Manganese in PDB 6p1u: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp

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

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 Cmp:
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 Cmp, PDB code: 6p1u 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)*	34.98 / 1.75
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	59.864, 68.825, 110.594, 90.00, 90.00, 90.00
*R / R_free (%)*	16.9 / 19.3

Other elements in 6p1u:

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

Chlorine	(Cl)	4 atoms
Sodium	(Na)	3 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 Cmp (pdb code 6p1u). 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 Cmp, PDB code: 6p1u:

Manganese binding site 1 out of 1 in 6p1u

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Manganese Binding Sites List in 6p1u

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 Cmp

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 Cmp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn501 b:22.0 occ:1.00	OD1	A:ASP332	1.9	20.6	1.0
	OD2	A:ASP330	1.9	22.0	1.0
	OP1	P:C5	1.9	22.6	0.8
	OD2	A:ASP418	2.0	19.1	1.0
	O	P:HOH201	2.5	15.4	0.2
	O2A	A:CTP509	2.5	9.5	0.2
	O3'	P:DA4	2.6	17.7	0.2
	CG	A:ASP330	2.8	22.3	1.0
	CG	A:ASP332	2.8	18.2	1.0
	CG	A:ASP418	3.0	20.5	1.0
	P	P:C5	3.0	24.0	0.8
	O3'	P:DA4	3.1	21.1	0.8
	OD1	A:ASP330	3.1	19.1	1.0
	OD2	A:ASP332	3.2	19.2	1.0
	NA	A:NA502	3.5	16.8	1.0
	CB	A:ASP418	3.6	18.3	1.0
	PA	A:CTP509	3.7	9.7	0.2
	C3'	P:DA4	3.8	19.3	0.2
	OD1	A:ASP418	4.0	21.6	1.0
	O5'	P:C5	4.1	22.8	0.8
	OP2	P:C5	4.1	24.4	0.8
	O5'	A:CTP509	4.1	7.4	0.2
	O1A	A:CTP509	4.1	10.8	0.2
	C3'	P:DA4	4.2	19.5	0.8
	CB	A:ASP330	4.2	19.3	1.0
	CB	A:ASP332	4.2	15.0	1.0
	C5'	P:C5	4.2	21.8	0.8
	C5'	P:DA4	4.2	19.6	0.8
	C5'	A:CTP509	4.3	6.7	0.2
	C4'	P:DA4	4.3	20.1	0.8
	C4'	P:DA4	4.3	19.8	0.2
	C5'	P:DA4	4.4	20.1	0.2
	O	A:VAL331	4.6	18.1	1.0
	O32	A:PPV508	4.6	17.2	0.3
	OP1	P:DA4	4.7	19.6	0.2
	CZ3	A:TRP434	4.7	25.0	1.0
	O2G	A:CTP509	4.7	18.3	0.2
	CA	A:ASP332	4.7	16.4	1.0
	NH2	A:ARG416	4.7	22.7	1.0
	N	A:ASP418	4.8	17.8	1.0
	CA	A:ASP418	4.8	16.6	1.0
	C	A:VAL331	4.8	18.7	1.0
	N	A:ASP332	4.9	16.0	1.0

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 05:49:58 2024

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