Calcium in PDB 5kfp: Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S, PDB code: 5kfp was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.84 / 1.70
*Space group*	P 6₁
*Cell size a, b, c (Å), α, β, γ (°)*	98.540, 98.540, 81.590, 90.00, 90.00, 120.00
*R / R_free (%)*	17.7 / 22.1

Other elements in 5kfp:

The structure of Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S (pdb code 5kfp). 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 with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S, PDB code: 5kfp:

Calcium binding site 1 out of 1 in 5kfp

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Calcium Binding Sites List in 5kfp

Calcium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Complex with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S

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 with Sp-Datp-Alpha-S: Reaction with 20 Mm MG2+ For 600S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca502 b:21.9 occ:0.05	MG	A:MG503	0.0	21.9	0.8
	O1	A:DPO509	1.6	23.3	0.3
	O5	A:DPO509	1.9	20.8	0.3
	O1B	A:STP508	2.0	18.8	0.6
	O1G	A:STP508	2.0	20.9	0.6
	OD2	A:ASP115	2.2	23.1	1.0
	OD1	A:ASP13	2.2	20.2	0.6
	OD1	A:ASP13	2.2	18.3	0.4
	O	A:MET14	2.3	18.2	1.0
	O2A	A:STP508	2.4	27.4	0.6
	OP1	P:AS9	2.4	27.3	0.3
	P1	A:DPO509	3.0	24.4	0.3
	PB	A:STP508	3.1	24.5	0.6
	P2	A:DPO509	3.1	24.4	0.3
	MG	A:MG504	3.1	26.5	0.5
	CG	A:ASP13	3.2	22.0	0.4
	PG	A:STP508	3.2	23.8	0.6
	CG	A:ASP13	3.2	22.8	0.6
	CG	A:ASP115	3.3	24.0	1.0
	C	A:MET14	3.4	17.8	1.0
	O4	A:DPO509	3.4	24.8	0.3
	PA	A:STP508	3.5	30.4	0.6
	O3B	A:STP508	3.6	25.1	0.6
	MG	A:MG501	3.6	26.4	0.5
	OD2	A:ASP13	3.6	21.8	0.4
	O3A	A:STP508	3.6	30.9	0.6
	OD2	A:ASP13	3.6	26.5	0.6
	OD1	A:ASP115	3.7	26.2	1.0
	O2	A:DPO509	3.8	30.7	0.3
	P	P:AS9	3.8	32.2	0.3
	O7	A:DPO509	3.8	22.1	0.3
	O2G	A:STP508	3.9	22.4	0.6
	C5'	A:STP508	3.9	28.4	0.6
	N	A:MET14	4.0	13.9	1.0
	O3	A:DPO509	4.0	23.2	0.3
	C5'	P:AS9	4.0	28.2	0.3
	NZ	A:LYS231	4.1	21.2	1.0
	O5'	P:AS9	4.1	28.8	0.3
	N	A:CYS16	4.2	16.4	1.0
	O5'	A:STP508	4.2	28.8	0.6
	CA	A:MET14	4.2	13.9	1.0
	C	A:ASP13	4.2	12.8	1.0
	O6	A:DPO509	4.3	27.4	0.3
	N	A:ASP15	4.3	13.8	1.0
	O2B	A:STP508	4.4	18.2	0.6
	O	A:HOH797	4.4	33.0	1.0
	CA	A:ASP15	4.4	15.0	1.0
	O3G	A:STP508	4.4	27.6	0.6
	CB	A:ASP13	4.5	15.6	0.6
	C	A:ASP15	4.5	18.8	1.0
	CB	A:ASP13	4.5	15.7	0.4
	CB	A:ASP115	4.5	18.8	1.0
	O	A:HOH680	4.5	36.1	1.0
	N	A:PHE17	4.6	13.8	1.0
	O	A:ASP13	4.6	14.2	1.0
	CB	A:MET14	4.7	15.3	1.0
	CA	A:ASP13	4.8	16.3	0.4
	CA	A:ASP13	4.8	16.2	0.6
	O3'	P:DT8	4.8	32.7	0.3
	CB	A:PHE17	4.8	14.3	1.0
	O	A:ASP115	4.8	16.8	1.0
	CA	A:CYS16	5.0	15.7	1.0

Reference:

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633

Page generated: Wed Jul 9 07:23:41 2025

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