Sodium in PDB 4ed2: Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion, PDB code: 4ed2 was solved by T.Nakamura, Y.Zhao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	26.95 / 1.71
*Space group*	P 6₁
*Cell size a, b, c (Å), α, β, γ (°)*	98.786, 98.786, 82.431, 90.00, 90.00, 120.00
*R / R_free (%)*	17 / 20.6

Other elements in 4ed2:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion (pdb code 4ed2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion, PDB code: 4ed2:

Sodium binding site 1 out of 1 in 4ed2

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Sodium Binding Sites List in 4ed2

Sodium binding site 1 out of 1 in the Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Eta - Dna Ternary Complex: at Crystal at pH 7.2 (Na+ Hepes) with 1 CA2+ Ion within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na501 b:16.7 occ:0.80	OE1	A:GLU116	2.0	19.3	0.2
	OD2	A:ASP115	2.2	13.3	1.0
	O3'	P:DT8	2.3	19.4	1.0
	OE1	A:GLU116	2.4	24.7	0.8
	O2A	P:DTP502	2.4	10.8	1.0
	OD2	A:ASP13	2.4	15.7	0.8
	CG	A:GLU116	2.5	14.6	0.2
	CD	A:GLU116	2.6	19.7	0.2
	OD1	A:ASP13	2.9	16.5	0.2
	O	A:HOH847	3.0	16.9	0.4
	C3'	P:DT8	3.1	15.0	1.0
	CG	A:ASP115	3.2	10.5	1.0
	CD	A:GLU116	3.5	22.6	0.8
	OD1	A:ASP115	3.5	11.6	1.0
	CA	A:CA503	3.5	10.0	1.0
	CG	A:ASP13	3.6	15.9	0.8
	OG	A:SER113	3.6	9.8	0.5
	PA	P:DTP502	3.6	10.0	1.0
	CG	A:ASP13	3.8	15.9	0.2
	OE2	A:GLU116	3.8	20.6	0.2
	CB	A:GLU116	3.9	14.4	0.2
	CB	A:GLU116	3.9	16.8	0.8
	C4'	P:DT8	4.0	14.4	1.0
	O5'	P:DTP502	4.1	9.3	1.0
	CG	A:GLU116	4.1	14.4	0.8
	C5'	P:DTP502	4.1	8.1	1.0
	OD1	A:ASP13	4.2	23.5	0.8
	O1A	P:DTP502	4.3	12.7	1.0
	O	P:HOH109	4.3	12.4	0.4
	OD2	A:ASP13	4.3	12.5	0.2
	C	A:ASP115	4.4	12.6	1.0
	OE2	A:GLU116	4.4	25.5	0.8
	C2'	P:DT8	4.4	20.4	1.0
	O	A:ASP115	4.4	13.0	1.0
	N	A:GLU116	4.5	11.1	1.0
	CB	A:ASP115	4.6	10.1	1.0
	C5'	P:DT8	4.6	20.0	0.5
	CB	A:ASP13	4.6	10.9	0.8
	C5'	P:DT8	4.7	20.4	0.5
	NZ	A:LYS224	4.7	23.2	0.8
	CA	A:GLU116	4.7	13.7	0.2
	CB	A:SER113	4.8	18.2	1.0
	O	A:HOH723	4.8	24.9	1.0
	CB	A:ASP13	4.8	11.2	0.2
	OG	A:SER113	4.8	20.4	0.5
	CA	A:GLU116	4.9	14.0	0.8
	CA	A:ASP115	4.9	10.3	1.0
	N	A:ASP115	4.9	10.2	1.0
	O3A	P:DTP502	5.0	11.7	1.0
	O1B	P:DTP502	5.0	7.9	1.0

Reference:

T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, W.Yang. Watching Dna Polymerase Eta Make A Phosphodiester Bond Nature V. 487 196 2012.
ISSN: ISSN 0028-0836
PubMed: 22785315
DOI: 10.1038/NATURE11181

Page generated: Mon Oct 7 15:08:47 2024

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