Manganese in PDB 6p1s: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp

Enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp, PDB code: 6p1s was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.39 / 1.75
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	59.880, 68.838, 110.562, 90.00, 90.00, 90.00
*R / R_free (%)*	17.2 / 19.6

Other elements in 6p1s:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp (pdb code 6p1s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp, PDB code: 6p1s:

Manganese binding site 1 out of 1 in 6p1s

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Manganese Binding Sites List in 6p1s

Manganese binding site 1 out of 1 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn502 b:19.4 occ:1.00	OD2	A:ASP330	1.9	21.1	1.0
	OD1	A:ASP332	1.9	18.2	1.0
	OD2	A:ASP418	2.0	18.9	1.0
	OP1	P:A5	2.1	25.2	1.0
	CG	A:ASP330	2.8	20.6	1.0
	CG	A:ASP332	2.9	18.8	1.0
	O3'	P:DA4	3.0	26.8	1.0
	CG	A:ASP418	3.0	19.5	1.0
	OD1	A:ASP330	3.0	18.1	1.0
	P	P:A5	3.1	24.9	1.0
	OD2	A:ASP332	3.2	18.6	1.0
	NA	A:NA503	3.5	21.7	1.0
	CB	A:ASP418	3.5	18.7	1.0
	OD1	A:ASP418	4.0	20.6	1.0
	C3'	P:DA4	4.1	25.5	1.0
	O5'	P:A5	4.1	18.4	1.0
	OP2	P:A5	4.2	24.0	1.0
	C5'	P:A5	4.2	15.9	1.0
	CB	A:ASP330	4.2	17.4	1.0
	CB	A:ASP332	4.2	13.7	1.0
	C4'	P:DA4	4.2	28.0	1.0
	C5'	P:DA4	4.2	26.1	1.0
	CE1	A:HIS329	4.3	24.8	0.6
	O	A:VAL331	4.6	16.7	1.0
	NH2	A:ARG416	4.6	19.7	1.0
	CZ3	A:TRP434	4.7	23.2	1.0
	CA	A:ASP332	4.7	15.1	1.0
	N	A:ASP418	4.7	16.7	1.0
	CA	A:ASP418	4.8	16.7	1.0
	C	A:VAL331	4.8	16.1	1.0
	N	A:ASP332	4.9	14.2	1.0
	O2B	A:ATP501	4.9	30.7	0.4

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680

Page generated: Sun Oct 6 05:49:09 2024

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