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Magnesium 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

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

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;

Protein crystallography data

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

Other elements in 5x8f:

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:

Calcium (Ca) 3 atoms
Sodium (Na) 33 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 27 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in 5x8f

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Magnesium binding site 1 out of 27 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 Magnesium with other atoms in the Mg 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:Mg503

b:22.5
occ:1.00
 O A:HOH877 2.2 38.2 1.0
O11 A:S0N501 2.2 27.9 1.0
O A:PHE219 2.3 28.0 1.0
O08 A:S0N501 2.3 26.5 1.0
O A:HOH850 2.3 32.7 1.0
O A:HOH964 2.4 38.2 1.0
P06 A:S0N501 3.5 25.9 1.0
C A:PHE219 3.5 24.0 1.0
P10 A:S0N501 3.5 31.2 1.0
O09 A:S0N501 3.7 25.3 1.0
O07 A:S0N501 4.1 26.4 1.0
O A:HOH883 4.2 35.7 1.0
O A:HOH771 4.3 24.0 1.0
O A:HOH991 4.3 60.9 1.0
CA A:SER220 4.3 26.2 1.0
N A:SER220 4.3 23.4 1.0
O12 A:S0N501 4.4 29.6 1.0
O13 A:S0N501 4.5 36.0 1.0
CA A:PHE219 4.5 18.5 1.0
O A:HOH1038 4.6 46.6 1.0
CD2 A:PHE219 4.6 22.4 1.0
N A:PHE219 4.7 21.7 1.0
CB A:PHE219 4.7 20.4 1.0
CB A:SER220 4.8 39.0 1.0
O05 A:S0N501 4.8 22.5 1.0

Magnesium binding site 2 out of 27 in 5x8f

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Magnesium binding site 2 out of 27 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 Magnesium with other atoms in the Mg 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:Mg504

b:39.2
occ:1.00
 OE2 A:GLU351 2.5 24.6 1.0
O B:HOH891 2.7 27.0 1.0
O B:TYR347 2.9 18.1 1.0
NA A:NA512 3.2 46.1 1.0
OG B:SER346 3.2 21.5 1.0
CD A:GLU351 3.4 26.4 1.0
O A:HOH678 3.5 33.7 1.0
NE2 B:GLN163 3.6 19.9 1.0
N B:ASN349 3.6 15.3 1.0
OE1 A:GLU351 3.6 28.9 1.0
CA B:PHE348 3.9 16.7 1.0
C B:TYR347 3.9 17.4 1.0
O A:HOH955 4.0 39.7 1.0
ND2 B:ASN354 4.0 17.5 1.0
O B:HOH917 4.0 36.6 1.0
CB B:SER346 4.2 20.5 1.0
C B:PHE348 4.2 19.3 1.0
N B:PHE348 4.3 13.7 1.0
CA B:ASN349 4.6 19.9 1.0
CD B:GLN163 4.6 22.8 1.0
CG A:GLU351 4.7 21.0 1.0
N B:ARG350 4.9 17.9 1.0

Magnesium binding site 3 out of 27 in 5x8f

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Magnesium binding site 3 out of 27 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 Magnesium with other atoms in the Mg 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:Mg505

b:43.9
occ:1.00
 O A:HIS406 2.3 47.4 1.0
O A:VAL409 2.4 43.3 1.0
O A:LEU404 2.4 37.6 1.0
O A:HOH880 2.6 52.4 1.0
C A:HIS406 3.4 46.4 1.0
C A:VAL409 3.5 36.2 1.0
C A:LEU404 3.6 38.0 1.0
O A:PRO407 3.9 50.7 1.0
N A:VAL409 3.9 39.6 1.0
C A:PRO407 4.0 46.6 1.0
N A:HIS406 4.0 38.1 1.0
CA A:PRO407 4.1 40.1 1.0
CA A:VAL409 4.1 31.4 1.0
C A:SER405 4.1 42.6 1.0
N A:PRO407 4.2 48.1 1.0
CB A:VAL409 4.3 34.5 1.0
CA A:HIS406 4.3 40.8 1.0
CA A:LEU404 4.4 35.3 1.0
O A:SER405 4.4 40.5 1.0
N A:SER405 4.5 33.6 1.0
CA A:SER405 4.5 33.3 1.0
N A:ALA410 4.6 34.4 1.0
O A:LEU403 4.8 30.7 1.0
N A:ALA408 4.8 35.3 1.0
CD2 A:HIS433 4.8 60.1 1.0
C A:ALA408 5.0 39.0 1.0
CA A:ALA410 5.0 33.2 1.0

