Magnesium in PDB 6vf2: Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min), PDB code: 6vf2 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)*	34.98 / 1.60
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.278, 62.297, 118.573, 90, 90, 90
*R / R_free (%)*	16.8 / 19.3

Other elements in 6vf2:

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) (pdb code 6vf2). 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:at Product State Ternary Complex, 50 Mm MG2+ (960 Min), PDB code: 6vf2:

Magnesium binding site 1 out of 1 in 6vf2

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Magnesium Binding Sites List in 6vf2

Magnesium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 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:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg509 b:20.4 occ:0.58	OD1	A:ASP332	1.9	33.7	1.0
	OD2	A:ASP418	1.9	28.7	1.0
	OP1	P:8GM5	2.1	34.4	1.0
	OD2	A:ASP330	2.1	57.1	1.0
	CG	A:ASP332	2.8	28.3	1.0
	CG	A:ASP330	2.9	43.3	1.0
	CG	A:ASP418	2.9	23.8	1.0
	OD2	A:ASP332	3.0	36.2	1.0
	P	P:8GM5	3.2	35.1	0.6
	O3'	P:DA4	3.3	44.5	1.0
	OD1	A:ASP330	3.3	40.2	1.0
	NA	A:NA503	3.5	35.2	0.5
	CB	A:ASP418	3.7	18.1	1.0
	OD1	A:ASP418	3.9	23.2	1.0
	CB	A:ASP330	4.0	26.7	1.0
	C5'	P:DA4	4.0	25.5	1.0
	C4'	P:DA4	4.1	34.6	1.0
	CB	A:ASP332	4.1	18.9	1.0
	OP2	P:8GM5	4.2	45.9	0.8
	C3'	P:DA4	4.3	42.5	1.0
	O5'	P:8GM5	4.3	36.6	0.3
	O	A:VAL331	4.4	21.0	1.0
	NH2	A:ARG416	4.5	21.2	1.0
	C	A:VAL331	4.6	18.6	1.0
	N	A:ASP418	4.6	17.4	1.0
	CA	A:ASP332	4.6	16.7	1.0
	C5'	P:8GM5	4.6	41.2	1.0
	N	A:ASP332	4.7	16.8	1.0
	CA	A:ASP418	4.8	16.2	1.0
	N	A:VAL331	4.8	20.1	1.0
	CZ3	A:TRP434	5.0	24.3	1.0
	C	A:ASP330	5.0	25.2	1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) To Be Published.

Page generated: Tue Oct 1 22:02:45 2024

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