Sodium in PDB 7kkg: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kkg 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) 45.88 / 1.64
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.67, 225.73, 200.88, 90, 90, 90
R / Rfree (%) 13.8 / 16.9

Other elements in 7kkg:

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site also contains other interesting chemical elements:

Magnesium (Mg) 21 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7kkg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kkg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7kkg

Go back to Sodium Binding Sites List in 7kkg
Sodium binding site 1 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:29.2
occ:1.00
 O A:HOH684 2.7 17.6 1.0
O A:HOH457 3.2 14.0 1.0
C2 A:EDO306 4.1 14.7 1.0
CB A:GLU160 4.1 18.1 1.0
O2 A:EDO306 4.3 14.3 1.0
O A:HOH481 4.4 20.3 1.0
O A:HOH760 4.5 24.4 1.0
O A:HOH584 4.5 16.6 1.0
O A:HOH609 4.6 17.6 1.0
C1 A:EDO306 4.9 14.8 1.0
CG A:GLU160 4.9 15.2 1.0
O A:HOH798 4.9 32.5 1.0

Sodium binding site 2 out of 3 in 7kkg

Go back to Sodium Binding Sites List in 7kkg
Sodium binding site 2 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na309

b:25.6
occ:1.00
 O C:HOH710 2.5 30.3 1.0
O C:HOH644 3.0 30.7 1.0
N C:GLU57 3.0 11.9 1.0
O C:HOH604 3.1 14.4 1.0
CB C:GLU57 3.5 15.4 1.0
N C:HIS56 3.5 10.5 1.0
CB C:THR55 3.5 11.3 1.0
OG1 C:THR55 3.7 11.6 1.0
CA C:GLU57 3.8 11.9 1.0
C C:HIS56 3.9 10.8 1.0
CB C:HIS56 3.9 10.1 1.0
CA C:HIS56 3.9 9.9 1.0
O F:HOH710 4.0 42.0 1.0
C C:THR55 4.2 10.3 1.0
CA C:THR55 4.4 11.4 1.0
OE1 C:GLU57 4.4 54.0 1.0
O C:HOH468 4.5 17.6 1.0
CG2 C:THR55 4.6 12.0 1.0
O C:HOH674 4.6 27.6 1.0
O C:HOH755 4.6 23.8 1.0
CG C:GLU57 4.8 30.4 1.0

Sodium binding site 3 out of 3 in 7kkg

Go back to Sodium Binding Sites List in 7kkg
Sodium binding site 3 out of 3 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na310

b:26.3
occ:1.00
 O B:HOH426 2.6 13.6 1.0
OE1 C:GLU191 2.8 12.5 1.0
O B:HOH626 3.1 12.8 1.0
CD C:GLU191 3.4 18.2 1.0
CA C:GLY170 3.4 13.7 1.0
CD1 C:ILE194 3.6 8.8 1.0
O B:HOH731 3.9 30.0 1.0
OE2 C:GLU191 3.9 21.4 1.0
CG1 C:ILE194 3.9 8.7 1.0
CG2 C:ILE194 3.9 6.7 1.0
CB B:ASP173 4.0 9.6 1.0
N C:GLY170 4.1 10.0 1.0
CB C:GLU191 4.2 10.0 1.0
CG C:GLU191 4.3 12.0 1.0
OD2 B:ASP173 4.4 11.8 1.0
O C:HOH426 4.5 24.3 1.0
C C:GLY170 4.6 18.9 1.0
CB C:ILE194 4.6 6.3 1.0
CG B:ASP173 4.7 7.6 1.0
O C:HOH562 4.8 35.3 1.0
N B:ASP173 4.9 10.0 1.0
CA B:ASP173 4.9 9.7 1.0

Reference:

S.Saran, M.Majdi Yazd, D.R.J.Palmer, D.A.R.Sanders. A Tight Dimer Interface N84 Residue, Plays A Critical Role in the Transmission of the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Fri Nov 5 16:04:25 2021

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