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Zinc in PDB 1ksp: 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: 1ksp 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 / 2.30
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 101.560, 101.560, 85.250, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex (pdb code 1ksp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex, PDB code: 1ksp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ksp

Go back to Zinc Binding Sites List in 1ksp
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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
A:Zn320

b:0.0
occ:1.00
OD2 A:ASP882 1.9 37.8 1.0
OE2 A:GLU710 2.5 64.7 1.0
OE1 A:GLU710 2.6 57.8 1.0
CG A:ASP882 2.7 28.6 1.0
CD A:GLU710 2.7 57.1 1.0
OD1 A:ASP882 2.9 35.8 1.0
O A:HOH70 3.5 41.7 1.0
NH2 A:ARG668 3.9 34.4 1.0
CB A:ASP882 4.0 25.7 1.0
CG A:GLU710 4.1 49.0 1.0
CG2 A:ILE709 4.3 23.8 1.0
N A:ASP882 4.7 23.6 1.0
CZ A:ARG668 4.7 33.5 1.0
O A:HOH36 4.7 34.8 1.0
NH1 A:ARG668 4.8 33.3 1.0
O A:HOH34 4.9 68.6 1.0
O A:HOH123 4.9 57.6 1.0
CA A:ASP882 4.9 24.5 1.0

Zinc binding site 2 out of 2 in 1ksp

Go back to Zinc Binding Sites List in 1ksp
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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
A:Zn3

b:74.4
occ:1.00
OE2 A:GLU905 1.9 55.9 1.0
NE2 A:HIS901 2.1 49.7 1.0
CD A:GLU905 2.8 48.5 1.0
CE1 A:HIS901 3.0 45.0 1.0
CD2 A:HIS901 3.1 42.0 1.0
OE1 A:GLU905 3.3 44.3 1.0
CG A:GLU905 3.8 46.0 1.0
ND1 A:HIS901 4.2 41.8 1.0
CG A:HIS901 4.2 38.2 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: Wed Dec 16 02:55:38 2020

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