Magnesium in PDB 1l3s: Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna.

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna.

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna.:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna., PDB code: 1l3s was solved by S.J.Johnson, J.S.Taylor, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 1.70
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	86.289, 93.254, 106.292, 90.00, 90.00, 90.00
*R / R_free (%)*	19.7 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna. (pdb code 1l3s). 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 Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna., PDB code: 1l3s:

Magnesium binding site 1 out of 1 in 1l3s

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Magnesium Binding Sites List in 1l3s

Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna.

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bacillus Dna Polymerase I Fragment Complexed to 9 Base Pairs of Duplex Dna. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg920 b:27.9 occ:1.00	OD1	A:ASP653	2.7	17.0	1.0
	O	A:TYR654	2.9	13.2	1.0
	O	A:HOH2525	3.0	17.3	1.0
	OD2	A:ASP830	3.1	16.4	1.0
	O	A:HOH2934	3.3	25.9	1.0
	CG	A:ASP653	3.7	15.9	1.0
	O	A:HOH2860	3.8	24.9	1.0
	O	A:HOH2512	3.8	12.2	1.0
	CB	A:ASP653	3.9	14.8	1.0
	CG	A:ASP830	4.0	15.7	1.0
	C	A:TYR654	4.0	13.3	1.0
	O	A:HOH2845	4.0	25.8	1.0
	OD1	A:ASP830	4.3	15.7	1.0
	O	A:HOH2977	4.4	36.2	1.0
	O	B:HOH2707	4.4	31.9	1.0
	N	A:TYR654	4.6	12.8	1.0
	CA	A:SER655	4.7	13.9	1.0
	C	A:ASP653	4.7	13.5	1.0
	OD2	A:ASP653	4.8	16.7	1.0
	O	A:HOH2645	4.8	34.4	1.0
	N	A:SER655	4.8	13.4	1.0
	CA	A:ASP653	5.0	13.9	1.0
	CA	A:TYR654	5.0	13.0	1.0

Reference:

S.J.Johnson, J.S.Taylor, L.S.Beese. Processive Dna Synthesis Observed in A Polymerase Crystal Suggests A Mechanism For the Prevention of Frameshift Mutations Proc.Natl.Acad.Sci.Usa V. 100 3895 2003.
ISSN: ISSN 0027-8424
PubMed: 12649320
DOI: 10.1073/PNAS.0630532100

Page generated: Sun Aug 10 00:37:34 2025

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