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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene 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- Monofluoromethylene Triphosphate, PDB code: 2pxi was solved by C.E.Mckenna, V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.09 / 2.10
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.600, 80.200, 55.400, 90.00, 107.80, 90.00
*R / R_free (%)*	20.6 / 27

Other elements in 2pxi:

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

Fluorine	(F)	1 atom
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- Monofluoromethylene Triphosphate (pdb code 2pxi). 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- Monofluoromethylene Triphosphate, PDB code: 2pxi:

Magnesium binding site 1 out of 1 in 2pxi

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Magnesium Binding Sites List in 2pxi

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- Monofluoromethylene 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- Monofluoromethylene Triphosphate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg339 b:18.2 occ:1.00	O1A	A:GFH338	1.9	16.2	1.0
	OD1	A:ASP190	2.0	20.9	1.0
	O1G	A:GFH338	2.1	22.2	1.0
	O	A:HOH348	2.1	19.1	1.0
	O2B	A:GFH338	2.2	15.5	1.0
	OD2	A:ASP192	2.2	16.7	1.0
	CG	A:ASP190	2.9	22.0	1.0
	CG	A:ASP192	3.1	17.5	1.0
	OD2	A:ASP190	3.2	24.8	1.0
	PA	A:GFH338	3.2	22.6	1.0
	PB	A:GFH338	3.3	16.9	1.0
	PG	A:GFH338	3.3	26.9	1.0
	OD1	A:ASP192	3.4	20.5	1.0
	NA	A:NA340	3.4	26.4	1.0
	O3A	A:GFH338	3.5	17.7	1.0
	O3G	A:GFH338	3.6	22.7	1.0
	C3B	A:GFH338	3.9	21.6	1.0
	O	A:ASP190	4.0	21.4	1.0
	O5'	A:GFH338	4.2	19.4	1.0
	C5'	A:GFH338	4.2	20.7	1.0
	O	A:HOH400	4.2	36.5	1.0
	C	A:ASP190	4.2	19.2	1.0
	CB	A:ASP190	4.2	17.1	1.0
	O	A:HOH365	4.2	17.9	1.0
	N	A:ASP190	4.3	18.2	1.0
	O2A	A:GFH338	4.3	20.5	1.0
	CB	A:ASP192	4.5	20.8	1.0
	CA	A:ASP190	4.5	18.2	1.0
	O2G	A:GFH338	4.6	27.3	1.0
	O1B	A:GFH338	4.6	21.3	1.0
	CA	A:GLY179	4.7	19.7	1.0
	N	A:MET191	4.7	18.7	1.0
	N	A:ASP192	4.8	21.1	1.0
	N	A:SER180	4.9	20.5	1.0
	C	A:MET191	4.9	21.1	1.0
	F3B	A:GFH338	5.0	23.0	1.0

Reference:

C.E.Mckenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson. (R)-Beta,Gamma-Fluoromethylene-Dgtp-Dna Ternary Complex with Dna Polymerase Beta. J.Am.Chem.Soc. V. 129 15412 2007.
ISSN: ISSN 0002-7863
PubMed: 18031037
DOI: 10.1021/JA072127V

Page generated: Wed Aug 14 02:19:34 2024

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