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Calcium 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
Sodium (Na) 5 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 1 out of 8 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 Calcium with other atoms in the Ca 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:Ca505

b:27.1
occ:1.00
 OG1 A:THR289 2.9 15.9 1.0
ND1 A:HIS196 3.1 21.3 1.0
O A:HOH755 3.2 30.8 1.0
O A:HOH947 3.3 17.6 1.0
N A:ILE197 3.3 18.4 1.0
O50 A:S0N501 3.5 21.4 1.0
CG2 A:ILE197 3.7 14.0 1.0
CA A:HIS196 3.8 17.0 1.0
C49 A:S0N501 3.8 16.7 1.0
CB A:THR289 3.8 15.9 1.0
CB A:HIS196 3.8 12.5 1.0
SD A:MET150 3.9 18.2 1.0
CG A:HIS196 3.9 23.3 1.0
CG2 A:THR289 4.0 15.8 1.0
C A:HIS196 4.0 14.0 1.0
CA A:THR289 4.1 13.8 1.0
CE1 A:HIS196 4.2 18.9 1.0
CB A:ILE197 4.2 16.9 1.0
CA A:ILE197 4.3 15.9 1.0
N48 A:S0N501 4.3 20.2 1.0
N A:THR289 4.4 16.9 1.0
C51 A:S0N501 4.4 17.6 1.0
C47 A:S0N501 4.5 19.5 1.0
O A:HOH725 4.6 23.1 1.0
O A:HOH916 4.7 17.2 1.0
O A:PHE195 5.0 20.2 1.0

Calcium binding site 2 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 2 out of 8 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 Calcium with other atoms in the Ca 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
A:Ca506

b:69.8
occ:1.00
 O A:PHE358 2.3 30.3 1.0
O A:GLU355 2.5 30.2 1.0
O A:HOH902 3.5 52.9 1.0
C A:PHE358 3.5 31.3 1.0
C A:GLU355 3.6 27.9 1.0
CA A:GLU355 4.0 26.8 1.0
N A:GLN359 4.4 33.7 1.0
CA A:GLN359 4.4 40.8 1.0
CA A:PHE358 4.5 26.2 1.0
O A:ASN354 4.6 24.1 1.0
N A:PHE358 4.6 23.9 1.0
N A:ALA356 4.7 31.4 1.0
CB A:PHE358 4.8 22.9 1.0
CB A:GLU355 4.8 31.1 1.0

Calcium binding site 3 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 3 out of 8 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 Calcium with other atoms in the Ca 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:Ca505

b:27.9
occ:1.00
 OG1 B:THR289 3.0 18.2 1.0
O B:HOH861 3.0 27.0 1.0
ND1 B:HIS196 3.2 21.7 1.0
O B:HOH928 3.2 15.8 1.0
N B:ILE197 3.3 13.7 1.0
O50 B:S0N501 3.4 20.1 1.0
CA B:HIS196 3.8 14.6 1.0
C49 B:S0N501 3.8 21.1 1.0
CB B:HIS196 3.9 15.0 1.0
CB B:THR289 3.9 14.8 1.0
CG2 B:ILE197 3.9 14.1 1.0
SD B:MET150 4.0 19.8 1.0
CG B:HIS196 4.0 17.5 1.0
CG2 B:THR289 4.0 15.9 1.0
C B:HIS196 4.0 12.6 1.0
CA B:THR289 4.2 18.4 1.0
CB B:ILE197 4.2 16.5 1.0
CE1 B:HIS196 4.3 22.7 1.0
N48 B:S0N501 4.3 20.8 1.0
CA B:ILE197 4.4 15.4 1.0
C51 B:S0N501 4.4 19.9 1.0
N B:THR289 4.4 18.2 1.0
C47 B:S0N501 4.5 16.6 1.0
O B:HOH895 4.6 20.5 1.0
O B:HOH831 4.7 23.6 1.0

Calcium binding site 4 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 4 out of 8 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 Calcium with other atoms in the Ca 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:Ca504

b:83.0
occ:1.00
 O D:HOH948 2.5 54.2 1.0
CD D:LYS457 4.1 63.2 1.0
CG D:LYS457 4.3 59.7 1.0
CA D:GLY483 4.5 64.9 1.0
CE D:LYS457 4.5 65.2 1.0
CE1 D:PHE459 4.6 47.5 1.0
O D:PHE458 4.8 47.4 1.0
CZ D:PHE459 4.8 46.4 1.0
CB D:LYS457 4.9 50.2 1.0
C D:GLY483 5.0 69.3 1.0
O D:GLU484 5.0 62.1 1.0