Magnesium binding site 4 out of 27 in 5x8f

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Magnesium binding site 4 out of 27 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 Magnesium with other atoms in the Mg 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:Mg506

b:37.3
occ:1.00
 O A:HOH706 2.0 44.0 1.0
O A:HOH934 2.5 39.7 1.0
N A:GLN142 2.9 21.2 1.0
O A:HOH741 3.2 29.7 1.0
O A:HOH610 3.3 77.0 1.0
O A:HOH995 3.5 62.9 1.0
CE2 A:PHE166 3.6 19.9 1.0
CG A:GLN142 3.6 29.0 1.0
CA A:MET141 3.6 17.7 1.0
CB A:GLN142 3.7 28.7 1.0
C A:MET141 3.7 20.0 1.0
O A:TYR140 3.8 25.9 1.0
CA A:GLN142 3.8 22.7 1.0
CD2 A:PHE166 4.0 15.6 1.0
O A:HOH1098 4.1 54.2 1.0
CB A:ALA145 4.2 22.7 1.0
O A:GLN142 4.4 20.6 1.0
CZ A:PHE166 4.4 17.5 1.0
CB A:MET141 4.5 16.9 1.0
N A:MET141 4.6 18.6 1.0
C A:TYR140 4.6 24.1 1.0
C A:GLN142 4.6 17.0 1.0
O A:HOH958 4.7 40.5 1.0
CD A:GLN142 4.8 33.3 1.0
NE2 A:GLN142 4.9 32.3 1.0
O A:MET141 4.9 24.3 1.0

Magnesium binding site 5 out of 27 in 5x8f

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Magnesium binding site 5 out of 27 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 Magnesium with other atoms in the Mg 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:Mg507

b:46.1
occ:1.00
 O A:HOH971 2.4 38.5 1.0
OD1 A:ASP144 2.5 47.6 1.0
O A:HOH1071 2.9 66.8 1.0
NZ A:LYS345 3.2 35.3 1.0
CG A:ASP144 3.3 45.7 1.0
O A:HOH981 3.4 49.3 1.0
OD2 A:ASP144 3.5 54.8 1.0
CB A:LYS345 3.5 15.7 1.0
CG A:LYS345 3.6 20.6 1.0
O A:HOH624 3.7 59.1 1.0
CA A:LYS345 3.7 18.1 1.0
O A:HOH707 3.7 23.2 1.0
CG2 A:THR165 3.9 18.2 1.0
CE A:LYS345 4.0 30.4 1.0
O A:HOH824 4.1 51.0 1.0
CD A:LYS345 4.4 21.9 1.0
N A:LYS345 4.5 17.3 1.0
O A:ASP144 4.6 23.5 1.0
CB A:ASP144 4.7 30.5 1.0
O B:HOH1080 4.8 73.7 1.0
C A:LYS345 4.9 23.9 1.0
CA A:ASP144 4.9 20.5 1.0
OG1 A:THR165 5.0 16.2 1.0

Magnesium binding site 6 out of 27 in 5x8f

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Magnesium binding site 6 out of 27 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 Magnesium with other atoms in the Mg 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
A:Mg508

b:36.3
occ:1.00
 O A:HOH1000 2.1 44.9 1.0
O A:HOH1051 2.4 41.2 1.0
O A:HOH981 2.7 49.3 1.0
O A:GLY340 2.8 14.8 1.0
O A:VAL343 2.9 16.3 1.0
O A:HOH933 3.7 22.7 1.0
CA A:PRO341 3.8 10.1 1.0
O A:HOH971 3.8 38.5 1.0
C A:VAL343 3.8 15.4 1.0
N A:VAL343 3.8 13.2 1.0
O A:HOH1045 3.8 40.6 1.0
C A:GLY340 3.9 13.7 1.0
C A:PRO341 3.9 14.0 1.0
CB A:VAL343 3.9 17.8 1.0
O A:PRO341 3.9 14.6 1.0
ND2 A:ASN168 4.1 15.8 1.0
CA A:VAL343 4.1 14.8 1.0
O A:HOH833 4.2 42.8 1.0
O A:HOH789 4.3 25.7 1.0
N A:PRO341 4.3 11.2 1.0
N A:ASN342 4.5 13.5 1.0
O A:HOH1081 4.5 54.9 1.0
CG1 A:VAL343 4.7 18.9 1.0
C A:ASN342 4.8 15.1 1.0
O A:MET344 4.8 18.1 1.0
CG2 A:VAL343 4.9 16.6 1.0

Magnesium binding site 7 out of 27 in 5x8f

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Magnesium binding site 7 out of 27 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 Magnesium with other atoms in the Mg 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
A:Mg509

