Magnesium in PDB 1l3v: Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues.

Enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues.

All present enzymatic activity of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues.:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues., PDB code: 1l3v 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)*	32.43 / 1.71
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	88.072, 93.378, 104.919, 90.00, 90.00, 90.00
*R / R_free (%)*	20.6 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues. (pdb code 1l3v). 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 Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues., PDB code: 1l3v:

Magnesium binding site 1 out of 1 in 1l3v

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Magnesium Binding Sites List in 1l3v

Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Dna Polymerase I Fragment Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues.

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 Product Complex with 15 Base Pairs of Duplex Dna Following Addition of Dttp, Datp, Dctp, and Dgtp Residues. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg920 b:31.3 occ:1.00	OD2	A:ASP830	2.8	20.2	1.0
	OD1	A:ASP653	2.8	18.6	1.0
	O	A:TYR654	2.9	14.9	1.0
	O	A:HOH2541	3.0	37.5	1.0
	O	A:HOH2525	3.1	22.2	1.0
	CG	A:ASP653	3.7	18.2	1.0
	CG	A:ASP830	3.7	18.8	1.0
	O	A:HOH2512	3.8	17.6	1.0
	CB	A:ASP653	3.8	16.4	1.0
	O	A:HOH2660	3.9	29.8	1.0
	OD1	A:ASP830	4.0	19.4	1.0
	C	A:TYR654	4.1	14.7	1.0
	O	A:HOH2814	4.2	27.8	1.0
	O	A:HOH2645	4.4	35.0	1.0
	N	A:TYR654	4.6	14.7	1.0
	C	A:ASP653	4.7	15.0	1.0
	OD2	A:ASP653	4.8	18.5	1.0
	CA	A:SER655	4.8	14.5	1.0
	CA	A:ASP653	4.9	15.3	1.0
	N	A:SER655	4.9	14.3	1.0
	CB	A:ASP830	5.0	18.0	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 00:37:49 2025

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