Magnesium in PDB 1kfs: Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex

Enzymatic activity of Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex

All present enzymatic activity of Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex, PDB code: 1kfs was solved by C.A.Brautigam, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 2.10
*Space group*	P 4₃
*Cell size a, b, c (Å), α, β, γ (°)*	101.700, 101.700, 85.800, 90.00, 90.00, 90.00
*R / R_free (%)*	19.5 / 21.9

Other elements in 1kfs:

The structure of Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex (pdb code 1kfs). 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 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex, PDB code: 1kfs:

Magnesium binding site 1 out of 1 in 1kfs

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Magnesium Binding Sites List in 1kfs

Magnesium binding site 1 out of 1 in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg2 b:36.9 occ:1.00	O	A:HOH4	1.9	18.8	1.0
	O	A:HOH292	2.1	40.9	1.0
	OD1	A:ASP355	2.2	34.6	1.0
	OP1	B:DG1007	2.3	23.0	1.0
	O	A:HOH171	2.5	35.9	1.0
	O3'	B:DC1006	2.6	23.6	1.0
	P	B:DG1007	3.1	18.6	1.0
	CG	A:ASP355	3.2	23.4	1.0
	OD2	A:ASP355	3.5	19.6	1.0
	ZN	A:ZN1	3.8	21.8	1.0
	C3'	B:DC1006	3.8	31.9	1.0
	OD1	A:ASP424	3.8	16.7	1.0
	C4'	B:DC1006	3.9	35.4	1.0
	O	A:THR356	4.0	16.3	1.0
	C5'	B:DG1007	4.0	14.2	1.0
	OD2	A:ASP424	4.1	17.6	1.0
	O5'	B:DG1007	4.1	19.5	1.0
	O	A:HOH18	4.2	20.0	1.0
	O	A:GLN419	4.2	19.0	1.0
	OP2	B:DG1007	4.3	19.3	1.0
	C5'	B:DC1006	4.3	32.9	1.0
	CG	A:ASP424	4.4	15.2	1.0
	C2'	B:DC1006	4.5	33.5	1.0
	O	A:HOH165	4.5	37.2	1.0
	CB	A:ASP355	4.6	21.1	1.0
	N	A:THR356	4.7	20.5	1.0
	CD2	A:TYR423	4.8	16.8	1.0
	OD2	A:ASP501	4.9	20.9	1.0
	CA	A:ASP355	5.0	17.6	1.0

Reference:

C.A.Brautigam, T.A.Steitz. Structural Principles For the Inhibition of the 3'-5' Exonuclease Activity of Escherichia Coli Dna Polymerase I By Phosphorothioates. J.Mol.Biol. V. 277 363 1998.
ISSN: ISSN 0022-2836
PubMed: 9514742
DOI: 10.1006/JMBI.1997.1586

Page generated: Sun Aug 10 00:08:40 2025

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