Zinc in PDB 1krp: 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: 1krp 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 / 2.20
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	101.600, 101.600, 85.200, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 25.5

The binding sites of Zinc atom in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex (pdb code 1krp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Mutant/Dna Complex, PDB code: 1krp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 B:Zn2 b:46.0 occ:1.00 OP1 B:PST1003 2.0 33.5 1.0 O A:HOH51 2.1 32.7 1.0 O A:HOH79 2.2 35.1 1.0 OD1 A:ASP355 2.3 34.8 1.0 O A:HOH48 2.3 42.7 1.0 O3' B:DT1002 2.8 31.6 1.0 P B:PST1003 3.1 29.1 1.0 CG A:ASP355 3.2 27.3 1.0 OD2 A:ASP355 3.4 34.2 1.0 OD1 A:ASP424 3.8 22.2 1.0 ZN A:ZN1 3.9 61.0 1.0 O A:THR356 4.0 20.3 1.0 O A:GLN419 4.0 26.8 1.0 O A:HOH63 4.0 26.9 1.0 C3' B:DT1002 4.0 30.2 1.0 OD2 A:ASP424 4.0 27.9 1.0 C5' B:PST1003 4.1 27.1 1.0 C4' B:DT1002 4.1 34.5 1.0 O5' B:PST1003 4.1 32.1 1.0 CG A:ASP424 4.3 22.3 1.0 O A:HOH140 4.5 42.4 1.0 SP B:PST1003 4.5 36.0 1.0 CB A:ASP355 4.6 26.4 1.0 C5' B:DT1002 4.6 31.9 1.0 N A:THR356 4.6 26.6 1.0 CD2 A:TYR423 4.8 22.3 1.0 C2' B:DT1002 4.8 30.1 1.0

Zinc binding site 2 out of 4 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:Zn1 b:61.0 occ:1.00 OD2 A:ASP355 2.3 34.2 1.0 OE2 A:GLU357 2.5 39.9 1.0 OD2 A:ASP501 2.5 37.6 1.0 OP1 B:PST1003 2.7 33.5 1.0 CD A:GLU357 3.4 33.6 1.0 CG A:ASP355 3.4 27.3 1.0 O B:HOH249 3.5 49.9 1.0 CG A:ASP501 3.5 34.7 1.0 CB A:ASP501 3.7 26.9 1.0 P B:PST1003 3.7 29.1 1.0 OE1 A:GLU357 3.7 31.9 1.0 CE1 A:TYR497 3.8 23.5 1.0 ZN B:ZN2 3.9 46.0 1.0 OD1 A:ASP355 4.0 34.8 1.0 SP B:PST1003 4.3 36.0 1.0 O A:THR356 4.3 20.3 1.0 O A:HOH48 4.3 42.7 1.0 OH A:TYR497 4.4 29.5 1.0 O5' B:PST1003 4.4 32.1 1.0 CZ A:TYR497 4.4 26.1 1.0 CD1 A:TYR497 4.6 20.6 1.0 OD1 A:ASP501 4.6 34.5 1.0 O A:HOH33 4.6 34.9 1.0 CB A:ASP355 4.6 26.4 1.0 CG A:GLU357 4.7 30.5 1.0 CA A:ALA498 4.7 18.7 1.0 O A:HOH51 4.7 32.7 1.0 O A:ALA498 4.8 25.3 1.0 O A:HOH140 4.8 42.4 1.0 C5' B:PST1003 4.9 27.1 1.0 O3' B:DT1002 5.0 31.6 1.0

Zinc binding site 3 out of 4 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:0.0 occ:1.00 OD2 A:ASP882 2.3 33.1 1.0 CG A:GLU710 3.2 56.1 1.0 CG A:ASP882 3.2 33.5 1.0 NH2 A:ARG668 3.4 39.1 1.0 OD1 A:ASP882 3.4 34.9 1.0 O A:HOH65 3.7 38.7 1.0 CD A:GLU710 3.8 70.3 1.0 CB A:GLU710 3.9 39.5 1.0 CG2 A:ILE709 4.0 25.1 1.0 OE2 A:GLU710 4.0 68.0 1.0 O A:HOH83 4.1 52.8 1.0 N A:GLU710 4.2 33.5 1.0 CZ A:ARG668 4.5 36.4 1.0 CB A:ASP882 4.6 27.4 1.0 OE1 A:GLU710 4.7 81.0 1.0 CA A:GLU710 4.7 35.0 1.0 O A:HOH34 4.8 41.8 1.0 NH1 A:ARG668 4.9 41.5 1.0 N A:ILE709 5.0 41.5 1.0

Zinc binding site 4 out of 4 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 4 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:87.0 occ:1.00 OE2 A:GLU905 1.9 53.8 1.0 NE2 A:HIS901 2.3 52.2 1.0 CD A:GLU905 2.6 49.9 1.0 O A:HOH177 2.9 70.6 1.0 CE1 A:HIS901 3.0 47.5 1.0 OE1 A:GLU905 3.0 39.8 1.0 CD2 A:HIS901 3.4 43.5 1.0 CG A:GLU905 3.8 47.7 1.0 ND1 A:HIS901 4.2 45.8 1.0 CG A:HIS901 4.4 40.8 1.0 CD1 A:LEU915 4.9 32.6 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