.0 CB B:ASN349 4.2 19.9 1.0 CD1 B:PHE348 4.5 17.3 1.0 C B:PHE348 4.5 19.3 1.0 CE1 B:PHE348 4.5 19.8 1.0 O A:HOH625 4.6 45.2 1.0 CA A:ASN349 4.6 22.3 0.5 OE1 A:GLU351 4.7 28.9 1.0 ND2 B:ASN349 4.7 24.2 1.0 CA A:ASN349 4.7 22.5 0.5 O A:HOH834 4.7 36.7 1.0 N A:ARG350 4.7 16.6 1.0 OD1 A:ASN349 4.8 19.3 0.5 CA B:PHE348 4.9 16.7 1.0 C B:ASN349 4.9 19.6 1.0 C A:ARG350 4.9 17.5 1.0

Sodium binding site 3 out of 33 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 Sodium with other atoms in the Na 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 A:Na513 b:46.7 occ:1.00 O A:HOH665 2.8 27.1 1.0 O A:HOH962 2.9 83.3 1.0 CG A:GLN61 2.9 34.0 1.0 O A:HOH622 3.1 52.5 1.0 OG A:SER109 3.1 37.6 1.0 CB A:GLN61 3.6 21.2 1.0 CB A:SER109 3.7 25.1 1.0 CD A:GLN61 4.2 54.3 1.0 OD2 A:ASP107 4.5 26.8 1.0 CE2 A:PHE110 4.5 17.3 1.0 NE2 A:GLN61 4.6 53.2 1.0 N A:GLN61 4.6 20.3 1.0 OD1 A:ASP107 4.7 24.1 1.0 CA A:GLN61 4.7 21.7 1.0 CZ A:PHE110 4.8 19.5 1.0 OE1 A:GLN217 4.8 41.6 1.0 NE2 A:GLN217 4.9 37.2 1.0

Sodium binding site 4 out of 33 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 Sodium with other atoms in the Na binding site number 4 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:Na514 b:48.9 occ:1.00 O A:PHE358 2.5 29.6 1.0 O A:GLU355 2.7 27.9 1.0 O A:HOH838 3.0 64.2 1.0 O A:HOH794 3.1 47.0 1.0 O A:HOH858 3.3 49.4 1.0 C A:GLU355 3.7 22.0 1.0 C A:PHE358 3.7 30.2 1.0 CA A:GLU355 4.0 22.2 1.0 O A:HOH915 4.0 55.8 1.0 CA A:GLN359 4.5 31.4 1.0 O A:ASN354 4.5 22.0 1.0 N A:GLN359 4.5 28.6 1.0 CB A:GLU355 4.6 24.8 1.0 CA A:PHE358 4.7 23.4 1.0 CB A:PHE358 4.8 22.9 1.0 N A:ALA356 4.9 23.5 1.0 N A:PHE358 4.9 22.4 1.0

Sodium binding site 5 out of 33 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 Sodium with other atoms in the Na binding site number 5 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:Na515 b:60.9 occ:1.00 O A:HOH1090 3.0 42.6 1.0 O C:HOH988 3.1 32.8 1.0 OE1 A:GLN14 3.2 40.8 1.0 O1 A:PEG516 3.5 50.2 1.0 CE A:MET10 3.6 39.1 1.0 SD A:MET10 3.8 34.4 1.0 O A:HOH1022 4.1 50.3 1.0 O C:HOH868 4.1 37.1 1.0 O A:HOH965 4.2 36.2 1.0 CD A:GLN14 4.2 31.8 1.0 C1 A:PEG516 4.3 44.7 1.0 NE2 A:GLN14 4.5 27.8 1.0 O A:HOH779 4.6 20.2 1.0 O A:HOH1078 4.6 54.8 1.0 CG A:MET10 4.8 23.0 1.0

Sodium binding site 6 out of 33 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 Sodium with other atoms in the Na binding site number 6 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:Na510 b:33.3 occ:1.00 O B:VAL343 2.7 15.5 1.0 O B:GLY340 2.8 14.2 1.0 O B:HOH976 2.8 43.7 1.0 O1 B:PEG520 3.3 38.2 1.0 C B:VAL343 3.6 17.1 1.0 N B:VAL343 3.7 13.2 1.0 CB B:VAL343 3.8 14.9 1.0 O B:HOH864 3.8 25.3 1.0 C B:GLY340 3.9 13.0 1.0 CA B:PRO341 3.9 12.2 1.0 CA B:VAL343 3.9 14.4 1.0 O B:HOH812 3.9 41.3 1.0 C B:PRO341 3.9 13.0 1.0 O B:HOH1014 3.9 43.5 1.0 ND2 B:ASN168 4.0 15.0 1.0 O B:PRO341 4.1 13.3 1.0 O B:HOH957 4.2 45.0 1.0 N B:PRO341 4.3 14.1 1.0 N B:ASN342 4.5 13.7 1.0 O B:HOH719 4.5 23.5 1.0 C1 B:PEG520 4.6 40.2 1.0 O B:MET344 4.6 17.1 1.0 CG1 B:VAL343 4.6 15.4 1.0 C B:ASN342 4.7 17.5 1.0 C3 B:PEG520 4.8 65.0 1.0 N B:MET344 4.8 13.8 1.0 CG2 B:VAL343 4.9 16.0 1.0

