Magnesium in PDB 3pnc: Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site

Enzymatic activity of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site

All present enzymatic activity of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site, PDB code: 3pnc 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)*	22.44 / 2.00
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.161, 62.254, 139.834, 90.00, 90.00, 90.00
*R / R_free (%)*	20.8 / 23.6

Other elements in 3pnc:

The structure of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site (pdb code 3pnc). 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 A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site, PDB code: 3pnc:

Magnesium binding site 1 out of 1 in 3pnc

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Magnesium Binding Sites List in 3pnc

Magnesium binding site 1 out of 1 in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal 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 A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg576 b:18.5 occ:1.00	O2B	A:1GC1	2.0	18.4	1.0
	OD2	A:ASP427	2.0	17.2	1.0
	O2A	A:1GC1	2.1	16.8	1.0
	O	A:HOH578	2.1	25.1	1.0
	OD1	A:ASP429	2.1	19.7	1.0
	O1G	A:1GC1	2.2	19.1	1.0
	CG	A:ASP429	3.1	20.6	1.0
	PB	A:1GC1	3.1	22.1	1.0
	CG	A:ASP427	3.1	20.9	1.0
	PA	A:1GC1	3.3	19.8	1.0
	NA	A:NA2	3.4	21.5	1.0
	PG	A:1GC1	3.4	23.4	1.0
	OD2	A:ASP429	3.4	20.1	1.0
	C3A	A:1GC1	3.5	20.8	1.0
	O3B	A:1GC1	3.6	22.7	1.0
	OD1	A:ASP427	3.6	22.1	1.0
	O1	A:TRS577	3.9	36.0	1.0
	C5'	A:1GC1	4.0	18.6	1.0
	O3G	A:1GC1	4.0	20.1	1.0
	O	A:ASP427	4.1	20.0	1.0
	O5'	A:1GC1	4.2	18.3	1.0
	O	A:HOH60	4.2	20.3	1.0
	C	A:ASP427	4.3	20.0	1.0
	OG	A:SER417	4.3	24.4	1.0
	N	A:SER417	4.3	23.6	1.0
	N	A:ASP427	4.4	20.0	1.0
	CB	A:ASP427	4.4	17.3	1.0
	O1B	A:1GC1	4.4	21.7	1.0
	O1A	A:1GC1	4.4	19.1	1.0
	CB	A:ASP429	4.5	20.7	1.0
	CA	A:GLY416	4.5	24.1	1.0
	CA	A:ASP427	4.6	18.8	1.0
	O2G	A:1GC1	4.7	22.2	1.0
	N	A:ASP429	4.8	21.0	1.0
	N	A:VAL428	4.8	20.2	1.0
	C1	A:TRS577	4.9	36.8	1.0
	C	A:GLY416	5.0	26.1	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: Thu Aug 15 09:39:31 2024

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