Magnesium in PDB 2isp: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate, PDB code: 2isp was solved by C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.Martinek, Y.Xiang, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.36 / 2.20
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.700, 80.400, 55.500, 90.00, 107.90, 90.00
*R / R_free (%)*	20.1 / 26.1

Other elements in 2isp:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate (pdb code 2isp). 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 Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate, PDB code: 2isp:

Magnesium binding site 1 out of 1 in 2isp

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Magnesium Binding Sites List in 2isp

Magnesium binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg339 b:17.1 occ:1.00	OD1	A:ASP190	1.8	14.9	1.0
	O1A	A:GGH338	1.9	13.4	1.0
	O2B	A:GGH338	2.1	11.7	1.0
	OD2	A:ASP192	2.1	19.8	1.0
	O	A:HOH348	2.1	19.9	1.0
	O1G	A:GGH338	2.1	17.8	1.0
	CG	A:ASP190	2.8	17.0	1.0
	CG	A:ASP192	3.1	16.9	1.0
	P2	A:GGH338	3.2	17.3	1.0
	P1	A:GGH338	3.2	17.4	1.0
	OD2	A:ASP190	3.3	16.7	1.0
	OD1	A:ASP192	3.4	19.6	1.0
	P3	A:GGH338	3.4	24.0	1.0
	NA	A:NA340	3.5	8.3	1.0
	O3A	A:GGH338	3.6	16.1	1.0
	O3G	A:GGH338	3.8	17.2	1.0
	O	A:ASP190	3.9	17.0	1.0
	C3B	A:GGH338	4.0	18.3	1.0
	O	A:HOH501	4.1	39.4	1.0
	O	A:HOH368	4.1	20.9	1.0
	C	A:ASP190	4.1	15.8	1.0
	O5'	A:GGH338	4.1	14.9	1.0
	C5'	A:GGH338	4.1	15.8	1.0
	CB	A:ASP190	4.1	15.3	1.0
	N	A:ASP190	4.2	15.7	1.0
	O2A	A:GGH338	4.3	15.4	1.0
	CA	A:ASP190	4.4	16.1	1.0
	CB	A:ASP192	4.4	17.1	1.0
	O1B	A:GGH338	4.6	18.4	1.0
	CA	A:GLY179	4.7	14.7	1.0
	N	A:MET191	4.7	15.6	1.0
	O2G	A:GGH338	4.7	24.6	1.0
	N	A:SER180	4.8	16.8	1.0
	N	A:ASP192	4.8	16.1	1.0
	C	A:MET191	4.8	16.3	1.0
	OG	A:SER180	5.0	17.2	1.0

Reference:

C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.K.Batra, V.Martinek, Y.Xiang, W.A.Beard, L.C.Pedersen, S.H.Wilson, C.E.Mckenna, J.Florian, A.Warshel, M.F.Goodman. Modifying the Beta,Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of Dna Polymerase Beta. Biochemistry V. 46 461 2007.
ISSN: ISSN 0006-2960
PubMed: 17209556
DOI: 10.1021/BI061517B

Page generated: Wed Aug 14 00:16:09 2024

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