Manganese in PDB 6u6b: Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

Enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

All present enzymatic activity of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b was solved by H.Ouzon-Shubeita, C.K.Vilas, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.14 / 3.11
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	53.430, 78.216, 53.965, 90.00, 110.57, 90.00
*R / R_free (%)*	22.2 / 26.8

Other elements in 6u6b:

Platinum	(Pt)	1 atom
Sodium	(Na)	2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site (pdb code 6u6b). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site, PDB code: 6u6b:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6u6b

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Manganese Binding Sites List in 6u6b

Manganese binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:73.6 occ:1.00	OD2	A:ASP190	1.8	43.0	1.0
	O3'	P:DC10	1.9	63.5	1.0
	OD1	A:ASP192	2.0	61.5	1.0
	OD2	A:ASP256	2.0	41.5	1.0
	O1A	A:DZ4405	2.5	61.7	1.0
	CG	A:ASP190	2.9	43.9	1.0
	C3'	P:DC10	3.0	72.4	1.0
	CG	A:ASP192	3.1	54.0	1.0
	CG	A:ASP256	3.2	31.4	1.0
	H3'	P:DC10	3.3	86.9	1.0
	H4'	P:DC10	3.3	84.1	1.0
	OD1	A:ASP190	3.4	44.3	1.0
	OD2	A:ASP192	3.5	55.2	1.0
	H5''	P:DC10	3.5	73.9	1.0
	HB2	A:ASP256	3.6	36.3	1.0
	C4'	P:DC10	3.6	70.1	1.0
	PA	A:DZ4405	3.6	47.3	1.0
	H5'	A:DZ4405	3.8	65.2	1.0
	O5'	A:DZ4405	3.9	49.4	1.0
	CB	A:ASP256	4.0	30.2	1.0
	MN	A:MN402	4.0	54.8	1.0
	C5'	P:DC10	4.0	61.5	1.0
	O2A	A:DZ4405	4.1	43.3	1.0
	H5'A	A:DZ4405	4.1	65.2	1.0
	C5'	A:DZ4405	4.2	54.4	1.0
	CB	A:ASP190	4.2	34.7	1.0
	OD1	A:ASP256	4.2	34.6	1.0
	HB2	A:ASP190	4.3	41.6	1.0
	H2''	P:DC10	4.3	78.3	1.0
	C2'	P:DC10	4.3	65.2	1.0
	HB3	A:ASP256	4.4	36.3	1.0
	CB	A:ASP192	4.4	47.1	1.0
	HB3	A:ASP190	4.4	41.6	1.0
	HA	A:ASP192	4.4	55.9	1.0
	HB3	A:ASP192	4.6	56.6	1.0
	O5'	P:DC10	4.6	60.5	1.0
	H	A:ASP256	4.8	45.5	1.0
	H5'	P:DC10	4.9	73.9	1.0
	CA	A:ASP192	4.9	46.5	1.0
	H2'	P:DC10	4.9	78.3	1.0
	O4'	P:DC10	4.9	61.9	1.0

Manganese binding site 2 out of 2 in 6u6b

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Manganese Binding Sites List in 6u6b

Manganese binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Dna Polymerase Beta Misinserting Dampnpp Opposite the 5'G of the Cisplatin Pt-Gg Intrastrand Crosslink with Manganese in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn402 b:54.8 occ:1.00	OD2	A:ASP192	1.8	55.2	1.0
	OD1	A:ASP190	1.9	44.3	1.0
	O2B	A:DZ4405	2.0	61.7	1.0
	O3G	A:DZ4405	2.1	57.7	1.0
	O1A	A:DZ4405	2.5	61.7	1.0
	CG	A:ASP192	3.0	54.0	1.0
	PB	A:DZ4405	3.0	39.8	1.0
	CG	A:ASP190	3.1	43.9	1.0
	PA	A:DZ4405	3.1	47.3	1.0
	N3A	A:DZ4405	3.2	65.8	1.0
	O5'	A:DZ4405	3.3	49.4	1.0
	PG	A:DZ4405	3.4	46.7	1.0
	H	A:SER180	3.4	47.6	1.0
	H	A:ASP190	3.4	47.4	1.0
	O	A:ASP190	3.5	45.7	1.0
	OD1	A:ASP192	3.5	61.5	1.0
	O3B	A:DZ4405	3.6	46.6	1.0
	HA3	A:GLY179	3.6	39.3	1.0
	OD2	A:ASP190	3.6	43.0	1.0
	HN3A	A:DZ4405	3.9	79.0	1.0
	MN	A:MN401	4.0	73.6	1.0
	C	A:ASP190	4.0	39.3	1.0
	HG	A:SER180	4.1	46.1	1.0
	HB2	A:ASP192	4.1	56.6	1.0
	CB	A:ASP192	4.2	47.1	1.0
	N	A:ASP190	4.2	39.5	1.0
	N	A:SER180	4.2	39.7	1.0
	OG	A:SER180	4.2	38.4	1.0
	H	A:ASP192	4.3	53.9	1.0
	O1G	A:DZ4405	4.3	55.3	1.0
	CB	A:ASP190	4.3	34.7	1.0
	O1B	A:DZ4405	4.3	32.1	1.0
	O2G	A:DZ4405	4.4	41.1	1.0
	CA	A:ASP190	4.4	31.4	1.0
	CA	A:GLY179	4.4	32.7	1.0
	HA2	A:GLY179	4.5	39.3	1.0
	C5'	A:DZ4405	4.5	54.4	1.0
	O2A	A:DZ4405	4.6	43.3	1.0
	N	A:ASP192	4.6	44.9	1.0
	H5'	A:DZ4405	4.6	65.2	1.0
	HB3	A:SER180	4.6	47.8	1.0
	H	A:GLY189	4.7	45.4	1.0
	HB3	A:ASP190	4.7	41.6	1.0
	HB3	A:ASP192	4.9	56.6	1.0
	N	A:MET191	4.9	40.9	1.0
	C	A:GLY179	4.9	33.1	1.0
	HA	A:MET191	4.9	43.2	1.0
	CB	A:SER180	4.9	39.8	1.0
	O3'	P:DC10	4.9	63.5	1.0
	CA	A:ASP192	5.0	46.5	1.0
	HB2	A:ASP190	5.0	41.6	1.0

Reference:

H.Ouzon-Shubeita, C.K.Vilas, S.Lee. Structures of the Mutagenic Bypass of the Major Cisplatin-Dna Lesion By Human Dna Polymerase Beta Reveal Insights Into Cisplatin-Induced Mutagenesis To Be Published.

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