Sodium in PDB 6nks: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp, PDB code: 6nks was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.27 / 2.35
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.607, 80.327, 55.391, 90.00, 108.13, 90.00
*R / R_free (%)*	18.9 / 25.5

Other elements in 6nks:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp (pdb code 6nks). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp, PDB code: 6nks:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nks

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Sodium Binding Sites List in 6nks

Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:39.8 occ:1.00	OD1	A:ASP192	2.4	35.6	1.0
	O1A	A:GFH401	2.5	29.2	1.0
	OD2	A:ASP190	2.6	37.5	1.0
	OD2	A:ASP256	2.7	40.9	1.0
	CG	A:ASP190	3.3	33.8	1.0
	OD1	A:ASP190	3.3	31.5	1.0
	CG	A:ASP192	3.4	31.5	1.0
	PA	A:GFH401	3.5	30.3	1.0
	C3'	P:DOC10	3.5	41.6	1.0
	O5'	A:GFH401	3.6	29.8	1.0
	OD2	A:ASP192	3.7	32.5	1.0
	MG	A:MG402	3.7	29.2	1.0
	CG	A:ASP256	3.7	37.9	1.0
	C5'	P:DOC10	3.9	48.5	1.0
	O2A	A:GFH401	3.9	35.4	1.0
	C5'	A:GFH401	3.9	28.3	1.0
	C4'	P:DOC10	4.0	46.6	1.0
	O5'	P:DOC10	4.2	44.7	1.0
	CB	A:ASP256	4.4	35.5	1.0
	OP1	P:DOC10	4.6	44.4	1.0
	OD1	A:ASP256	4.6	32.7	1.0
	CB	A:ASP190	4.6	31.4	1.0
	CB	A:ASP192	4.7	26.9	1.0
	O	A:MET191	4.8	27.9	1.0
	NH2	A:ARG254	4.8	36.9	1.0
	C2'	P:DOC10	4.8	37.5	1.0
	O1G	A:GFH401	4.8	36.6	1.0
	O3A	A:GFH401	4.9	25.7	1.0

Sodium binding site 2 out of 3 in 6nks

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Sodium Binding Sites List in 6nks

Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:33.1 occ:1.00	O	A:THR101	2.3	32.8	1.0
	O	A:HOH528	2.3	34.7	1.0
	OP1	P:DG9	2.5	31.9	1.0
	O	A:ILE106	2.5	30.4	1.0
	O	A:VAL103	2.7	31.1	1.0
	O	A:HOH554	3.0	35.6	1.0
	C	A:THR101	3.3	34.4	1.0
	P	P:DG9	3.5	31.9	1.0
	C	A:VAL103	3.5	32.7	1.0
	C	A:ILE106	3.5	32.5	1.0
	OP2	P:DG9	3.6	36.8	1.0
	N	A:ILE106	3.9	33.7	1.0
	CA	A:SER104	4.0	27.1	1.0
	CA	A:THR101	4.0	31.3	1.0
	N	A:GLY105	4.1	31.4	1.0
	N	A:SER104	4.1	25.8	1.0
	N	A:VAL103	4.2	33.7	1.0
	C	A:ARG102	4.2	33.0	1.0
	CA	A:ILE106	4.3	30.6	1.0
	N	A:ARG102	4.3	33.6	1.0
	C	A:SER104	4.4	29.5	1.0
	CA	A:ARG102	4.5	32.0	1.0
	O3'	P:DC8	4.5	30.5	1.0
	N	A:GLY107	4.5	32.3	1.0
	CA	A:VAL103	4.5	32.8	1.0
	CB	A:THR101	4.6	29.8	1.0
	O5'	P:DG9	4.6	37.8	1.0
	CB	A:ILE106	4.7	32.7	1.0
	O	A:ARG102	4.7	35.8	1.0
	CA	A:GLY107	4.7	33.9	1.0
	C	A:GLY105	4.8	34.0	1.0
	O	A:LEU100	4.9	32.4	1.0
	CA	A:GLY105	5.0	34.9	1.0

Sodium binding site 3 out of 3 in 6nks

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Sodium Binding Sites List in 6nks

Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Chf Analog of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na405 b:54.6 occ:1.00	O	A:LYS60	2.7	46.3	1.0
	O	A:LEU62	2.8	42.1	1.0
	OP1	D:DC3	3.0	49.1	1.0
	C	A:LEU62	3.3	42.4	1.0
	O	A:VAL65	3.5	41.6	1.0
	CA	A:PRO63	3.6	44.1	1.0
	N	A:PRO63	3.7	44.0	1.0
	C	A:LYS60	3.8	44.7	1.0
	C	A:LYS61	3.9	45.4	1.0
	N	A:LEU62	4.0	45.8	1.0
	O	A:LYS61	4.0	51.1	1.0
	CA	A:LEU62	4.2	39.1	1.0
	P	D:DC3	4.2	49.4	1.0
	N	A:GLY64	4.4	43.2	1.0
	CA	A:LYS61	4.4	44.1	1.0
	C	A:PRO63	4.5	44.5	1.0
	OP2	D:DC3	4.6	49.5	1.0
	N	A:LYS61	4.6	46.4	1.0
	C	A:VAL65	4.6	40.7	1.0
	CB	A:PRO63	4.7	41.2	1.0
	N	A:VAL65	4.8	37.6	1.0
	CA	A:LYS60	4.8	41.4	1.0
	CG	A:LYS60	4.9	45.5	1.0
	CD	A:PRO63	4.9	40.6	1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.

Page generated: Tue Oct 8 12:16:45 2024

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