Calcium binding site 5 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 5 out of 8 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 Calcium with other atoms in the Ca 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:Ca501

b:40.8
occ:1.00
 O C:HOH664 2.8 17.8 1.0
NZ C:LYS205 2.9 14.3 1.0
CE C:LYS205 3.2 18.0 1.0
OG C:SER201 3.4 16.2 1.0
CB C:ALA202 3.4 19.1 1.0
CA C:ALA202 3.5 18.9 1.0
N C:ALA202 3.5 17.0 1.0
CZ2 C:TRP188 3.6 16.6 1.0
CE2 C:TRP188 3.6 14.2 1.0
CD C:LYS205 3.6 12.6 1.0
NE1 C:TRP188 3.9 15.9 1.0
CH2 C:TRP188 4.1 17.1 1.0
OG C:SER237 4.1 17.4 1.0
CD2 C:TRP188 4.1 11.1 1.0
O C:SER198 4.1 17.7 1.0
C C:SER201 4.2 16.8 1.0
O C:HOH700 4.3 16.2 1.0
CG C:LYS205 4.4 10.3 1.0
O62 C:S0N508 4.4 17.6 1.0
CD1 C:TRP188 4.5 15.4 1.0
CD1 C:ILE190 4.6 16.0 1.0
CZ3 C:TRP188 4.6 16.7 1.0
CB C:SER201 4.6 11.7 1.0
CE3 C:TRP188 4.6 16.7 1.0
O C:SER201 4.6 14.0 1.0
CG C:TRP188 4.7 12.6 1.0
C C:ALA202 4.9 15.5 1.0
CA C:SER201 5.0 15.5 1.0

Calcium binding site 6 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 6 out of 8 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 Calcium with other atoms in the Ca binding site number 6 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:Ca502

b:72.3
occ:1.00
 O C:HOH968 4.0 49.4 1.0
O C:HOH977 4.4 57.5 1.0

Calcium binding site 7 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 7 out of 8 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 Calcium with other atoms in the Ca binding site number 7 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:Ca503

b:55.1
occ:1.00
 OG C:SER299 2.8 53.2 1.0
OD1 C:ASN179 3.2 19.3 1.0
N C:SER299 3.2 30.7 1.0
ND2 C:ASN179 3.4 16.7 1.0
C C:LEU298 3.5 31.5 1.0
O C:THR297 3.6 31.6 1.0
CD2 C:PHE283 3.6 20.2 1.0
CA C:SER299 3.6 36.7 1.0
CG2 C:THR297 3.7 36.2 1.0
CG C:ASN179 3.7 23.1 1.0
C C:THR297 3.7 29.0 1.0
CB C:SER299 3.8 44.7 1.0
N C:LEU298 3.8 26.1 1.0
CB C:THR297 4.0 30.8 1.0
CE2 C:PHE283 4.0 28.1 1.0
CA C:LEU298 4.0 30.7 1.0
O C:LEU298 4.1 35.5 1.0
O C:HOH905 4.2 51.5 1.0
CA C:THR297 4.5 18.9 1.0
CG C:PHE283 4.8 21.5 1.0

Calcium binding site 8 out of 8 in 5x8g

Go back to Calcium Binding Sites List in 5x8g
Calcium binding site 8 out of 8 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 Calcium with other atoms in the Ca binding site number 8 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:Ca504

b:30.0
occ:1.00
 O C:HOH687 1.9 83.1 1.0
O29 C:S0N508 3.0 35.4 1.0
NZ C:LYS86 3.1 47.6 1.0
O C:HOH857 3.2 56.9 1.0
CE C:LYS86 3.4 46.0 1.0
N18 C:S0N508 3.5 32.8 1.0
C27 C:S0N508 3.6 30.4 1.0
C19 C:S0N508 3.7 35.7 1.0
C28 C:S0N508 3.8 33.3 1.0
C21 C:S0N508 3.9 34.5 1.0
N C:TYR452 3.9 34.1 1.0
N20 C:S0N508 3.9 27.0 1.0
CB C:LYS451 4.0 38.9 1.0
C17 C:S0N508 4.0 31.6 1.0
CD2 C:TYR452 4.0 33.5 1.0
CB C:TYR452 4.0 27.4 1.0
N26 C:S0N508 4.2 22.0 1.0
O C:HOH991 4.3 60.1 1.0
CD C:LYS86 4.3 44.2 1.0
CA C:TYR452 4.4 33.8 1.0
CD C:LYS451 4.5 66.6 1.0
CG C:TYR452 4.5 28.7 1.0
C C:LYS451 4.6 36.2 1.0
C22 C:S0N508 4.6 28.1 1.0
CA C:LYS451 4.8 38.5 1.0
CG C:LYS86 4.8 39.3 1.0
CG C:LYS451 4.8 55.2 1.0
C25 C:S0N508 4.9 30.0 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 14:50:10 2024

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