Sodium in PDB 6nky: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky 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)*	21.98 / 2.09
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.643, 80.158, 55.251, 90.00, 107.89, 90.00
*R / R_free (%)*	19.9 / 25.6

Other elements in 6nky:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp (pdb code 6nky). 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nky

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Sodium Binding Sites List in 6nky

Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na402 b:31.2 occ:1.00	OD2	A:ASP190	2.1	34.5	1.0
	OD1	A:ASP192	2.2	32.6	1.0
	OD2	A:ASP256	2.2	34.5	1.0
	O	A:HOH537	2.4	41.6	1.0
	O1A	A:GFH408	2.5	27.9	1.0
	CG	A:ASP190	3.1	30.6	1.0
	CG	A:ASP192	3.2	27.5	1.0
	C3'	P:2DT10	3.4	41.3	1.0
	CG	A:ASP256	3.4	33.5	1.0
	PA	A:GFH408	3.5	31.1	1.0
	OD1	A:ASP190	3.5	31.4	1.0
	OD2	A:ASP192	3.6	26.7	1.0
	O5'	A:GFH408	3.6	30.9	1.0
	MG	A:MG401	3.6	26.5	1.0
	O2A	A:GFH408	3.8	28.7	1.0
	C5'	A:GFH408	3.9	31.2	1.0
	CB	A:ASP256	4.0	34.7	1.0
	C4'	P:2DT10	4.1	41.2	1.0
	C5'	P:2DT10	4.3	39.8	1.0
	OD1	A:ASP256	4.4	33.0	1.0
	CB	A:ASP190	4.4	29.0	1.0
	CB	A:ASP192	4.5	30.5	1.0
	O5'	P:2DT10	4.6	37.9	1.0
	O1G	A:GFH408	4.6	25.8	1.0
	C2'	P:2DT10	4.6	37.3	1.0
	OP1	P:2DT10	4.7	37.8	1.0
	NH2	A:ARG254	4.8	34.9	1.0
	O	A:MET191	4.9	29.4	1.0
	O3A	A:GFH408	4.9	30.0	1.0

Sodium binding site 2 out of 3 in 6nky

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Sodium Binding Sites List in 6nky

Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:29.5 occ:1.00	O	A:THR101	2.3	32.8	1.0
	OP1	P:DT9	2.4	29.4	1.0
	O	A:ILE106	2.4	27.6	1.0
	O	A:VAL103	2.5	28.9	1.0
	O	P:HOH101	2.5	31.0	1.0
	O	A:HOH666	3.2	43.3	1.0
	C	A:THR101	3.3	35.3	1.0
	C	A:VAL103	3.4	32.0	1.0
	P	P:DT9	3.5	33.8	1.0
	C	A:ILE106	3.5	28.6	1.0
	OP2	P:DT9	3.6	28.8	1.0
	N	A:ILE106	3.8	31.4	1.0
	CA	A:SER104	3.9	31.8	1.0
	O	A:HOH662	4.0	42.8	1.0
	N	A:GLY105	4.0	29.8	1.0
	N	A:SER104	4.0	29.2	1.0
	CA	A:THR101	4.1	31.4	1.0
	N	A:VAL103	4.1	30.0	1.0
	CA	A:ILE106	4.1	28.8	1.0
	C	A:ARG102	4.2	29.5	1.0
	C	A:SER104	4.3	31.8	1.0
	N	A:ARG102	4.3	29.4	1.0
	O3'	P:DC8	4.4	29.1	1.0
	CA	A:VAL103	4.4	30.9	1.0
	CA	A:ARG102	4.5	33.1	1.0
	N	A:GLY107	4.5	32.9	1.0
	CB	A:ILE106	4.5	32.0	1.0
	CB	A:THR101	4.6	34.8	1.0
	O	A:ARG102	4.6	32.5	1.0
	C	A:GLY105	4.6	33.8	1.0
	O5'	P:DT9	4.7	33.5	1.0
	CA	A:GLY107	4.8	32.9	1.0
	CA	A:GLY105	4.9	32.5	1.0
	O	A:LEU100	4.9	28.2	1.0

Sodium binding site 3 out of 3 in 6nky

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Sodium Binding Sites List in 6nky

Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue 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 "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:40.4 occ:1.00	O	A:LYS60	2.3	38.4	1.0
	O	A:LEU62	2.3	41.5	1.0
	O	A:VAL65	2.4	41.0	1.0
	OP1	D:DC3	2.7	42.0	1.0
	O	D:HOH102	3.1	41.9	1.0
	C	A:LEU62	3.4	40.8	1.0
	C	A:LYS60	3.4	41.7	1.0
	C	A:VAL65	3.5	36.2	1.0
	P	D:DC3	3.8	42.3	1.0
	CA	A:PRO63	4.0	42.5	1.0
	OP2	D:DC3	4.0	35.9	1.0
	N	A:VAL65	4.0	36.6	1.0
	N	A:PRO63	4.0	44.0	1.0
	N	A:LEU62	4.1	41.6	1.0
	C	A:LYS61	4.1	44.0	1.0
	CA	A:LYS60	4.1	40.0	1.0
	CA	A:VAL65	4.2	38.4	1.0
	CG	A:LYS60	4.3	37.4	1.0
	N	A:GLY64	4.3	39.2	1.0
	O	A:LYS61	4.3	41.1	1.0
	CA	A:LEU62	4.3	43.0	1.0
	N	A:LYS61	4.4	42.0	1.0
	CB	A:VAL65	4.5	39.0	1.0
	C	A:PRO63	4.5	45.5	1.0
	CA	A:LYS61	4.6	41.8	1.0
	N	A:GLY66	4.6	35.5	1.0
	O3'	D:DT2	4.7	39.4	1.0
	CB	A:LYS60	4.8	36.3	1.0
	CA	A:GLY66	4.9	39.1	1.0
	O	A:ALA59	4.9	39.8	1.0
	CD	A:LYS60	4.9	42.0	1.0
	C	A:GLY64	5.0	38.4	1.0
	O5'	D:DC3	5.0	45.8	1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp To Be Published.

Page generated: Tue Oct 8 12:18:14 2024

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