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

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

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

Protein crystallography data

The structure of A Bacillus Dna Polymerase I Product Complex Bound to A Guanine-Thymine Mismatch After Three Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, and Dttp., PDB code: 1nkb 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)*	33.84 / 2.00
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	88.239, 93.698, 105.444, 90.00, 90.00, 90.00
*R / R_free (%)*	20.5 / 24.4

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 Three Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, and Dttp. (pdb code 1nkb). 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 Three Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, and Dttp., PDB code: 1nkb:

Magnesium binding site 1 out of 1 in 1nkb

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Magnesium Binding Sites List in 1nkb

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

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 Three Rounds of Primer Extension, Following Incorporation of Dctp, Dgtp, and Dttp. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg950 b:30.8 occ:1.00	O	A:TYR654	2.7	17.2	1.0
	OD2	A:ASP653	2.8	24.5	1.0
	OD2	A:ASP830	2.9	19.8	1.0
	O	A:HOH2511	2.9	29.5	1.0
	O	A:HOH2771	3.3	30.4	1.0
	CG	A:ASP653	3.8	24.7	1.0
	O	A:HOH2510	3.8	23.8	1.0
	CG	A:ASP830	3.9	21.0	1.0
	C	A:TYR654	3.9	19.1	1.0
	O	A:HOH2790	3.9	31.5	1.0
	CB	A:ASP653	3.9	22.8	1.0
	OD1	A:ASP830	4.2	20.4	1.0
	O	A:HOH2563	4.4	34.1	1.0
	CA	A:SER655	4.5	20.4	1.0
	N	A:TYR654	4.6	19.2	1.0
	N	A:SER655	4.7	18.5	1.0
	C	A:ASP653	4.7	20.4	1.0
	N	A:GLN656	4.8	20.0	1.0
	CA	A:TYR654	4.9	18.1	1.0
	OD1	A:ASP653	4.9	24.4	1.0
	CA	A:ASP653	5.0	21.0	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: Sun Aug 10 01:46:43 2025

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