Magnesium in PDB 1nkc: A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp.

Enzymatic activity of A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp.

All present enzymatic activity of A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp.:
2.7.7.7;

Protein crystallography data

The structure of A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp., PDB code: 1nkc was solved by S.J.Johnson, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	26.76 / 1.80
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	87.802, 93.491, 105.475, 90.00, 90.00, 90.00
*R / R_free (%)*	18.6 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp. (pdb code 1nkc). 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 A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp., PDB code: 1nkc:

Magnesium binding site 1 out of 1 in 1nkc

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Magnesium Binding Sites List in 1nkc

Magnesium binding site 1 out of 1 in the A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp.

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Five Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, Dttp, and Datp. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg920 b:26.0 occ:1.00	OD2	A:ASP653	2.7	15.1	1.0
	O	A:TYR654	2.9	12.6	1.0
	OD2	A:ASP830	3.0	14.6	1.0
	O	A:HOH2801	3.0	13.3	1.0
	O	A:HOH2805	3.3	27.3	1.0
	O	A:HOH2807	3.6	10.5	1.0
	CG	A:ASP653	3.6	14.4	1.0
	CB	A:ASP653	3.8	12.6	1.0
	CG	A:ASP830	3.9	14.2	1.0
	C	A:TYR654	4.0	12.4	1.0
	O	A:HOH3069	4.0	22.5	1.0
	OD1	A:ASP830	4.3	12.4	1.0
	O	A:HOH2929	4.5	26.7	1.0
	N	A:TYR654	4.6	10.6	1.0
	CA	A:SER655	4.7	11.2	1.0
	C	A:ASP653	4.7	10.6	1.0
	OD1	A:ASP653	4.8	15.1	1.0
	N	A:SER655	4.8	12.0	1.0
	N	A:GLN656	4.9	10.3	1.0
	CA	A:ASP653	4.9	10.6	1.0

Reference:

S.J.Johnson, L.S.Beese. Structures of Mismatch Replication Errors Observed in A Dna Polymerase. Cell(Cambridge,Mass.) V. 116 803 2004.
ISSN: ISSN 0092-8674
PubMed: 15035983
DOI: 10.1016/S0092-8674(04)00252-1

Page generated: Tue Aug 13 10:05:36 2024

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