Manganese in PDB 4klt: Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min, PDB code: 4klt was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.76 / 1.98
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	55.082, 78.596, 54.980, 90.00, 112.43, 90.00
*R / R_free (%)*	22.9 / 29.3

Other elements in 4klt:

The structure of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min (pdb code 4klt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min, PDB code: 4klt:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4klt

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Manganese Binding Sites List in 4klt

Manganese binding site 1 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn403 b:65.7 occ:1.00	OD1	A:ASP124	2.5	39.7	1.0
	CG	A:ASP124	3.3	36.4	1.0
	OD2	A:ASP124	3.4	31.5	1.0
	O	A:HOH567	4.1	39.1	1.0
	NZ	A:LYS127	4.3	46.1	1.0
	OG1	A:THR121	4.5	33.2	1.0
	CB	A:ASP124	4.8	29.2	1.0

Manganese binding site 2 out of 4 in 4klt

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Manganese Binding Sites List in 4klt

Manganese binding site 2 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn404 b:52.4 occ:0.60	OD2	A:ASP192	2.3	27.5	1.0
	O22	A:PPV406	2.3	33.6	0.6
	OD1	A:ASP190	2.4	33.8	1.0
	O21	A:PPV406	2.4	25.8	0.6
	O	A:HOH627	2.4	38.0	1.0
	P2	A:PPV406	3.2	44.0	0.6
	MN	A:MN405	3.3	33.0	0.4
	O32	A:PPV406	3.3	26.6	0.6
	CG	A:ASP190	3.4	40.7	1.0
	CG	A:ASP192	3.5	32.7	1.0
	P1	A:PPV406	3.5	34.7	0.6
	O	A:HOH686	3.6	47.3	1.0
	OPP	A:PPV406	3.8	52.6	0.6
	O	A:ASP190	3.9	32.0	1.0
	OD2	A:ASP190	4.0	31.7	1.0
	O31	A:PPV406	4.1	38.9	0.6
	OG	A:SER180	4.1	30.1	1.0
	OD1	A:ASP192	4.1	26.1	1.0
	CA	A:GLY179	4.2	33.8	1.0
	N	A:SER180	4.3	31.9	1.0
	C	A:ASP190	4.3	28.0	1.0
	N	A:ASP190	4.3	30.7	1.0
	O	A:HOH504	4.4	22.3	1.0
	O	A:HOH634	4.5	37.3	1.0
	CB	A:ASP192	4.6	23.6	1.0
	O12	A:PPV406	4.6	38.7	0.6
	CB	A:ASP190	4.6	28.0	1.0
	CA	A:ASP190	4.7	27.6	1.0
	MN	A:MN405	4.7	29.5	0.4
	C5'	P:DA11	4.7	44.7	1.0
	O11	A:PPV406	4.8	43.6	0.6
	O5'	P:DA11	4.8	47.4	1.0
	C	A:GLY179	4.9	35.9	1.0
	N	A:ASP192	4.9	29.0	1.0

Manganese binding site 3 out of 4 in 4klt

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Manganese Binding Sites List in 4klt

Manganese binding site 3 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn405 b:33.0 occ:0.40	MN	A:MN405	0.0	33.0	0.4
	MN	A:MN405	1.8	29.5	0.4
	O	A:HOH634	2.4	37.3	1.0
	OD1	A:ASP192	2.5	26.1	1.0
	O	A:HOH686	2.6	47.3	1.0
	O5'	P:DA11	2.6	47.4	1.0
	OD2	A:ASP192	2.7	27.5	1.0
	OD2	A:ASP190	2.7	31.7	1.0
	CG	A:ASP192	2.9	32.7	1.0
	O	P:HOH128	3.0	24.8	1.0
	OD1	A:ASP190	3.2	33.8	1.0
	MN	A:MN404	3.3	52.4	0.6
	CG	A:ASP190	3.4	40.7	1.0
	C5'	P:DA11	3.4	44.7	1.0
	O3'	P:DC10	3.5	47.5	1.0
	P	P:DA11	3.8	48.0	1.0
	C3'	P:DC10	4.0	38.2	1.0
	O32	A:PPV406	4.1	26.6	0.6
	OD2	A:ASP256	4.3	34.0	1.0
	CB	A:ASP192	4.4	23.6	1.0
	OP2	P:DA11	4.5	46.4	1.0
	O21	A:PPV406	4.5	25.8	0.6
	C4'	P:DA11	4.7	52.5	1.0
	O	P:HOH118	4.7	35.6	1.0
	OP1	P:DA11	4.8	51.9	1.0
	CB	A:ASP190	4.9	28.0	1.0
	C4'	P:DC10	4.9	37.2	1.0
	O22	A:PPV406	5.0	33.6	0.6

Manganese binding site 4 out of 4 in 4klt

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Manganese Binding Sites List in 4klt

Manganese binding site 4 out of 4 in the Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Beta Mismatched Product Complex with MN2+, 30 Min within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn405 b:29.5 occ:0.40	MN	A:MN405	0.0	29.5	0.4
	MN	A:MN405	1.8	33.0	0.4
	O	P:HOH128	2.1	24.8	1.0
	OD1	A:ASP192	2.2	26.1	1.0
	OD2	A:ASP190	2.5	31.7	1.0
	OD2	A:ASP256	2.6	34.0	1.0
	O	A:HOH634	3.0	37.3	1.0
	CG	A:ASP192	3.3	32.7	1.0
	CG	A:ASP256	3.3	32.0	1.0
	O3'	P:DC10	3.4	47.5	1.0
	CG	A:ASP190	3.4	40.7	1.0
	OD2	A:ASP192	3.6	27.5	1.0
	O5'	P:DA11	3.7	47.4	1.0
	OD1	A:ASP190	3.7	33.8	1.0
	C3'	P:DC10	3.8	38.2	1.0
	CB	A:ASP256	4.0	17.5	1.0
	O	P:HOH118	4.0	35.6	1.0
	C5'	P:DC10	4.0	37.2	1.0
	OD1	A:ASP256	4.0	28.6	1.0
	C4'	P:DC10	4.2	37.2	1.0
	P	P:DA11	4.2	48.0	1.0
	O	A:HOH686	4.3	47.3	1.0
	CB	A:ASP192	4.6	23.6	1.0
	CB	A:ASP190	4.7	28.0	1.0
	O	A:MET191	4.7	25.1	1.0
	MN	A:MN404	4.7	52.4	0.6
	OP2	P:DA11	4.7	46.4	1.0
	OP1	P:DC10	4.7	26.6	1.0
	O5'	P:DC10	4.8	31.2	1.0
	NH2	A:ARG254	4.8	24.4	1.0
	C5'	P:DA11	4.8	44.7	1.0

Reference:

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048

Page generated: Sat Oct 5 20:03:47 2024

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