Zinc in PDB 1kfs: 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;

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 / Rfree (%)	19.5 / 21.9

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex, PDB code: 1kfs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 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:Zn1 b:21.8 occ:1.00 OD2 A:ASP501 1.9 20.9 1.0 OD2 A:ASP355 1.9 19.6 1.0 OE2 A:GLU357 2.0 17.7 1.0 OP1 B:DG1007 2.2 23.0 1.0 CD A:GLU357 3.0 15.5 1.0 CG A:ASP501 3.0 17.2 1.0 CG A:ASP355 3.0 23.4 1.0 P B:DG1007 3.3 18.6 1.0 OE1 A:GLU357 3.4 23.6 1.0 CB A:ASP501 3.5 15.2 1.0 OD1 A:ASP355 3.5 34.6 1.0 OP2 B:DG1007 3.7 19.3 1.0 MG B:MG2 3.8 36.9 1.0 CE2 A:TYR497 3.8 14.1 1.0 O A:THR356 4.1 16.3 1.0 OD1 A:ASP501 4.1 18.2 1.0 O5' B:DG1007 4.1 19.5 1.0 CG A:GLU357 4.2 17.4 1.0 CB A:ASP355 4.3 21.1 1.0 O3' B:DC1006 4.4 23.6 1.0 O A:HOH4 4.4 18.8 1.0 CD2 A:TYR497 4.4 17.9 1.0 O A:HOH168 4.5 25.2 1.0 C5' B:DG1007 4.5 14.2 1.0 CA A:ALA498 4.5 11.8 1.0 CZ A:TYR497 4.6 17.8 1.0 O A:HOH292 4.7 40.9 1.0 O A:ALA498 4.7 15.2 1.0 OH A:TYR497 4.7 18.7 1.0 C A:THR356 5.0 19.2 1.0 O A:TYR497 5.0 16.1 1.0

Zinc binding site 2 out of 3 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:66.9 occ:1.00 OE2 A:GLU905 2.0 46.0 1.0 O A:HOH294 2.2 60.1 1.0 NE2 A:HIS901 2.5 43.4 1.0 CD A:GLU905 2.8 44.5 1.0 OE1 A:GLU905 3.2 41.3 1.0 CD2 A:HIS901 3.2 40.5 1.0 CE1 A:HIS901 3.6 42.1 1.0 CG A:GLU905 4.0 41.8 1.0 CG A:HIS901 4.5 37.4 1.0 ND1 A:HIS901 4.6 41.5 1.0

Zinc binding site 3 out of 3 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 3 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:99.7 occ:1.00 OD2 A:ASP882 2.1 35.4 1.0 CG A:ASP882 2.9 30.3 1.0 OD1 A:ASP882 3.1 28.1 1.0 NH2 A:ARG668 3.5 47.2 1.0 O A:HOH206 3.7 43.2 1.0 CG A:GLU710 4.1 45.5 1.0 CG2 A:ILE709 4.3 18.3 1.0 CB A:ASP882 4.3 22.3 1.0 CD A:GLU710 4.3 56.4 1.0 OE2 A:GLU710 4.4 61.6 1.0 CZ A:ARG668 4.4 44.9 1.0 CB A:GLU710 4.7 33.8 1.0 NH1 A:ARG668 4.8 41.7 1.0 N A:ASP882 4.9 24.3 1.0 N A:GLU710 5.0 27.7 1.0

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