b:40.3
occ:1.00
 O A:HOH653 2.2 47.2 1.0
OH A:TYR395 2.7 17.8 1.0
OG A:SER153 3.0 18.7 0.6
O A:HOH906 3.1 50.4 1.0
O A:HOH884 3.6 50.6 1.0
CE1 A:TYR395 3.6 16.6 1.0
CZ A:TYR395 3.6 19.8 1.0
O A:HOH603 3.8 70.9 1.0
CB A:SER153 3.8 21.5 0.6
CA A:SER153 3.8 14.3 0.6
CA A:SER153 3.9 15.4 0.4
CB A:SER153 3.9 20.4 0.4
O1P A:AMP502 3.9 32.2 0.6
ND2 A:ASN393 4.1 22.0 1.0
NH2 A:ARG383 4.2 25.9 1.0
NH1 A:ARG383 4.3 20.6 1.0
N A:SER153 4.3 14.7 1.0
CD2 A:LEU386 4.4 19.6 1.0
OG A:SER153 4.4 24.3 0.4
O3' A:AMP502 4.5 45.3 0.6
OG1 A:THR152 4.6 22.8 1.0
CZ A:ARG383 4.6 24.3 1.0
CD1 A:LEU386 4.8 14.7 1.0
OE2 A:GLU290 4.9 17.7 1.0
CD1 A:TYR395 4.9 16.0 1.0
O5' A:AMP502 4.9 58.2 0.6
CE2 A:TYR395 4.9 17.7 1.0

Magnesium binding site 8 out of 27 in 5x8f

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Magnesium binding site 8 out of 27 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 Magnesium with other atoms in the Mg 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
A:Mg510

b:50.8
occ:1.00
 O A:HOH984 2.5 72.3 1.0
OE1 A:GLU33 2.8 26.2 1.0
O A:THR28 3.0 30.9 1.0
OG1 A:THR28 3.0 40.0 1.0
CD A:GLU33 3.5 34.6 1.0
OE2 A:GLU33 3.5 39.2 1.0
C A:THR28 3.6 32.8 1.0
CB A:THR28 4.0 38.8 1.0
CG2 A:THR30 4.0 28.0 1.0
O A:HOH923 4.2 57.7 1.0
N A:THR30 4.2 21.1 1.0
N A:VAL29 4.2 26.5 1.0
CA A:VAL29 4.3 23.3 1.0
CA A:THR28 4.4 30.1 1.0
C A:VAL29 4.6 23.4 1.0
CG A:GLU33 5.0 23.1 1.0
CD1 A:ILE20 5.0 33.6 1.0

Magnesium binding site 9 out of 27 in 5x8f

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Magnesium binding site 9 out of 27 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 Magnesium with other atoms in the Mg 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:Mg502

b:27.9
occ:1.00
 O08 B:S0N501 2.2 27.7 1.0
O B:HOH958 2.3 30.0 1.0
O B:PHE219 2.4 24.9 1.0
O B:HOH954 2.5 51.9 1.0
O B:HOH941 2.6 35.9 1.0
O11 B:S0N501 2.6 40.9 1.0
P06 B:S0N501 3.5 28.7 1.0
C B:PHE219 3.6 27.0 1.0
P10 B:S0N501 3.8 35.0 1.0
O09 B:S0N501 3.8 31.9 1.0
O07 B:S0N501 4.2 31.9 1.0
O B:HOH736 4.3 27.2 1.0
CD2 B:PHE219 4.4 29.2 1.0
O12 B:S0N501 4.4 33.5 1.0
CA B:PHE219 4.5 21.1 1.0
N B:SER220 4.5 22.5 1.0
CB B:PHE219 4.6 27.1 1.0
O B:HOH797 4.6 32.5 1.0
CA B:SER220 4.6 33.4 1.0
N B:PHE219 4.7 22.7 1.0
O B:HOH634 4.7 41.5 1.0
O05 B:S0N501 4.7 23.8 1.0
O B:HOH605 4.9 58.6 1.0
CG B:PHE219 5.0 24.0 1.0

Magnesium binding site 10 out of 27 in 5x8f

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Magnesium binding site 10 out of 27 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 Magnesium with other atoms in the Mg 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:Mg503

b:32.8
occ:1.00
 O B:HOH639 2.0 45.9 1.0
OD1 B:ASN179 3.1 21.9 1.0
N B:SER299 3.2 33.0 1.0
C B:LEU298 3.2 30.3 1.0
O B:THR297 3.3 37.1 1.0
C B:THR297 3.3 24.3 1.0
OG B:SER299 3.3 47.7 1.0
N B:LEU298 3.3 30.1 1.0
CG2 B:THR297 3.3 20.8 1.0
CD2 B:PHE283 3.4 23.7 1.0
CA B:LEU298 3.6 31.2 1.0
CA B:SER299 3.6 36.4 1.0
O B:LEU298 3.7 34.9 1.0
O B:HOH809 3.7 30.0 1.0
ND2 B:ASN179 3.7 15.4 1.0
CG B:ASN179 3.8 19.8 1.0
CB B:THR297 3.8 17.3 1.0
CE2 B:PHE283 3.9 24.0 1.0
CB B:SER299 4.0 32.3 1.0
CA B:THR297 4.2 16.8 1.0
O B:HOH758 4.3 52.1 1.0
O B:HOH959 4.3 51.6 1.0
CG B:PHE283 4.5 19.6 1.0
CB B:PHE283 4.8 18.6 1.0
CD2 B:LEU180 4.9 18.4 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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