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Magnesium 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:

Calcium (Ca) 8 atoms
Sodium (Na) 5 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 5x8g

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Magnesium binding site 1 out of 9 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 Magnesium with other atoms in the Mg 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:Mg502

b:19.1
occ:1.00
 O11 A:S0N501 2.1 34.0 1.0
O A:HOH881 2.2 36.5 1.0
O08 A:S0N501 2.3 25.4 1.0
O A:HOH912 2.3 34.3 1.0
O A:HOH946 2.4 37.2 1.0
O A:PHE219 2.5 30.2 1.0
P10 A:S0N501 3.4 33.6 1.0
P06 A:S0N501 3.5 25.7 1.0
C A:PHE219 3.6 23.3 1.0
O09 A:S0N501 3.8 33.1 1.0
O07 A:S0N501 4.1 24.5 1.0
O12 A:S0N501 4.2 36.5 1.0
O A:HOH749 4.2 24.6 1.0
O A:HOH898 4.4 34.8 1.0
O A:HOH926 4.5 52.8 1.0
CD2 A:PHE219 4.5 25.5 1.0
N A:SER220 4.5 24.0 1.0
CA A:PHE219 4.6 23.4 1.0
CA A:SER220 4.6 26.3 1.0
O13 A:S0N501 4.7 42.5 1.0
N A:PHE219 4.7 25.2 1.0
CB A:PHE219 4.7 25.2 1.0
O A:HOH969 4.8 45.4 1.0
O05 A:S0N501 4.8 21.2 1.0
O A:HOH985 4.8 48.7 1.0
NH2 A:ARG218 5.0 29.4 1.0

Magnesium binding site 2 out of 9 in 5x8g

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Magnesium binding site 2 out of 9 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 Magnesium with other atoms in the Mg 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:Mg503

b:28.7
occ:1.00
 CD2 A:HIS71 3.0 13.1 1.0
ND2 A:ASN7 3.0 18.1 1.0
O A:HIS71 3.1 20.8 1.0
CB A:HIS71 3.4 16.6 1.0
CA A:HIS71 3.5 17.5 1.0
CB A:PHE74 3.5 14.9 1.0
CG A:HIS71 3.5 15.4 1.0
OD1 A:ASN7 3.7 18.6 1.0
C A:HIS71 3.7 19.0 1.0
CG A:LEU75 3.7 24.7 1.0
CG A:ASN7 3.8 19.0 1.0
CD2 A:PHE74 3.8 15.2 1.0
CB A:LEU9 3.9 15.8 1.0
CD2 A:LEU75 4.0 25.5 1.0
CD2 A:LEU9 4.1 17.1 1.0
CG A:PHE74 4.1 18.4 1.0
NE2 A:HIS71 4.2 19.3 1.0
N A:LEU75 4.3 21.3 1.0
CD1 A:LEU75 4.3 21.2 1.0
CA A:PHE74 4.6 19.8 1.0
CE A:MET141 4.6 19.8 1.0
CG A:LEU9 4.6 18.3 1.0
C A:PHE74 4.7 19.8 1.0
ND1 A:HIS71 4.8 17.2 1.0
N A:HIS71 4.8 16.9 1.0
N A:LEU9 4.8 18.7 1.0
CB A:LEU75 4.9 24.2 1.0
N A:ALA72 5.0 18.0 1.0
CA A:LEU75 5.0 26.5 1.0
CE2 A:PHE74 5.0 21.1 1.0

Magnesium binding site 3 out of 9 in 5x8g

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Magnesium binding site 3 out of 9 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 Magnesium with other atoms in the Mg 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
A:Mg504

b:64.6
occ:1.00
 O A:GLU116 3.7 72.4 1.0
O A:HOH906 3.9 64.8 1.0
C A:VAL119 4.2 40.1 1.0
O A:VAL119 4.3 39.1 1.0
N A:GLN120 4.3 34.8 1.0
N A:VAL119 4.5 43.8 1.0
CA A:VAL119 4.7 39.8 1.0
CA A:GLN120 4.7 41.2 1.0
C A:GLU116 4.7 61.9 1.0
C A:ILE118 4.8 51.8 1.0
O A:HIS117 4.8 70.4 1.0
C A:HIS117 4.8 66.7 1.0
O A:ILE118 4.9 55.4 1.0

Magnesium binding site 4 out of 9 in 5x8g

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Magnesium binding site 4 out of 9 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 Magnesium with other atoms in the Mg 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
B:Mg502

b:24.9
occ:1.00
 O08 B:S0N501 2.2 24.8 1.0
O B:HOH916 2.4 65.6 1.0
O B:HOH898 2.4 37.0 1.0
O B:PHE219 2.4 31.2 1.0
O B:HOH942 2.5 44.8 1.0
O11 B:S0N501 2.7 39.0 1.0
P06 B:S0N501 3.5 32.8 1.0
P10 B:S0N501 3.6 35.4 1.0
C B:PHE219 3.6 38.5 1.0
O09 B:S0N501 3.8 35.9 1.0
O12 B:S0N501 4.0 39.5 1.0
O07 B:S0N501 4.3 33.7 1.0
O B:HOH865 4.3 43.0 1.0
CD2 B:PHE219 4.4 33.9 1.0
O B:HOH799 4.4 28.8 1.0
CA B:PHE219 4.5 26.9 1.0
N B:SER220 4.6 35.2 1.0
CB B:PHE219 4.6 28.6 1.0
CA B:SER220 4.7 38.7 1.0
O05 B:S0N501 4.7 21.7 1.0
N B:PHE219 4.7 27.5 1.0
NH2 B:ARG218 4.9 49.1 1.0
CG B:PHE219 5.0 27.5 1.0

