Manganese in PDB 3pmn: Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

All present enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn was solved by K.Bebenek, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.27 / 2.20
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.390, 62.417, 139.881, 90.00, 90.00, 90.00
*R / R_free (%)*	21.3 / 24.3

Other elements in 3pmn:

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site (pdb code 3pmn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 3pmn

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Manganese Binding Sites List in 3pmn

Manganese binding site 1 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ 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 Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn2 b:23.2 occ:1.00	OD2	A:ASP490	2.1	27.0	1.0
	OD1	A:ASP427	2.1	21.6	1.0
	OD2	A:ASP429	2.1	24.4	1.0
	O2A	A:1GC1	2.3	20.7	1.0
	O	A:HOH577	2.4	19.0	1.0
	O3'	C:DG6	2.5	21.3	1.0
	CG	A:ASP427	3.1	24.8	1.0
	CG	A:ASP490	3.2	28.0	1.0
	CG	A:ASP429	3.2	24.3	1.0
	PA	A:1GC1	3.3	23.8	1.0
	OD2	A:ASP427	3.5	23.0	1.0
	C3'	C:DG6	3.5	19.6	1.0
	MG	A:MG576	3.5	17.9	1.0
	O1A	A:1GC1	3.5	23.6	1.0
	OD1	A:ASP429	3.6	22.7	1.0
	O5'	A:1GC1	3.8	24.4	1.0
	CB	A:ASP490	3.8	24.7	1.0
	O	A:HOH3	4.0	25.8	1.0
	C5'	A:1GC1	4.1	23.7	1.0
	OD1	A:ASP490	4.2	26.8	1.0
	C4'	C:DG6	4.2	21.2	1.0
	C5'	C:DG6	4.2	17.2	1.0
	CB	A:ASP427	4.4	23.5	1.0
	CB	A:ASP429	4.5	24.2	1.0
	NH2	A:ARG488	4.5	18.0	1.0
	O5'	C:DG6	4.6	22.2	1.0
	C2'	C:DG6	4.7	20.2	1.0
	O	C:HOH7	4.8	33.5	1.0
	O1G	A:1GC1	4.8	22.0	1.0
	OP1	C:DG6	4.8	19.7	1.0
	O2B	A:1GC1	4.9	20.5	1.0
	C3A	A:1GC1	4.9	24.3	1.0

Manganese binding site 2 out of 3 in 3pmn

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Manganese Binding Sites List in 3pmn

Manganese binding site 2 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ 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 Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn6 b:45.3 occ:1.00	OD1	A:ASP382	2.1	28.8	1.0
	O	A:HOH590	2.5	38.3	1.0
	ND1	A:HIS486	2.6	28.3	1.0
	O	A:HOH588	2.6	21.1	1.0
	O	A:HOH589	2.7	33.7	1.0
	CL	A:CL8	3.0	55.1	1.0
	CG	A:ASP382	3.2	28.8	1.0
	CE1	A:HIS486	3.3	30.6	1.0
	N	A:HIS486	3.6	28.1	1.0
	OD2	A:ASP382	3.6	25.2	1.0
	CG	A:HIS486	3.7	28.2	1.0
	CB	A:HIS486	4.0	24.6	1.0
	CA	A:ARG485	4.4	30.3	1.0
	NH1	A:ARG478	4.4	39.1	1.0
	C	A:ARG485	4.4	30.8	1.0
	CA	A:HIS486	4.4	26.4	1.0
	ND1	A:HIS379	4.4	26.3	1.0
	CB	A:ASP382	4.5	26.1	1.0
	NE2	A:HIS486	4.6	31.4	1.0
	O	A:HOH37	4.6	27.9	1.0
	O	A:ARG484	4.7	29.0	1.0
	CD2	A:HIS486	4.7	29.5	1.0
	O	A:HOH638	4.7	53.4	1.0
	CE1	A:HIS379	4.9	27.9	1.0

Manganese binding site 3 out of 3 in 3pmn

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Manganese Binding Sites List in 3pmn

Manganese binding site 3 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn7 b:85.8 occ:1.00	NE2	A:HIS530	2.2	36.0	1.0
	OP1	B:DA8	2.4	31.2	1.0
	O	A:HOH30	2.5	30.6	1.0
	O	A:HOH602	2.7	52.9	1.0
	CE1	A:HIS530	2.8	34.0	1.0
	CD2	A:HIS530	3.4	32.4	1.0
	O	A:HOH596	3.6	35.6	1.0
	P	B:DA8	3.7	31.0	1.0
	O3'	B:DT7	3.9	28.1	1.0
	C5'	B:DA8	4.0	30.9	1.0
	ND1	A:HIS530	4.1	34.9	1.0
	O	A:HOH598	4.1	53.2	1.0
	O	B:HOH327	4.2	58.3	1.0
	O5'	B:DA8	4.2	30.5	1.0
	OG1	A:THR471	4.3	45.4	1.0
	CG	A:HIS530	4.3	33.5	1.0
	OE2	A:GLU529	4.8	32.6	1.0
	OP2	B:DA8	5.0	31.8	1.0

Reference:

K.Bebenek, L.C.Pedersen, T.A.Kunkel. Replication Infidelity Via A Mismatch with Watson-Crick Geometry. Proc.Natl.Acad.Sci.Usa V. 108 1862 2011.
ISSN: ISSN 0027-8424
PubMed: 21233421
DOI: 10.1073/PNAS.1012825108

Page generated: Sat Oct 5 17:32:08 2024

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