Magnesium in PDB 2fmp: Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site

Enzymatic activity of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site

All present enzymatic activity of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site, PDB code: 2fmp was solved by V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, 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)*	17.18 / 1.65
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.900, 80.400, 55.300, 90.00, 107.50, 90.00
*R / R_free (%)*	17.9 / 21.7

Other elements in 2fmp:

The structure of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site (pdb code 2fmp). 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 Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site, PDB code: 2fmp:

Magnesium binding site 1 out of 1 in 2fmp

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Magnesium Binding Sites List in 2fmp

Magnesium binding site 1 out of 1 in the Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta with A Terminated Gapped Dna Substrate and Ddctp with Sodium in the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1339 b:11.1 occ:1.00	O1G	A:DCT1338	2.0	27.0	0.5
	O2B	A:DCT1338	2.0	11.4	1.0
	OD2	A:ASP192	2.0	13.6	1.0
	OD1	A:ASP190	2.1	12.2	1.0
	O1A	A:DCT1338	2.1	14.8	1.0
	O	A:HOH1409	2.2	12.9	1.0
	O	A:HOH1408	2.2	9.6	0.5
	CG	A:ASP192	3.1	10.8	1.0
	PB	A:DCT1338	3.1	12.5	1.0
	CG	A:ASP190	3.2	16.6	1.0
	PG	A:DCT1338	3.3	22.9	0.5
	PA	A:DCT1338	3.3	13.1	1.0
	NA	A:NA1340	3.4	15.4	1.0
	OD1	A:ASP192	3.5	12.7	1.0
	O3A	A:DCT1338	3.5	11.1	1.0
	O3B	A:DCT1338	3.6	13.9	1.0
	OD2	A:ASP190	3.7	21.5	1.0
	O3G	A:DCT1338	3.9	15.5	0.5
	O	A:ASP190	4.0	13.0	1.0
	C5'	A:DCT1338	4.1	10.3	1.0
	O5'	A:DCT1338	4.2	12.0	1.0
	C	A:ASP190	4.2	11.2	1.0
	O	A:HOH1413	4.3	13.0	1.0
	OG	A:SER180	4.3	13.3	1.0
	O	A:HOH1568	4.4	28.1	1.0
	N	A:ASP190	4.4	10.3	1.0
	CB	A:ASP192	4.4	8.6	1.0
	N	A:SER180	4.4	12.5	1.0
	O2A	A:DCT1338	4.4	13.4	1.0
	CB	A:ASP190	4.4	11.9	1.0
	CA	A:GLY179	4.5	12.0	1.0
	O1B	A:DCT1338	4.5	15.3	1.0
	O2G	A:DCT1338	4.5	41.2	0.5
	CA	A:ASP190	4.6	8.6	1.0
	N	A:ASP192	4.7	9.7	1.0
	O	P:HOH11	4.8	38.4	1.0
	N	A:MET191	4.8	10.4	0.5
	N	A:MET191	4.8	9.7	0.5
	O	A:HOH1407	4.9	10.8	0.5
	C	A:MET191	4.9	10.7	0.5

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson. Magnesium-Induced Assembly of A Complete Dna Polymerase Catalytic Complex. Structure V. 14 757 2006.
ISSN: ISSN 0969-2126
PubMed: 16615916
DOI: 10.1016/J.STR.2006.01.011

Page generated: Mon Dec 14 07:23:14 2020

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