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Magnesium in PDB 7kpe: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site, PDB code: 7kpe was solved by S.Saran, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.88 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.2, 231.95, 199.8, 90, 90, 90
R / Rfree (%) 20 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site (pdb code 7kpe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site, PDB code: 7kpe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7kpe

Go back to Magnesium Binding Sites List in 7kpe
Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:30.0
occ:1.00
 O A:HOH441 1.7 25.1 1.0
O A:HOH468 2.1 28.9 1.0
O A:HOH485 2.3 27.6 1.0
OD2 A:ASP227 2.4 31.1 1.0
CG A:ASP227 3.3 28.5 1.0
OD1 A:ASP227 3.7 32.3 1.0
O A:HOH464 4.4 32.0 1.0
O A:HOH563 4.6 29.3 1.0
CB A:ASP227 4.7 25.4 1.0

Magnesium binding site 2 out of 7 in 7kpe

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Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:30.0
occ:1.00
 O B:HOH401 1.8 30.0 1.0
O B:HOH484 1.9 30.0 1.0
OD2 B:ASP227 2.1 28.1 1.0
CG B:ASP227 3.1 25.6 1.0
OD1 B:ASP227 3.5 27.2 1.0
O B:HOH426 3.7 28.8 1.0
O B:HOH565 4.1 32.8 1.0
CB B:ASP227 4.4 28.5 1.0
O B:HOH537 4.4 30.1 1.0

Magnesium binding site 3 out of 7 in 7kpe

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Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:30.0
occ:1.00
 NH1 C:ARG184 3.6 34.2 1.0
CE C:LYS3 3.8 33.3 1.0
CE2 C:PHE156 3.8 26.9 1.0
CZ C:ARG184 3.9 39.1 1.0
CZ C:PHE156 4.0 26.8 1.0
NE C:ARG184 4.1 35.1 1.0
CD C:ARG184 4.2 34.1 1.0
CD C:LYS3 4.4 32.0 1.0
O C:HOH541 4.5 41.1 1.0
NH2 C:ARG184 4.5 38.6 1.0
CG C:LYS3 4.6 37.4 1.0
CD2 C:PHE156 4.7 24.5 1.0
CB C:ARG184 4.9 28.7 1.0
NZ C:LYS3 5.0 24.9 1.0

Magnesium binding site 4 out of 7 in 7kpe

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Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:30.0
occ:1.00
 O C:HOH428 2.7 32.2 1.0
N C:GLY82 3.3 25.0 1.0
O B:HOH413 3.5 34.9 1.0
O C:LEU105 3.5 26.6 1.0
N C:ALA81 3.5 23.8 1.0
O C:HOH444 3.7 37.8 1.0
CA C:GLY80 3.7 31.6 1.0
N C:VAL107 3.7 22.8 1.0
C C:LEU105 3.9 24.5 1.0
C C:GLY80 3.9 27.1 1.0
CA C:GLY82 3.9 26.4 1.0
CD2 C:LEU105 4.0 21.6 1.0
CG C:LEU105 4.1 25.8 1.0
CB C:VAL107 4.2 25.6 1.0
CA C:SER106 4.2 24.5 1.0
N C:SER106 4.2 23.0 1.0
CG1 C:VAL107 4.3 22.4 1.0
CB C:LEU105 4.3 21.8 1.0
C C:ALA81 4.4 28.0 1.0
C C:SER106 4.5 24.6 1.0
O C:HOH415 4.5 31.6 1.0
CA C:ALA81 4.5 25.1 1.0
CA C:VAL107 4.6 28.1 1.0
O C:VAL45 4.6 31.2 1.0
CA C:GLY46 4.7 28.2 1.0
O C:HOH550 4.7 36.5 1.0
CA C:LEU105 4.8 25.9 1.0
C C:GLY82 4.9 24.6 1.0
CD2 C:TYR137 4.9 27.7 1.0
O C:GLY80 4.9 27.2 1.0
O C:GLY82 4.9 24.5 1.0