Sodium binding site 7 out of 33 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 Sodium with other atoms in the Na binding site number 7 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:Na511 b:64.4 occ:1.00 O B:HOH922 2.5 53.7 1.0 O B:HOH906 2.9 59.9 1.0 O B:HOH890 3.2 43.4 1.0 O B:THR365 3.2 22.9 1.0 O B:HOH993 3.3 69.6 1.0 OE2 B:GLU290 3.3 19.0 1.0 OG B:SER153 3.4 19.7 0.6 O B:HOH646 3.5 31.0 1.0 CD B:GLU290 3.9 16.0 1.0 OH B:TYR347 4.0 17.4 1.0 C B:THR365 4.1 20.7 1.0 OE1 B:GLU290 4.2 15.6 1.0 OG B:SER153 4.2 24.0 0.5 CB B:SER153 4.4 24.1 0.6 O B:HOH819 4.4 41.4 1.0 CB B:SER153 4.5 22.9 0.5 CA B:THR365 4.5 18.8 1.0 O B:HOH756 4.5 18.9 1.0 NH1 B:ARG383 4.6 26.7 1.0 CG B:GLU290 4.9 15.5 1.0 O B:LYS364 4.9 26.9 1.0 SD B:MET288 4.9 25.2 1.0 NH2 B:ARG383 5.0 32.0 1.0

Sodium binding site 8 out of 33 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 Sodium with other atoms in the Na binding site number 8 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:Na512 b:38.5 occ:1.00 O B:HOH878 2.5 27.0 1.0 N B:SER352 2.8 20.7 1.0 O B:HOH1023 2.9 58.2 1.0 CB B:SER352 3.2 37.0 1.0 N B:GLU351 3.3 21.2 1.0 CA B:SER352 3.6 24.2 1.0 O B:HOH926 3.7 36.8 1.0 C B:ARG350 3.8 22.3 1.0 C B:GLU351 3.9 24.0 1.0 CA B:GLU351 4.0 25.8 1.0 CA B:ARG350 4.1 14.5 1.0 CB B:GLU351 4.2 25.1 1.0 O B:HOH999 4.3 53.1 1.0 OG B:SER352 4.4 58.4 1.0 O B:ARG350 4.4 21.1 1.0 N B:ALA353 4.5 22.6 1.0 C B:SER352 4.6 21.2 1.0

Sodium binding site 9 out of 33 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 Sodium with other atoms in the Na binding site number 9 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:Na513 b:58.4 occ:1.00 O B:HOH613 2.5 41.7 1.0 O B:LEU76 2.9 20.6 1.0 O B:HOH786 3.1 34.2 1.0 OE2 B:GLU138 3.2 46.5 1.0 C B:LEU76 3.6 22.5 1.0 CB B:LYS52 3.6 25.1 1.0 CA B:LEU76 3.9 14.4 1.0 CG B:GLU138 4.1 22.7 1.0 CD B:GLU138 4.1 35.2 1.0 N B:LYS52 4.2 21.4 1.0 CD2 B:LEU76 4.2 21.4 1.0 CA B:LYS52 4.3 22.3 1.0 CG B:LYS52 4.4 25.1 1.0 CB B:LEU76 4.5 16.9 1.0 O B:GLU136 4.5 28.1 1.0 O B:LEU75 4.6 18.8 1.0 CD B:LYS52 4.6 28.0 1.0 N B:GLY77 4.7 17.6 1.0

Sodium binding site 10 out of 33 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 Sodium with other atoms in the Na binding site number 10 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:Na514 b:70.2 occ:1.00 CD B:ARG40 2.8 47.9 1.0 O B:HOH710 3.1 40.8 1.0 O B:HOH1094 3.1 72.2 1.0 CG B:ARG40 3.9 29.5 1.0 NE2 B:GLN44 4.3 30.1 1.0 O B:MET128 4.4 36.5 1.0 O B:HOH1036 4.6 55.0 1.0 O B:GLU130 4.8 33.9 1.0

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