Magnesium in PDB 7kz2: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kz2 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) 46.03 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.58, 231.8, 200.62, 90, 90, 90
R / Rfree (%) 18.6 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group (pdb code 7kz2). 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, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kz2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7kz2

Go back to Magnesium Binding Sites List in 7kz2
Magnesium binding site 1 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:30.0
occ:1.00
 OD2 B:ASP227 2.0 38.6 1.0
O B:HOH500 2.1 32.0 1.0
O B:HOH542 2.3 38.5 1.0
CG B:ASP227 2.8 36.5 1.0
OD1 B:ASP227 3.1 39.1 1.0
O B:HOH444 4.1 29.6 1.0
O B:HOH574 4.2 35.5 1.0
CB B:ASP227 4.2 34.2 1.0
O B:HOH528 4.4 27.8 1.0

Magnesium binding site 2 out of 3 in 7kz2

Go back to Magnesium Binding Sites List in 7kz2
Magnesium binding site 2 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:30.0
occ:1.00
 O B:HOH410 2.1 30.0 1.0
O B:HOH439 2.1 39.5 1.0
O B:HOH438 2.4 28.6 1.0
O B:HOH435 4.1 26.0 1.0
OD1 B:ASP102 4.3 32.5 1.0
O B:THR73 4.4 34.6 1.0
OD2 B:ASP102 4.4 29.6 1.0
O B:VAL75 4.4 26.7 1.0
O B:CYS70 4.5 28.6 1.0
CG B:ASP102 4.8 29.9 1.0
O B:HOH419 5.0 27.0 1.0

Magnesium binding site 3 out of 3 in 7kz2

Go back to Magnesium Binding Sites List in 7kz2
Magnesium binding site 3 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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, Y110F Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg309

b:30.0
occ:1.00
 N C:VAL107 3.2 26.4 1.0
N C:GLY82 3.3 29.5 1.0
O B:HOH454 3.3 37.6 1.0
O C:LEU105 3.5 24.5 1.0
CB C:VAL107 3.7 25.8 1.0
CA C:GLY82 3.8 29.2 1.0
N C:ALA81 3.8 27.5 1.0
CG1 C:VAL107 3.8 22.9 1.0
C C:LEU105 3.9 25.9 1.0
CA C:SER106 4.0 22.2 1.0
N C:SER106 4.0 24.2 1.0
CA C:VAL107 4.0 24.9 1.0
C C:SER106 4.0 23.4 1.0
CA C:GLY80 4.1 30.5 1.0
CD2 C:LEU105 4.1 24.0 1.0
CG C:LEU105 4.2 24.5 1.0
C C:GLY80 4.3 29.3 1.0
CD2 C:TYR137 4.3 30.0 1.0
C C:ALA81 4.4 26.8 1.0
CB C:LEU105 4.4 22.1 1.0
CA C:ALA81 4.7 26.0 1.0
C C:GLY82 4.7 26.0 1.0
CA C:LEU105 4.8 24.6 1.0
CE2 C:TYR137 4.9 31.8 1.0
O C:GLY82 4.9 23.9 1.0
O C:VAL45 5.0 36.9 1.0
CG2 C:VAL107 5.0 25.2 1.0

Reference:

S.Saran, D.A.R.Sanders. B-Factor Analysis Suggest That L-Lysine and R, R-Bislysine Allosterically Inhibit Cj.Dhdps Enzyme By Decreasing Protein Dynamics. To Be Published.
Page generated: Wed Oct 2 23:01:25 2024

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