Magnesium 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:

Manganese	(Mn)	3 atoms
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 in 3pmn

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Magnesium Binding Sites List in 3pmn

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg576 b:17.9 occ:1.00	OD2	A:ASP427	1.9	23.0	1.0
	O2A	A:1GC1	2.0	20.7	1.0
	O1G	A:1GC1	2.0	22.0	1.0
	O2B	A:1GC1	2.0	20.5	1.0
	O	A:HOH578	2.1	21.7	1.0
	OD1	A:ASP429	2.2	22.7	1.0
	CG	A:ASP427	2.9	24.8	1.0
	PB	A:1GC1	3.1	23.6	1.0
	CG	A:ASP429	3.2	24.3	1.0
	PA	A:1GC1	3.2	23.8	1.0
	PG	A:1GC1	3.3	25.6	1.0
	OD1	A:ASP427	3.3	21.6	1.0
	O3B	A:1GC1	3.4	25.1	1.0
	OD2	A:ASP429	3.5	24.4	1.0
	C3A	A:1GC1	3.5	24.3	1.0
	MN	A:MN2	3.5	23.2	1.0
	O	A:HOH3	3.5	25.8	1.0
	O3G	A:1GC1	4.0	20.3	1.0
	C5'	A:1GC1	4.0	23.7	1.0
	O	A:ASP427	4.1	24.9	1.0
	O5'	A:1GC1	4.1	24.4	1.0
	O	A:HOH4	4.2	26.1	1.0
	CB	A:ASP427	4.2	23.5	1.0
	C	A:ASP427	4.3	26.1	1.0
	N	A:ASP427	4.3	24.5	1.0
	O1A	A:1GC1	4.4	23.6	1.0
	O1B	A:1GC1	4.4	23.8	1.0
	O2G	A:1GC1	4.5	21.2	1.0
	OG	A:SER417	4.5	27.2	1.0
	CA	A:ASP427	4.5	24.3	1.0
	CB	A:ASP429	4.5	24.2	1.0
	N	A:SER417	4.5	29.8	1.0
	O	A:HOH577	4.6	19.0	1.0
	CA	A:GLY416	4.7	31.2	1.0
	N	A:VAL428	4.8	25.0	1.0
	N	A:ASP429	4.8	25.6	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: Mon Aug 11 02:07:08 2025

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