Magnesium binding site 5 out of 9 in 5x8g

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Magnesium binding site 5 out of 9 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 Magnesium with other atoms in the Mg 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
B:Mg503

b:55.1
occ:1.00
 O B:HOH751 2.4 44.2 1.0
O B:HOH894 2.4 36.0 1.0
O B:THR28 2.7 33.4 1.0
OG1 B:THR28 3.2 50.3 1.0
O B:HOH905 3.6 54.3 1.0
C B:THR28 3.8 29.9 1.0
O B:HOH936 4.0 30.0 1.0
N B:THR28 4.1 35.4 1.0
OE1 B:GLU33 4.2 39.5 1.0
OE2 B:GLU33 4.3 27.0 1.0
CA B:THR28 4.3 32.1 1.0
CB B:THR28 4.3 35.0 1.0
O B:HOH973 4.7 52.6 1.0
CD B:GLU33 4.7 31.7 1.0
N B:VAL29 5.0 23.3 1.0

Magnesium binding site 6 out of 9 in 5x8g

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Magnesium binding site 6 out of 9 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 Magnesium with other atoms in the Mg 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
B:Mg504

b:54.3
occ:1.00
 O B:VAL119 4.3 30.1 1.0
C B:HIS117 4.4 61.2 1.0
O B:HIS117 4.4 69.9 1.0
C B:VAL119 4.4 36.1 1.0
CA B:HIS117 4.5 56.7 1.0
N B:VAL119 4.7 41.6 1.0
O B:GLU116 4.7 59.2 1.0
N B:GLN120 4.8 31.1 1.0
C B:GLU116 4.8 48.2 1.0
N B:HIS117 4.8 43.1 1.0
N B:ILE118 4.8 48.4 1.0
CA B:VAL119 4.9 33.4 1.0

Magnesium binding site 7 out of 9 in 5x8g

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Magnesium binding site 7 out of 9 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 Magnesium with other atoms in the Mg 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
D:Mg502

b:19.2
occ:1.00
 O11 D:S0N501 2.2 67.1 1.0
O D:HOH868 2.2 32.8 1.0
O D:PHE219 2.3 26.2 1.0
O08 D:S0N501 2.3 31.8 1.0
P10 D:S0N501 3.4 68.5 1.0
C D:PHE219 3.5 23.1 1.0
P06 D:S0N501 3.6 52.4 1.0
O12 D:S0N501 3.8 72.8 1.0
O09 D:S0N501 3.9 61.4 1.0
O07 D:S0N501 4.3 52.0 1.0
CA D:SER220 4.3 23.9 1.0
N D:SER220 4.3 22.0 1.0
CA D:PHE219 4.5 19.1 1.0
CD2 D:PHE219 4.6 26.5 1.0
CB D:PHE219 4.6 17.7 1.0
O D:HOH790 4.7 40.4 1.0
N D:PHE219 4.7 19.0 1.0
O13 D:S0N501 4.7 61.2 1.0
O D:HOH774 4.7 33.5 1.0
O05 D:S0N501 4.8 46.1 1.0
CB D:SER220 4.9 20.7 1.0

Magnesium binding site 8 out of 9 in 5x8g

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Magnesium binding site 8 out of 9 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 Magnesium with other atoms in the Mg 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
D:Mg503

b:45.3
occ:1.00
 O D:GLN359 2.7 45.4 1.0
NZ D:LYS320 2.8 35.9 1.0
CD1 D:TRP362 3.5 33.2 1.0
C D:GLN359 3.6 53.5 1.0
CE D:LYS320 3.7 38.4 1.0
CB D:GLN359 3.9 42.3 1.0
CE D:MET337 3.9 37.9 1.0
CG D:TRP362 3.9 26.2 1.0
CB D:TRP362 4.0 24.4 1.0
CB D:ASN360 4.1 59.4 1.0
OE2 D:GLU322 4.1 50.4 1.0
CA D:GLN359 4.3 47.3 1.0
NE1 D:TRP362 4.4 34.9 1.0
N D:ASN360 4.5 58.7 1.0
O D:ASN360 4.6 50.7 1.0
CA D:ASN360 4.7 54.4 1.0
OE1 D:GLU322 4.8 48.1 1.0
C D:ASN360 4.8 51.7 1.0
CD D:GLU322 4.8 50.3 1.0
CD2 D:TRP362 4.9 23.7 1.0
N D:TRP362 4.9 31.5 1.0

Magnesium binding site 9 out of 9 in 5x8g

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Magnesium binding site 9 out of 9 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 Magnesium with other atoms in the Mg binding site number 9 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:Mg509

b:24.6
occ:1.00
 O C:HOH861 2.2 31.9 1.0
O C:PHE219 2.3 30.4 1.0
O12 C:S0N508 2.3 65.9 1.0
O08 C:S0N508 2.4 33.6 1.0
C C:PHE219 3.5 27.1 1.0
P10 C:S0N508 3.6 62.2 1.0
P06 C:S0N508 3.7 39.0 1.0
O09 C:S0N508 4.1 49.0 1.0
O11 C:S0N508 4.2 57.2 1.0
O07 C:S0N508 4.2 35.1 1.0
CA C:SER220 4.3 25.0 1.0
N C:SER220 4.4 22.8 1.0
O C:HOH815 4.4 36.4 1.0
CD2 C:PHE219 4.5 29.5 1.0
CA C:PHE219 4.6 22.5 1.0
CB C:PHE219 4.7 24.3 1.0
N C:PHE219 4.8 22.5 1.0
O13 C:S0N508 4.9 58.6 1.0
O05 C:S0N508 5.0 36.4 1.0
CB C:SER220 5.0 23.2 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 Sep 30 09:09:20 2024

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