Magnesium in PDB 6cr8: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.28 / 2.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.585, 78.601, 55.473, 90.00, 107.14, 90.00
*R / R_free (%)*	19.1 / 24.8

Other elements in 6cr8:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue (pdb code 6cr8). 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 Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue, PDB code: 6cr8:

Magnesium binding site 1 out of 1 in 6cr8

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Magnesium Binding Sites List in 6cr8

Magnesium binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R & S Isomers), Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg402 b:27.6 occ:1.00	O1A	A:VA4401	1.9	19.6	1.0
	OD1	A:ASP190	2.0	30.2	1.0
	O1B	A:VA4401	2.1	22.1	1.0
	OD2	A:ASP192	2.1	20.0	1.0
	O1G	A:VA4401	2.1	27.6	1.0
	O	A:HOH594	2.4	24.6	1.0
	CG	A:ASP190	3.0	28.5	1.0
	PA	A:VA4401	3.0	33.0	1.0
	PB	A:VA4401	3.0	28.1	1.0
	CG	A:ASP192	3.2	24.6	1.0
	O3A	A:VA4401	3.3	27.2	1.0
	OD2	A:ASP190	3.4	36.4	1.0
	PG	A:VA4401	3.4	36.2	1.0
	OD1	A:ASP192	3.5	28.6	1.0
	C3B	A:VA4401	3.8	31.5	1.0
	C5'	A:VA4401	3.8	20.3	1.0
	NA	A:NA405	3.9	47.0	1.0
	O3G	A:VA4401	3.9	30.0	1.0
	O5'	A:VA4401	3.9	20.6	1.0
	O	A:HOH644	4.1	37.1	1.0
	O2A	A:VA4401	4.1	23.4	1.0
	O	A:ASP190	4.3	21.4	1.0
	CB	A:ASP190	4.3	21.3	1.0
	N	A:ASP190	4.3	22.4	1.0
	O2B	A:VA4401	4.4	24.0	1.0
	CA	A:GLY179	4.4	20.2	1.0
	C	A:ASP190	4.5	25.5	1.0
	CB	A:ASP192	4.5	21.7	1.0
	CA	A:ASP190	4.6	25.1	1.0
	O2G	A:VA4401	4.6	38.0	1.0
	N	A:SER180	4.7	22.6	1.0
	O	A:HOH604	4.7	19.8	1.0
	OG	A:SER180	4.8	26.8	1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418

Page generated: Mon Sep 30 22:41:52 2024

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