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Magnesium in PDB 7kr7: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site, PDB code: 7kr7 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) 45.80 / 2.22
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.8, 231.24, 199.54, 90, 90, 90
R / Rfree (%) 14.9 / 18.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site (pdb code 7kr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site, PDB code: 7kr7:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7kr7

Go back to Magnesium Binding Sites List in 7kr7
Magnesium binding site 1 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:41.0
occ:1.00
 OD2 A:ASP227 1.8 51.1 1.0
CG A:ASP227 2.3 41.8 1.0
OD1 A:ASP227 2.7 40.3 1.0
O A:HOH407 3.2 13.3 1.0
CB A:ASP227 3.4 36.8 1.0
O A:HOH557 4.5 30.5 1.0
CA A:ASP227 4.7 25.1 1.0
O A:HIS223 4.8 21.6 1.0

Magnesium binding site 2 out of 3 in 7kr7

Go back to Magnesium Binding Sites List in 7kr7
Magnesium binding site 2 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:11.7
occ:1.00
 N C:GLY82 3.2 21.6 1.0
O C:HOH461 3.2 29.1 1.0
N C:VAL107 3.2 17.9 1.0
O C:LEU105 3.5 19.3 1.0
CA C:GLY82 3.6 21.7 1.0
O B:HOH409 3.7 25.8 1.0
N C:ALA81 3.7 21.6 1.0
C C:LEU105 3.8 20.0 1.0
CB C:VAL107 3.8 17.7 1.0
CA C:SER106 3.8 18.5 1.0
N C:SER106 3.9 18.3 1.0
C C:SER106 4.0 20.4 1.0
CG1 C:VAL107 4.0 13.0 1.0
CA C:GLY80 4.1 23.9 1.0
CA C:VAL107 4.1 16.9 1.0
CG C:LEU105 4.2 16.7 1.0
C C:GLY80 4.2 23.4 1.0
CD2 C:LEU105 4.3 13.8 1.0
C C:ALA81 4.3 20.4 1.0
CB C:LEU105 4.4 18.0 1.0
CD2 C:TYR137 4.4 17.6 1.0
C C:GLY82 4.6 19.7 1.0
CA C:ALA81 4.6 18.9 1.0
CA C:LEU105 4.7 20.8 1.0
O C:GLY82 4.9 17.9 1.0
O C:VAL45 4.9 26.9 1.0
CE2 C:TYR137 5.0 16.6 1.0

Magnesium binding site 3 out of 3 in 7kr7

Go back to Magnesium Binding Sites List in 7kr7
Magnesium binding site 3 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56A Mutant with Pyruvate Bound in the Active Site and L-Lysine at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:11.5
occ:1.00
 O F:HOH443 3.0 27.2 1.0
N F:GLY82 3.2 18.4 1.0
N F:VAL107 3.2 16.7 1.0
O D:HOH427 3.3 24.7 1.0
O F:LEU105 3.6 18.3 1.0
CA F:GLY82 3.6 20.8 1.0
N F:ALA81 3.8 17.5 1.0
CB F:VAL107 3.8 15.6 1.0
CA F:SER106 3.9 18.6 1.0
C F:LEU105 3.9 18.2 1.0
C F:SER106 4.0 16.9 1.0
N F:SER106 4.0 18.3 1.0
CG1 F:VAL107 4.0 13.2 1.0
CA F:VAL107 4.1 16.8 1.0
CA F:GLY80 4.1 17.6 1.0
CG F:LEU105 4.2 19.2 1.0
C F:GLY80 4.3 18.5 1.0
C F:ALA81 4.3 18.7 1.0
CD2 F:LEU105 4.3 15.5 1.0
CD2 F:TYR137 4.4 20.2 1.0
O F:HOH495 4.5 38.0 1.0
CB F:LEU105 4.5 18.4 1.0
CA F:ALA81 4.7 18.3 1.0
C F:GLY82 4.7 21.7 1.0
CA F:LEU105 4.8 17.0 1.0
O F:VAL45 4.9 23.5 1.0
CA F:GLY46 5.0 24.5 1.0
CE2 F:TYR137 5.0 20.2 1.0
O F:GLY82 5.0 21.2 1.0

Reference:

S.Saran, Y.Skovpen, M.M.Yazdi, D.R.J.Palmer, D.A.R.Sanders. Allosteric Site Residue 'H56' Caps the Inhibitor at the Tight Dimer Interface For Transmitting the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Wed Oct 2 22:33:20 2024

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