Magnesium binding site 5 out of 7 in 7kpe

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Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:30.0
occ:1.00
 N D:VAL107 3.2 23.7 1.0
N D:GLY82 3.4 30.0 1.0
O D:LEU105 3.5 30.0 1.0
O A:HOH467 3.7 39.7 1.0
CA D:GLY82 3.8 30.0 1.0
CB D:VAL107 3.8 29.4 1.0
CG1 D:VAL107 3.8 25.4 1.0
C D:LEU105 3.9 30.0 1.0
CA D:SER106 3.9 30.0 1.0
N D:ALA81 4.0 30.0 1.0
CD2 D:LEU105 4.0 20.0 1.0
N D:SER106 4.0 30.0 1.0
CG D:LEU105 4.0 20.0 1.0
C D:SER106 4.0 30.0 1.0
CA D:VAL107 4.1 23.9 1.0
CA D:GLY80 4.2 30.0 1.0
CD2 D:TYR137 4.4 29.5 1.0
CB D:LEU105 4.4 20.0 1.0
C D:GLY80 4.5 30.0 1.0
C D:ALA81 4.5 30.0 1.0
C D:GLY82 4.8 30.0 1.0
CA D:LEU105 4.8 30.0 1.0
CA D:ALA81 4.8 30.0 1.0
O D:GLY82 5.0 30.0 1.0

Magnesium binding site 6 out of 7 in 7kpe

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Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:30.0
occ:1.00
 O D:HOH454 2.1 32.2 1.0
OD1 D:ASP40 2.2 26.0 1.0
O D:HOH481 2.2 44.6 1.0
O D:HOH480 2.3 33.7 1.0
CG D:ASP40 3.4 28.3 1.0
O D:HOH411 4.0 38.0 1.0
CB D:ASP40 4.2 29.6 1.0
OD2 D:ASP40 4.3 29.6 1.0
CA D:ASP40 4.3 26.7 1.0
OXT D:ACT305 4.3 20.0 1.0
O D:GLY38 4.4 29.9 1.0
O D:ACT305 4.5 20.0 1.0
NE2 D:HIS223 4.5 28.4 1.0
O D:ILE39 4.7 28.7 1.0
CE1 D:HIS223 4.8 25.4 1.0
N D:ASP40 4.8 27.4 1.0
C D:ACT305 4.9 20.0 1.0
C D:ILE39 5.0 29.5 1.0

Magnesium binding site 7 out of 7 in 7kpe

Go back to Magnesium Binding Sites List in 7kpe
Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:30.0
occ:1.00
 N E:GLY82 3.0 31.0 1.0
N E:VAL107 3.1 25.7 1.0
O E:LEU105 3.3 30.4 1.0
O E:HOH434 3.3 34.0 1.0
CA E:GLY82 3.4 30.6 1.0
C E:LEU105 3.6 30.3 1.0
N E:ALA81 3.6 28.1 1.0
CA E:SER106 3.6 26.3 1.0
O E:HOH538 3.6 41.5 1.0
N E:SER106 3.7 31.6 1.0
C E:SER106 3.8 32.0 1.0
CB E:VAL107 3.9 28.6 1.0
CG1 E:VAL107 3.9 26.4 1.0
O F:HOH430 4.0 38.4 1.0
CA E:VAL107 4.1 27.7 1.0
C E:ALA81 4.1 32.2 1.0
CA E:GLY80 4.2 32.6 1.0
C E:GLY80 4.2 30.6 1.0
CG E:LEU105 4.3 29.7 1.0
CB E:LEU105 4.3 31.3 1.0
CD2 E:LEU105 4.3 27.8 1.0
O E:HOH429 4.4 38.6 1.0
CA E:ALA81 4.4 29.2 1.0
C E:GLY82 4.5 30.8 1.0
O E:HOH534 4.6 39.5 1.0
CA E:LEU105 4.6 29.4 1.0
CD2 E:TYR137 4.7 30.3 1.0
O E:GLY82 4.8 30.9 1.0
CB E:SER106 5.0 30.6 1.0

Reference:

S.Saran, M.Majdi Yazdi, I.Chung, D.A.R.Sanders. The Allosteric Site Residue, E88 Interacts with the Inhibitors to Transmit the Allosteric Inhibition Signals in Cj.Dhdps By Forming A Hydrogen Bond. To Be Published.
Page generated: Wed Oct 2 22:33:19 2024

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