Magnesium in PDB 7ko1: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site, PDB code: 7ko1 was solved by S.Saran, M.Majdi Yazdi, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.16, 232.65, 201.86, 90, 90, 90
R / Rfree (%) 17.9 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site (pdb code 7ko1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site, PDB code: 7ko1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7ko1

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Magnesium binding site 1 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:55.3
occ:1.00
 OD2 A:ASP227 2.0 48.8 1.0
CG A:ASP227 2.6 33.8 1.0
OD1 A:ASP227 2.7 42.9 1.0
CB A:ASP227 4.0 33.7 1.0

Magnesium binding site 2 out of 9 in 7ko1

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Magnesium binding site 2 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:51.6
occ:1.00
 O A:LYS291 3.8 38.5 1.0
O A:TYR293 4.1 37.9 1.0
C A:TYR293 4.2 35.1 1.0
N A:TYR293 4.3 42.5 1.0
C A:LYS292 4.4 41.8 1.0
N A:LYS294 4.4 32.2 1.0
CA A:TYR293 4.6 38.1 1.0
O A:LYS292 4.7 45.6 1.0
CA A:LYS292 4.7 39.7 1.0
C A:LYS291 4.8 43.4 1.0
CA A:LYS294 4.8 40.2 1.0

Magnesium binding site 3 out of 9 in 7ko1

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Magnesium binding site 3 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:48.2
occ:1.00
 O A:LYS71 3.6 39.2 1.0
O A:GLY72 4.3 36.8 1.0
CA A:GLY72 4.4 29.7 1.0
C A:GLY72 4.5 37.0 1.0
CG2 A:THR73 4.7 27.7 1.0
C A:LYS71 4.7 33.0 1.0

Magnesium binding site 4 out of 9 in 7ko1

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Magnesium binding site 4 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:40.2
occ:1.00
 O B:HOH402 2.2 38.0 1.0
OD2 B:ASP227 2.3 42.6 1.0
CG B:ASP227 2.9 41.6 1.0
OD1 B:ASP227 3.0 42.0 1.0
CB B:ASP227 4.3 37.4 1.0
O B:HOH401 4.8 47.7 1.0

Magnesium binding site 5 out of 9 in 7ko1

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Magnesium binding site 5 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:48.2
occ:1.00
 NE C:ARG142 3.4 46.6 1.0
ND2 C:ASN252 3.7 29.4 1.0
NH2 C:ARG142 3.9 34.5 1.0
CE2 C:PHE248 4.0 29.7 1.0
C1 C:KPI166 4.0 35.3 1.0
CZ C:ARG142 4.1 42.3 1.0
OH C:TYR137 4.1 32.6 1.0
CZ C:PHE248 4.2 26.9 1.0
CD C:ARG142 4.3 39.7 1.0
CG2 C:THR47 4.3 31.2 1.0
CB C:ASN252 4.4 28.1 1.0
CG C:ASN252 4.5 31.3 1.0
CB C:THR47 4.7 36.1 1.0
O2 C:KPI166 4.8 28.4 1.0

Magnesium binding site 6 out of 9 in 7ko1

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Magnesium binding site 6 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:50.1
occ:1.00
 CZ C:ARG184 3.8 39.0 1.0
NH1 C:ARG184 3.8 44.9 1.0
NE C:ARG184 4.0 36.4 1.0
CE2 C:PHE156 4.0 34.1 1.0
CE C:LYS3 4.2 41.9 1.0
NH2 C:ARG184 4.2 47.4 1.0
CD C:ARG184 4.2 34.0 1.0
CZ C:PHE156 4.3 34.6 1.0
CD2 C:PHE156 4.8 31.4 1.0
CD C:LYS3 4.9 39.7 1.0
CB C:ARG184 5.0 33.2 1.0
CG C:LYS3 5.0 40.0 1.0

Magnesium binding site 7 out of 9 in 7ko1

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Magnesium binding site 7 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active 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, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:48.6
occ:1.00
 OD2 E:ASP88 3.3 57.2 1.0
O F:LEU54 3.6 44.5 1.0
OD1 E:ASP88 3.7 53.9 1.0
O F:ALA52 3.7 39.7 1.0
CG E:ASP88 3.8 49.1 1.0
C F:LEU54 4.0 43.6 1.0
C F:THR53 4.2 36.4 1.0
CB E:ALA85 4.3 33.0 1.0
N F:THR55 4.3 43.0 1.0
CA F:THR55 4.3 48.6 1.0
N F:LEU54 4.4 39.0 1.0
O F:THR53 4.4 39.5 1.0
CA F:THR53 4.5 40.9 1.0
C F:ALA52 4.7 40.2 1.0
CG2 F:THR55 4.8 35.4 1.0
CA F:LEU54 4.8 42.3 1.0
CB E:ASP88 5.0 32.4 1.0
N F:THR53 5.0 38.6 1.0

Magnesium binding site 8 out of 9 in 7ko1

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Magnesium binding site 8 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:40.0
occ:1.00
 O F:ARG157 3.2 33.5 1.0
OE1 F:GLU160 4.0 52.3 1.0
C F:ARG157 4.1 35.3 1.0
CA F:GLU160 4.1 41.3 1.0
N F:GLU160 4.2 41.4 1.0
C F:CYS159 4.3 38.6 1.0
NZ F:LYS3 4.5 36.6 1.0
C F:ASP158 4.5 34.0 1.0
CB F:GLU160 4.5 36.3 1.0
O F:HOH460 4.5 37.5 1.0
N F:CYS159 4.6 31.0 1.0
O F:ASP158 4.6 40.2 1.0
O F:PHE156 4.6 32.4 1.0
O F:CYS159 4.6 37.0 1.0
N F:ASP158 4.8 30.4 1.0
CA F:ARG157 4.8 34.1 1.0
CA F:ASP158 4.9 33.0 1.0
CA F:CYS159 4.9 36.9 1.0
CD F:GLU160 4.9 43.4 1.0

Magnesium binding site 9 out of 9 in 7ko1

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Magnesium binding site 9 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:41.0
occ:1.00
 CD2 F:PHE248 3.0 40.9 1.0
NZ E:LYS113 3.2 39.9 1.0
N F:ASN252 3.3 34.1 1.0
NH2 F:ARG142 3.4 38.6 1.0
CE2 F:PHE248 3.4 41.1 1.0
CA F:SER251 3.7 36.1 1.0
CH3 F:ACT304 3.9 40.0 1.0
CB F:ASN252 4.0 29.7 1.0
C F:SER251 4.0 37.0 1.0
CE E:LYS113 4.2 47.2 1.0
CG F:PHE248 4.2 41.4 1.0
CA F:ASN252 4.2 35.2 1.0
CZ F:ARG142 4.3 40.6 1.0
CB F:SER251 4.3 35.4 1.0
O F:GLU250 4.4 34.8 1.0
OXT F:ACT304 4.5 49.8 1.0
C F:ACT304 4.5 54.8 1.0
CB F:PHE248 4.6 36.0 1.0
NE F:ARG142 4.6 48.0 1.0
OG F:SER251 4.7 35.8 1.0
N F:SER251 4.8 29.3 1.0
CZ F:PHE248 4.8 43.4 1.0
O F:ASN252 4.9 35.5 1.0
C F:GLU250 4.9 37.3 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 22:29:32 2024

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