Sodium in PDB 6nl0: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 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 CF2 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 CF2 Analogue of Dgtp, PDB code: 6nl0 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)*	21.23 / 1.97
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.317, 79.933, 55.119, 90.00, 107.97, 90.00
*R / R_free (%)*	19.3 / 23.7

Other elements in 6nl0:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

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 CF2 Analogue of Dgtp (pdb code 6nl0). 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 CF2 Analogue of Dgtp, PDB code: 6nl0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nl0

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Sodium Binding Sites List in 6nl0

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 CF2 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 CF2 Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na402 b:29.6 occ:1.00	OD1	A:ASP192	2.2	26.7	1.0
	OD2	A:ASP190	2.2	30.9	1.0
	OD2	A:ASP256	2.3	32.5	1.0
	O1A	A:GFF405	2.5	27.4	1.0
	CG	A:ASP190	2.9	30.1	1.0
	OD1	A:ASP190	3.0	29.0	1.0
	CG	A:ASP192	3.2	25.2	1.0
	MG	A:MG401	3.4	27.4	1.0
	CG	A:ASP256	3.4	31.9	1.0
	OD2	A:ASP192	3.5	28.7	1.0
	P1	A:GFF405	3.6	29.9	1.0
	C3'	P:2DT10	3.7	31.3	1.0
	O5'	A:GFF405	3.9	29.5	1.0
	CB	A:ASP256	4.0	29.1	1.0
	O2A	A:GFF405	4.1	31.6	1.0
	C5'	A:GFF405	4.1	29.3	1.0
	CB	A:ASP190	4.2	27.9	1.0
	C4'	P:2DT10	4.3	33.4	1.0
	C5'	P:2DT10	4.4	27.8	1.0
	OD1	A:ASP256	4.4	28.6	1.0
	CB	A:ASP192	4.5	26.2	1.0
	O	A:HOH620	4.6	32.5	1.0
	O1G	A:GFF405	4.6	31.1	1.0
	O	A:MET191	4.7	24.7	1.0
	O5'	P:2DT10	4.8	28.9	1.0
	NH2	A:ARG254	4.8	28.2	1.0
	OP1	P:2DT10	4.9	29.5	1.0
	C	A:MET191	4.9	29.3	1.0
	C2'	P:2DT10	4.9	31.7	1.0
	CA	A:ASP192	4.9	28.0	1.0

Sodium binding site 2 out of 3 in 6nl0

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Sodium Binding Sites List in 6nl0

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 CF2 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 CF2 Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:27.2 occ:1.00	O	A:THR101	2.3	26.3	1.0
	O	A:ILE106	2.3	24.6	1.0
	O	A:VAL103	2.5	26.9	1.0
	O	P:HOH104	2.5	27.8	1.0
	OP1	P:DT9	2.5	27.0	1.0
	O	A:HOH665	2.8	34.9	1.0
	C	A:THR101	3.3	26.4	1.0
	C	A:VAL103	3.4	27.5	1.0
	C	A:ILE106	3.4	28.8	1.0
	P	P:DT9	3.5	27.5	1.0
	OP2	P:DT9	3.6	24.5	1.0
	O	A:HOH656	3.8	50.0	1.0
	N	A:ILE106	3.8	26.1	1.0
	CA	A:THR101	3.9	29.5	1.0
	CA	A:SER104	4.0	27.4	1.0
	N	A:VAL103	4.1	26.6	1.0
	N	A:GLY105	4.1	28.8	1.0
	N	A:SER104	4.1	22.2	1.0
	CA	A:ILE106	4.1	26.4	1.0
	C	A:ARG102	4.2	28.6	1.0
	N	A:ARG102	4.3	28.6	1.0
	CA	A:VAL103	4.4	26.8	1.0
	C	A:SER104	4.4	28.5	1.0
	CB	A:THR101	4.4	29.9	1.0
	O3'	P:DC8	4.4	27.7	1.0
	N	A:GLY107	4.5	29.2	1.0
	CB	A:ILE106	4.5	28.4	1.0
	CA	A:ARG102	4.5	28.9	1.0
	C	A:GLY105	4.7	30.6	1.0
	O	A:ARG102	4.7	27.9	1.0
	O5'	P:DT9	4.7	30.0	1.0
	CA	A:GLY107	4.8	28.1	1.0
	O	A:LEU100	4.9	27.1	1.0
	CA	A:GLY105	4.9	29.6	1.0

Sodium binding site 3 out of 3 in 6nl0

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Sodium Binding Sites List in 6nl0

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 CF2 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 CF2 Analogue of Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:40.6 occ:1.00	O	A:LEU62	2.4	42.4	1.0
	O	A:HOH611	2.4	42.8	1.0
	O	A:LYS60	2.5	41.7	1.0
	O	A:VAL65	2.5	39.2	1.0
	OP1	D:DC3	2.6	38.6	1.0
	O	D:HOH101	2.8	41.6	1.0
	C	A:LEU62	3.3	40.4	1.0
	C	A:LYS60	3.6	43.7	1.0
	C	A:VAL65	3.6	39.4	1.0
	P	D:DC3	3.7	38.3	1.0
	N	A:VAL65	3.9	36.3	1.0
	CA	A:PRO63	3.9	41.9	1.0
	N	A:LEU62	4.0	40.2	1.0
	N	A:PRO63	4.0	43.4	1.0
	OP2	D:DC3	4.0	37.6	1.0
	C	A:LYS61	4.1	46.5	1.0
	N	A:GLY64	4.1	37.4	1.0
	CA	A:VAL65	4.2	36.2	1.0
	CA	A:LEU62	4.3	39.5	1.0
	O	A:LYS61	4.3	46.6	1.0
	CA	A:LYS60	4.3	42.0	1.0
	C	A:PRO63	4.3	40.7	1.0
	N	A:LYS61	4.5	40.9	1.0
	CB	A:VAL65	4.5	37.4	1.0
	CD	A:LYS60	4.5	44.1	1.0
	CA	A:LYS61	4.5	43.4	1.0
	N	A:GLY66	4.6	34.8	1.0
	O3'	D:DT2	4.6	42.2	1.0
	C	A:GLY64	4.8	36.6	1.0
	O	A:ALA59	4.8	42.0	1.0
	CG	A:LYS60	4.9	44.7	1.0
	O5'	D:DC3	4.9	41.6	1.0
	CA	A:GLY66	4.9	36.9	1.0

Reference:

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

Page generated: Tue Oct 8 12:18:27 2024

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