Magnesium in PDB 6vf9: Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min), PDB code: 6vf9 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.93 / 1.56
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.2, 62.13, 118.533, 90, 90, 90
*R / R_free (%)*	16.5 / 18.2

Other elements in 6vf9:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) (pdb code 6vf9). 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 Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min), PDB code: 6vf9:

Magnesium binding site 1 out of 1 in 6vf9

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Magnesium Binding Sites List in 6vf9

Magnesium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg505 b:26.2 occ:0.74	O	P:HOH101	1.9	33.7	1.0
	OD2	A:ASP418	1.9	28.4	1.0
	OD1	A:ASP332	2.0	37.7	1.0
	OD2	A:ASP330	2.1	42.8	1.0
	CG	A:ASP332	2.8	28.4	1.0
	OD2	A:ASP332	2.9	35.3	1.0
	CG	A:ASP330	3.0	36.9	1.0
	CG	A:ASP418	3.0	23.5	1.0
	NA	A:NA507	3.5	33.2	0.7
	OD1	A:ASP330	3.5	35.0	1.0
	O3'	P:DA4	3.5	35.9	1.0
	C5'	P:DA4	3.6	24.6	1.0
	CB	A:ASP418	3.8	17.2	1.0
	C4'	P:DA4	3.9	24.3	1.0
	OD1	A:ASP418	3.9	23.3	1.0
	CB	A:ASP330	4.1	27.8	1.0
	CB	A:ASP332	4.2	16.6	1.0
	C3'	P:DA4	4.3	30.3	1.0
	NH2	A:ARG416	4.5	18.5	1.0
	O	A:VAL331	4.6	20.5	1.0
	CA	A:ASP332	4.8	14.9	1.0
	C	A:VAL331	4.8	18.6	1.0
	O5'	P:DA4	4.8	21.6	1.0
	OP1	P:DA4	4.8	22.7	1.0
	N	A:ASP332	4.9	16.0	1.0
	N	A:ASP418	4.9	16.6	1.0
	CA	A:ASP418	5.0	15.6	1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) To Be Published.

Page generated: Tue Oct 1 22:03:27 2024

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