Atomistry » Magnesium » PDB 7koc-7kum » 7kpe
Atomistry »
  Magnesium »
    PDB 7koc-7kum »
      7kpe »

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

Go back to Magnesium Binding Sites List in 7kpe
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

Go back to Magnesium Binding Sites List in 7kpe
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

Go back to Magnesium Binding Sites List in 7kpe
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

Go back to Magnesium Binding Sites List in 7kpe
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

Go back to Magnesium Binding Sites List in 7kpe
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

Last articles

Ni in 5F5A
Ni in 5F5C
Ni in 5FF5
Ni in 5FG6
Ni in 5DOU
Ni in 5CK0
Ni in 5D7Z
Ni in 5DOT
Ni in 5DQV
Ni in 5DQW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy