Magnesium in PDB 1lv5: Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp

Enzymatic activity of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp

All present enzymatic activity of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp, PDB code: 1lv5 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)*	39.70 / 1.95
*Space group*	P 3₁
*Cell size a, b, c (Å), α, β, γ (°)*	91.681, 91.681, 190.116, 90.00, 90.00, 120.00
*R / R_free (%)*	21.8 / 26.1

Other elements in 1lv5:

The structure of Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp (pdb code 1lv5). 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 the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp, PDB code: 1lv5:

Magnesium binding site 1 out of 1 in 1lv5

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Magnesium Binding Sites List in 1lv5

Magnesium binding site 1 out of 1 in the Crystal Structure of the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp

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 the Closed Conformation of Bacillus Dna Polymerase I Fragment Bound to Dna and Dctp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg205 b:34.5 occ:1.00	OD1	A:ASP830	2.7	22.2	1.0
	O2A	A:DCP201	2.7	30.1	1.0
	OD2	A:ASP653	2.9	36.3	1.0
	MN	A:MN1	3.5	40.6	1.0
	C3'	C:DA29	3.6	32.5	1.0
	PA	A:DCP201	3.6	28.8	1.0
	CG	A:ASP830	3.9	23.2	1.0
	O1A	A:DCP201	3.9	29.0	1.0
	CG	A:ASP653	3.9	36.1	1.0
	C4'	C:DA29	4.1	32.9	1.0
	O5'	A:DCP201	4.1	29.3	1.0
	C5'	C:DA29	4.1	30.9	1.0
	CB	A:GLU831	4.3	32.1	1.0
	O	A:VAL828	4.4	28.4	1.0
	OD1	A:ASP653	4.4	36.4	1.0
	OD2	A:ASP830	4.4	23.9	1.0
	C5'	A:DCP201	4.5	27.1	1.0
	OP1	C:DA29	4.6	32.4	1.0
	O	A:ASP830	4.7	25.2	1.0
	C	A:ASP830	4.8	26.4	1.0
	O5'	C:DA29	4.8	31.5	1.0
	O2G	A:DCP201	4.8	33.2	1.0
	C2'	C:DA29	4.8	34.3	1.0
	O2B	A:DCP201	4.9	33.0	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: Tue Aug 13 08:35:10 2024

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