Zinc in PDB 2kzz: Klenow Fragment with Normal Substrate and Zinc Only

All present enzymatic activity of Klenow Fragment with Normal Substrate and Zinc Only:
2.7.7.7;

The structure of Klenow Fragment with Normal Substrate and Zinc Only, PDB code: 2kzz was solved by C.A.Brautigam, S.Sun, J.A.Piccirilli, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.25
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	101.700, 101.700, 85.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 25.1

The binding sites of Zinc atom in the Klenow Fragment with Normal Substrate and Zinc Only (pdb code 2kzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Klenow Fragment with Normal Substrate and Zinc Only, PDB code: 2kzz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Klenow Fragment with Normal Substrate and Zinc Only


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Klenow Fragment with Normal Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:77.5 occ:1.00 O3' B:DC1006 2.5 31.3 1.0 OP1 B:DG1007 2.6 33.2 1.0 OD1 A:ASP355 2.6 43.1 1.0 P B:DG1007 3.1 24.1 1.0 C3' B:DC1006 3.5 37.5 1.0 CG A:ASP355 3.6 32.5 1.0 C4' B:DC1006 3.6 38.2 1.0 OD2 A:ASP424 3.7 23.7 1.0 OD2 A:ASP355 3.8 24.2 1.0 OD1 A:ASP424 3.8 23.2 1.0 O A:THR356 3.8 25.7 1.0 C5' B:DG1007 3.9 24.5 1.0 O5' B:DG1007 3.9 27.6 1.0 ZN A:ZN1 3.9 26.6 1.0 C2' B:DC1006 4.0 38.0 1.0 CG A:ASP424 4.2 20.9 1.0 C5' B:DC1006 4.3 40.3 1.0 OP2 B:DG1007 4.3 25.4 1.0 O A:GLN419 4.3 23.5 1.0 O A:HOH71 4.4 29.5 1.0 CD2 A:TYR423 4.6 18.3 1.0 N A:THR356 4.6 30.2 1.0 O4' B:DC1006 4.8 35.8 1.0 CB A:ASP355 4.9 31.2 1.0 C A:THR356 4.9 24.0 1.0 OD2 A:ASP501 5.0 25.2 1.0 CE2 A:TYR423 5.0 21.8 1.0

Zinc binding site 2 out of 3 in the Klenow Fragment with Normal Substrate and Zinc Only


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Klenow Fragment with Normal Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:26.6 occ:1.00 OD2 A:ASP501 1.9 25.2 1.0 OD2 A:ASP355 2.0 24.2 1.0 OE2 A:GLU357 2.0 19.1 1.0 OP1 B:DG1007 2.0 33.2 1.0 CG A:ASP501 3.0 24.2 1.0 CD A:GLU357 3.0 24.6 1.0 CG A:ASP355 3.1 32.5 1.0 OE1 A:GLU357 3.3 26.9 1.0 P B:DG1007 3.3 24.1 1.0 CB A:ASP501 3.4 20.8 1.0 OD1 A:ASP355 3.6 43.1 1.0 OP2 B:DG1007 3.7 25.4 1.0 CE2 A:TYR497 3.7 19.6 1.0 ZN B:ZN2 3.9 77.5 1.0 OD1 A:ASP501 4.1 26.1 1.0 O A:THR356 4.1 25.7 1.0 O5' B:DG1007 4.2 27.6 1.0 CD2 A:TYR497 4.3 18.8 1.0 CG A:GLU357 4.3 23.4 1.0 O3' B:DC1006 4.3 31.3 1.0 CB A:ASP355 4.4 31.2 1.0 CA A:ALA498 4.5 18.5 1.0 O A:HOH34 4.5 50.5 1.0 CZ A:TYR497 4.5 20.9 1.0 C5' B:DG1007 4.6 24.5 1.0 O A:ALA498 4.7 28.8 1.0 OH A:TYR497 4.7 25.1 1.0 O A:TYR497 5.0 19.9 1.0 CA A:ASP501 5.0 20.4 1.0

Zinc binding site 3 out of 3 in the Klenow Fragment with Normal Substrate and Zinc Only


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Klenow Fragment with Normal Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:0.0 occ:1.00 O A:HOH170 2.5 39.5 1.0 CD2 A:LEU825 2.8 55.9 1.0 O A:TYR824 3.0 38.8 1.0 CG A:LEU825 3.3 51.4 1.0 CD2 A:LEU823 3.3 28.1 1.0 CG A:LEU823 3.5 31.4 1.0 CA A:LEU825 3.5 47.2 1.0 C A:TYR824 3.7 40.5 1.0 CD1 A:LEU823 3.8 29.2 1.0 CB A:LEU825 3.9 48.2 1.0 N A:LEU825 3.9 41.2 1.0 CB A:ALA842 4.1 42.3 1.0 CD A:PRO826 4.4 53.8 1.0 CD1 A:LEU825 4.6 54.4 1.0 N A:TYR824 4.8 38.3 1.0 C A:LEU825 4.8 49.5 1.0 C A:LEU823 4.9 37.4 1.0 CA A:TYR824 4.9 40.2 1.0 CB A:LEU823 4.9 32.1 1.0 O A:LEU823 5.0 38.9 1.0

C.A.Brautigam, S.Sun, J.A.Piccirilli, T.A.Steitz. Structures of Normal Single-Stranded Dna and Deoxyribo-3'-S-Phosphorothiolates Bound to the 3'-5' Exonucleolytic Active Site of Dna Polymerase I From Escherichia Coli. Biochemistry V. 38 696 1999.
ISSN: ISSN 0006-2960
PubMed: 9888810
DOI: 10.1021/BI981537G