Magnesium in PDB 7u7l: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product

Enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product, PDB code: 7u7l was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	42.10 / 1.47
*Space group*	P 6₁
*Cell size a, b, c (Å), α, β, γ (°)*	98.164, 98.164, 81.882, 90, 90, 120
*R / R_free (%)*	18.7 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product (pdb code 7u7l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product, PDB code: 7u7l:

Magnesium binding site 1 out of 1 in 7u7l

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Magnesium Binding Sites List in 7u7l

Magnesium binding site 1 out of 1 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 1.0 Mm MG2+ For 300S with Flipped-Out Product within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg501 b:25.9 occ:0.55	OD1	A:ASP13	1.9	35.1	1.0
	O	A:MET14	2.1	27.8	1.0
	O1	A:DPO505	2.2	15.7	0.4
	O5	A:DPO505	2.3	27.5	0.4
	O	A:HOH678	2.8	33.8	0.7
	P1	A:DPO505	3.1	29.5	0.4
	CG	A:ASP13	3.1	34.3	1.0
	C	A:MET14	3.2	21.3	1.0
	P2	A:DPO505	3.3	24.8	0.4
	O4	A:DPO505	3.4	21.6	0.4
	O2	A:DPO505	3.6	29.7	0.4
	OD2	A:ASP115	3.7	28.2	1.0
	N	A:MET14	3.8	17.3	1.0
	C5'	P:DG9	3.9	26.2	0.3
	CG	A:ASP115	3.9	24.9	1.0
	OD2	A:ASP13	3.9	45.9	1.0
	O7	A:DPO505	3.9	17.0	0.4
	CB	A:ASP115	4.0	18.6	1.0
	C	A:ASP13	4.1	18.0	1.0
	CB	A:ASP13	4.1	21.8	1.0
	N	A:CYS16	4.1	17.8	1.0
	CA	A:MET14	4.1	20.2	1.0
	OP1	P:DG9	4.2	26.8	0.3
	N	A:ASP15	4.2	15.7	1.0
	CA	A:ASP15	4.2	17.9	1.0
	O	A:ASP115	4.3	22.0	1.0
	C	A:ASP15	4.3	18.4	1.0
	CA	A:ASP13	4.5	18.7	1.0
	O3	A:DPO505	4.5	22.5	0.4
	O6	A:DPO505	4.6	26.0	0.4
	OD1	A:ASP115	4.6	19.9	1.0
	O	A:ASP13	4.6	21.2	1.0
	N	A:PHE17	4.6	14.1	1.0
	CB	A:MET14	4.7	21.9	1.0
	O5'	P:DG9	4.9	24.6	0.3
	C4'	P:DG9	4.9	20.3	0.3
	CA	A:CYS16	4.9	15.9	1.0
	O	A:HOH617	4.9	29.9	0.7
	CB	A:PHE17	4.9	14.0	1.0

Reference:

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3

Page generated: Thu Oct 3 09:50:12 2024

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