Calcium in PDB 4ecs: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec

Enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec, PDB code: 4ecs 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)*	30.10 / 1.95
*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 (%)*	17.9 / 23.5

Other elements in 4ecs:

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec (pdb code 4ecs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec, PDB code: 4ecs:

Calcium binding site 1 out of 1 in 4ecs

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Calcium Binding Sites List in 4ecs

Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca504 b:8.8 occ:0.30	MG	A:MG505	0.0	8.0	0.7
	O7	P:DPO502	2.1	8.6	0.1
	O2	P:DPO502	2.1	9.9	0.1
	O1B	P:DTP501	2.2	9.9	0.8
	O3G	P:DTP501	2.2	8.1	0.8
	O2A	P:DTP501	2.2	12.6	0.8
	OD1	A:ASP13	2.2	9.4	0.2
	OD1	A:ASP13	2.3	14.1	0.8
	OD1	A:ASP115	2.3	9.0	1.0
	OP1	P:DA9	2.4	12.9	0.1
	O	A:MET14	2.4	9.4	1.0
	OD2	A:ASP13	2.9	21.6	0.8
	CG	A:ASP13	2.9	9.7	0.8
	P1	P:DPO502	3.2	10.0	0.1
	PB	P:DTP501	3.2	9.6	0.8
	CG	A:ASP115	3.3	13.5	1.0
	PA	P:DTP501	3.4	14.9	0.8
	MG	A:MG503	3.4	15.8	0.8
	O1	P:DPO502	3.4	11.9	0.1
	CG	A:ASP13	3.4	11.4	0.2
	P2	P:DPO502	3.4	11.5	0.1
	PG	P:DTP501	3.5	11.4	0.8
	O3A	P:DTP501	3.5	12.1	0.8
	OD2	A:ASP115	3.5	10.7	1.0
	C	A:MET14	3.6	5.8	1.0
	O3B	P:DTP501	3.7	13.5	0.8
	O4	P:DPO502	3.8	12.7	0.1
	P	P:DA9	3.8	13.9	0.1
	C5'	P:DTP501	4.0	10.9	0.8
	NZ	A:LYS231	4.0	11.1	1.0
	O5	P:DPO502	4.0	10.6	0.1
	N	A:MET14	4.1	5.5	1.0
	O	A:HOH603	4.1	17.9	1.0
	OD2	A:ASP13	4.1	16.0	0.2
	O5'	P:DTP501	4.2	11.3	0.8
	O2G	P:DTP501	4.2	10.4	0.8
	O	A:HOH714	4.2	21.3	1.0
	C5'	P:DA9	4.3	11.4	0.1
	O5'	P:DA9	4.3	12.2	0.1
	C	A:ASP13	4.4	6.7	1.0
	CA	A:MET14	4.4	7.5	1.0
	CB	A:ASP13	4.4	8.1	0.8
	CB	A:ASP13	4.5	8.7	0.2
	O3	P:DPO502	4.6	11.0	0.1
	N	A:ASP15	4.6	6.9	1.0
	N	A:CYS16	4.6	7.4	1.0
	O2B	P:DTP501	4.6	11.5	0.8
	CB	A:ASP115	4.6	6.4	1.0
	O6	P:DPO502	4.7	11.2	0.1
	CA	A:ASP15	4.7	10.2	1.0
	O1G	P:DTP501	4.7	11.1	0.8
	O1A	P:DTP501	4.7	16.5	0.8
	O3'	P:DT8	4.7	16.1	0.1
	C	A:ASP15	4.7	11.9	1.0
	OP2	P:DA9	4.8	15.9	0.1
	O	A:ASP13	4.8	10.0	1.0
	N	A:PHE17	4.8	8.0	1.0
	CA	A:ASP13	4.8	9.3	0.2
	CB	A:MET14	4.8	7.0	1.0
	CE	A:LYS231	4.8	27.3	1.0
	CA	A:ASP13	4.9	9.3	0.8
	CB	A:PHE17	4.9	5.1	1.0
	O3'	P:DT8	4.9	15.3	0.8
	O	A:ASP115	5.0	9.2	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: Sat Jul 13 23:53:59 2024

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