Magnesium in PDB 1zjn: Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp

Enzymatic activity of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp, PDB code: 1zjn was solved by V.K.Batra, W.A.Beard, D.D.Shock, 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)*	30.39 / 2.61
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	49.100, 79.500, 55.100, 90.00, 106.20, 90.00
*R / R_free (%)*	22.8 / 23.4

Other elements in 1zjn:

The structure of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp (pdb code 1zjn). 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 Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp, PDB code: 1zjn:

Magnesium binding site 1 out of 1 in 1zjn

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Magnesium Binding Sites List in 1zjn

Magnesium binding site 1 out of 1 in the Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Complexed with Dna Containing An A-A Mismatched Primer Terminus with Dgtp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg339 b:46.5 occ:1.00	O2B	A:DGT338	2.0	31.0	1.0
	O	A:HOH377	2.1	48.7	1.0
	O1G	A:DGT338	2.1	45.0	1.0
	O1A	A:DGT338	2.1	28.6	1.0
	OD1	A:ASP190	2.2	35.9	1.0
	OD2	A:ASP192	2.4	38.6	1.0
	CG	A:ASP190	3.2	35.4	1.0
	PB	A:DGT338	3.2	36.0	1.0
	CG	A:ASP192	3.4	34.5	1.0
	PA	A:DGT338	3.4	31.1	1.0
	PG	A:DGT338	3.4	46.3	1.0
	OD2	A:ASP190	3.6	35.5	1.0
	O3B	A:DGT338	3.7	40.4	1.0
	O3A	A:DGT338	3.7	35.4	1.0
	OD1	A:ASP192	3.8	35.8	1.0
	O5'	A:DGT338	4.0	38.0	1.0
	O	A:ASP190	4.0	33.2	1.0
	NA	A:NA340	4.1	37.0	1.0
	C	A:ASP190	4.2	32.4	1.0
	N	A:ASP190	4.3	34.1	1.0
	O3G	A:DGT338	4.3	45.0	1.0
	N	A:SER180	4.3	36.0	1.0
	CA	A:GLY179	4.3	34.5	1.0
	O	A:HOH349	4.4	29.6	1.0
	CB	A:ASP190	4.4	34.2	1.0
	C5'	A:DGT338	4.5	38.6	1.0
	O2G	A:DGT338	4.5	46.0	1.0
	OG	A:SER180	4.5	36.3	1.0
	CB	A:ASP192	4.6	32.4	1.0
	CA	A:ASP190	4.6	33.0	1.0
	O1B	A:DGT338	4.6	34.2	1.0
	O2A	A:DGT338	4.6	33.2	1.0
	N	A:MET191	4.7	31.1	1.0
	N	A:ASP192	4.7	32.0	1.0
	C	A:GLY179	4.9	35.5	1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Nucleotide-Induced Dna Polymerase Active Site Motions Accommodating A Mutagenic Dna Intermediate. Structure V. 13 1225 2005.
ISSN: ISSN 0969-2126
PubMed: 16084394
DOI: 10.1016/J.STR.2005.05.010

Page generated: Tue Aug 13 20:10:15 2024

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