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 / R_free (%)*	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

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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

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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

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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: Mon Aug 18 10:23:35 2025

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