Magnesium in PDB 4fo6: Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus.

Enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus.

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus.:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus., PDB code: 4fo6 was solved by R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.03 / 2.01
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	55.780, 63.655, 141.470, 90.00, 90.00, 90.00
*R / R_free (%)*	19 / 23.1

Other elements in 4fo6:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus. also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus. (pdb code 4fo6). 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 Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus., PDB code: 4fo6:

Magnesium binding site 1 out of 1 in 4fo6

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Magnesium Binding Sites List in 4fo6

Magnesium binding site 1 out of 1 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus.

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with A Datp Analog Opposite A Templating T and An Rcmp at the Primer Terminus. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:15.8 occ:1.00	OD1	A:ASP429	2.0	16.1	1.0
	OD1	A:ASP427	2.0	17.4	1.0
	O2B	A:F2A606	2.0	18.7	1.0
	O	A:HOH701	2.1	22.0	1.0
	O1A	A:F2A606	2.1	11.2	1.0
	O3G	A:F2A606	2.2	19.1	1.0
	CG	A:ASP427	3.0	22.9	1.0
	CG	A:ASP429	3.1	19.4	1.0
	PB	A:F2A606	3.2	18.4	1.0
	PA	A:F2A606	3.4	19.3	1.0
	PG	A:F2A606	3.4	24.0	1.0
	OD2	A:ASP427	3.4	23.0	1.0
	OD2	A:ASP429	3.5	18.2	1.0
	MN	A:MN604	3.5	18.9	1.0
	C3A	A:F2A606	3.6	15.3	1.0
	O3B	A:F2A606	3.7	22.1	1.0
	O	A:HOH782	3.9	23.7	1.0
	O2G	A:F2A606	4.0	23.3	1.0
	C5'	A:F2A606	4.0	19.2	1.0
	O	A:ASP427	4.1	19.5	1.0
	O5'	A:F2A606	4.2	19.4	1.0
	N	A:ASP427	4.3	20.1	1.0
	O	A:HOH702	4.3	21.6	1.0
	CB	A:ASP427	4.3	16.6	1.0
	OG	A:SER417	4.3	23.5	1.0
	CB	A:ASP429	4.3	20.9	1.0
	C	A:ASP427	4.3	16.3	1.0
	N	A:SER417	4.5	23.5	1.0
	O2A	A:F2A606	4.5	21.9	1.0
	O	A:HOH823	4.5	18.4	1.0
	O1B	A:F2A606	4.5	25.0	1.0
	CA	A:ASP427	4.6	19.0	1.0
	CA	A:GLY416	4.6	20.5	1.0
	O1G	A:F2A606	4.6	22.9	1.0
	N	A:ASP429	4.7	15.8	1.0
	O3'	P:C6	5.0	14.0	1.0

Reference:

R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek. The Catalytic Cycle For Ribonucleotide Incorporation By Human Dna Pol Lambda Nucleic Acids Res. V. 40 1 2012.
ISSN: ISSN 0305-1048
PubMed: 22584622
DOI: 10.1093/NAR/GKS413

Page generated: Fri Aug 16 15:13:35 2024

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