Potassium in PDB 7jza: Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

Enzymatic activity of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

All present enzymatic activity of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site, PDB code: 7jza was solved by A.J.Board, R.C.J.Dobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	33.36 / 1.82
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	121.299, 121.299, 109.781, 90, 90, 120
*R / R_free (%)*	13.6 / 16.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site (pdb code 7jza). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site, PDB code: 7jza:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 7jza

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Potassium Binding Sites List in 7jza

Potassium binding site 1 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

Mono view

Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K301 b:23.3 occ:1.00	O	A:HOH634	2.6	32.1	1.0
	O	A:ILE157	2.7	17.1	1.0
	O	A:ALA152	2.7	19.4	1.0
	O	A:VAL154	2.7	20.7	1.0
	O	A:HOH651	2.9	47.2	1.0
	O	A:LYS155	3.1	21.2	1.0
	C	A:LYS155	3.7	22.0	1.0
	C	A:ILE157	3.7	16.7	1.0
	C	A:VAL154	3.8	18.4	1.0
	C	A:ALA152	3.8	18.7	1.0
	CA	A:LYS155	4.0	25.7	1.0
	N	A:ILE157	4.1	14.8	1.0
	O	A:HOH624	4.2	46.8	1.0
	N	A:LYS155	4.4	22.3	1.0
	CA	A:ILE157	4.4	15.1	1.0
	CA	A:ALA152	4.4	17.1	1.0
	N	A:ASN156	4.6	18.5	1.0
	N	A:VAL154	4.6	20.6	1.0
	C	A:LYS153	4.6	25.2	1.0
	N	A:ILE158	4.6	15.2	1.0
	CG2	A:ILE158	4.7	25.1	1.0
	CA	A:ILE158	4.7	16.3	1.0
	N	A:LYS153	4.8	16.8	1.0
	CA	A:VAL154	4.8	21.1	1.0
	C	A:ASN156	4.9	17.0	1.0
	CB	A:ILE157	4.9	15.3	1.0
	O	A:LYS153	4.9	23.7	1.0
	CA	A:LYS153	4.9	21.3	1.0

Potassium binding site 2 out of 3 in 7jza

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Potassium Binding Sites List in 7jza

Potassium binding site 2 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

Mono view

Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:K301 b:18.4 occ:1.00	O	B:ILE157	2.7	12.7	1.0
	O	B:ALA152	2.7	15.1	1.0
	O	B:HOH669	2.7	28.0	1.0
	O	B:VAL154	2.7	19.8	1.0
	O	B:HOH658	2.9	36.8	1.0
	O	B:HOH678	3.0	47.1	1.0
	O	B:LYS155	3.2	17.6	1.0
	C	B:LYS155	3.7	18.5	1.0
	C	B:ALA152	3.7	14.8	1.0
	C	B:ILE157	3.7	13.1	1.0
	C	B:VAL154	3.8	20.6	1.0
	CA	B:LYS155	4.0	20.9	1.0
	N	B:ILE157	4.2	12.9	1.0
	O	B:HOH593	4.3	38.7	1.0
	N	B:LYS155	4.3	19.6	1.0
	CA	B:ALA152	4.3	13.9	1.0
	O	B:HOH665	4.5	39.8	1.0
	CA	B:ILE157	4.5	12.8	1.0
	N	B:VAL154	4.6	18.4	1.0
	N	B:ASN156	4.6	15.3	1.0
	C	B:LYS153	4.6	23.2	1.0
	N	B:ILE158	4.7	12.6	1.0
	CA	B:ILE158	4.7	14.2	1.0
	N	B:LYS153	4.8	14.1	1.0
	CA	B:VAL154	4.8	18.9	1.0
	CB	B:ILE157	4.9	12.1	1.0
	O	B:LYS153	4.9	20.0	1.0
	CA	B:LYS153	4.9	17.8	1.0
	CD1	B:PHE181	4.9	12.4	1.0
	CB	B:ALA152	5.0	14.3	1.0
	CG2	B:ILE158	5.0	25.1	1.0

Potassium binding site 3 out of 3 in 7jza

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Potassium Binding Sites List in 7jza

Potassium binding site 3 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

Mono view

Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:K304 b:32.3 occ:1.00	O	B:THR126	2.7	20.7	1.0
	O	B:ALA123	2.8	15.4	1.0
	O	B:HOH409	2.8	39.2	1.0
	O	B:HOH662	2.9	44.6	1.0
	O	B:HOH541	2.9	23.8	1.0
	O	B:GLU124	3.3	22.5	1.0
	C	B:GLU124	3.7	21.9	1.0
	ND2	B:ASN156	3.9	16.1	1.0
	C	B:THR126	3.9	19.2	1.0
	C	B:ALA123	3.9	15.0	1.0
	OD1	B:ASN156	3.9	22.7	1.0
	CA	B:GLU124	3.9	18.1	1.0
	O	B:HOH571	4.0	39.8	1.0
	CG	B:ASN156	4.1	15.9	1.0
	OD1	B:ASP127	4.3	38.0	1.0
	N	B:THR126	4.3	18.1	1.0
	N	B:GLU124	4.3	13.9	1.0
	N	B:HIS125	4.6	19.9	1.0
	CA	B:ASP127	4.6	19.5	1.0
	N	B:ASP127	4.6	18.6	1.0
	CA	B:THR126	4.7	18.4	1.0

Reference:

A.J.Board, R.C.J.Dobson. Mapping the Uncharted Water Channel of Dhdps To Be Published.

Page generated: Mon Aug 12 19:11:27 2024

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