Zinc in PDB 2kfz: Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only

All present enzymatic activity of Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only:
2.7.7.7;

The structure of Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only, PDB code: 2kfz 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 / 2.03
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	102.900, 102.900, 86.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.5

The structure of Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only (pdb code 2kfz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only, PDB code: 2kfz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Klenow Fragment with Bridging-Sulfur 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 Bridging-Sulfur Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:39.1 occ:1.00 OD2 A:ASP355 2.0 31.1 1.0 OE2 A:GLU357 2.1 25.6 1.0 OP1 B:DG1007 2.1 55.4 1.0 OD2 A:ASP501 2.2 30.7 1.0 CG A:ASP355 3.0 30.6 1.0 CD A:GLU357 3.0 24.2 1.0 CG A:ASP501 3.3 26.2 1.0 OE1 A:GLU357 3.4 26.7 1.0 OD1 A:ASP355 3.4 43.9 1.0 P B:DG1007 3.5 48.0 1.0 CB A:ASP501 3.7 21.3 1.0 CE1 A:TYR497 3.8 19.6 1.0 O A:THR356 4.0 18.8 1.0 OP2 B:DG1007 4.2 51.7 1.0 ZN A:ZN2 4.3 0.0 1.0 CG A:GLU357 4.3 21.6 1.0 CB A:ASP355 4.3 21.8 1.0 OD1 A:ASP501 4.4 26.1 1.0 S B:US11006 4.4 54.2 1.0 CD1 A:TYR497 4.5 18.9 1.0 O A:HOH4 4.5 43.6 1.0 O5' B:DG1007 4.5 51.8 1.0 CA A:ALA498 4.6 13.3 1.0 CZ A:TYR497 4.6 25.0 1.0 OH A:TYR497 4.6 21.0 1.0 O A:HOH168 4.7 36.2 1.0 O A:ALA498 4.8 19.0 1.0 C5' B:DG1007 4.8 43.4 1.0 C A:THR356 4.9 16.5 1.0

Zinc binding site 2 out of 4 in the Klenow Fragment with Bridging-Sulfur 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 Bridging-Sulfur Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:0.0 occ:1.00 OD1 A:ASP355 2.3 43.9 1.0 O A:HOH4 2.8 43.6 1.0 S B:US11006 3.1 54.2 1.0 CG A:ASP355 3.3 30.6 1.0 O A:GLN419 3.4 22.0 1.0 O A:HOH18 3.5 31.0 1.0 OD2 A:ASP424 3.7 27.3 1.0 OD1 A:ASP424 3.8 23.6 1.0 OD2 A:ASP355 3.8 31.1 1.0 O A:HOH165 3.9 65.1 1.0 OP1 B:DG1007 3.9 55.4 1.0 C4' B:US11006 4.1 58.6 1.0 CG A:ASP424 4.2 23.0 1.0 C3' B:US11006 4.3 58.5 1.0 P B:DG1007 4.3 48.0 1.0 ZN A:ZN1 4.3 39.1 1.0 C5' B:US11006 4.4 57.7 1.0 CB A:ASP355 4.4 21.8 1.0 C A:GLN419 4.6 21.9 1.0 O A:THR356 4.7 18.8 1.0 CA A:ASP355 4.8 19.1 1.0 N A:THR356 4.8 22.3 1.0 CB A:GLN419 4.8 17.2 1.0 O A:ASN420 4.9 22.2 1.0 N A:GLN419 5.0 18.3 1.0

Zinc binding site 3 out of 4 in the Klenow Fragment with Bridging-Sulfur 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 Bridging-Sulfur Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:70.7 occ:1.00 OE2 A:GLU905 2.1 51.6 1.0 O A:HOH293 2.2 70.0 1.0 NE2 A:HIS901 2.4 48.1 1.0 CD A:GLU905 3.0 50.4 1.0 CD2 A:HIS901 3.3 42.9 1.0 OE1 A:GLU905 3.5 47.6 1.0 CE1 A:HIS901 3.5 45.2 1.0 CG A:GLU905 4.1 46.9 1.0 CG A:HIS901 4.5 39.0 1.0 ND1 A:HIS901 4.6 43.0 1.0

Zinc binding site 4 out of 4 in the Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Klenow Fragment with Bridging-Sulfur Substrate and Zinc Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn320 b:0.0 occ:1.00 OE2 A:GLU710 2.3 72.8 1.0 OD2 A:ASP882 2.3 37.8 1.0 CG A:ASP882 3.1 33.9 1.0 CD A:GLU710 3.1 66.4 1.0 OD1 A:ASP882 3.2 33.5 1.0 O A:HOH206 3.3 43.9 1.0 OE1 A:GLU710 3.4 68.9 1.0 NH2 A:ARG668 3.9 42.8 1.0 CG A:GLU710 4.3 53.1 1.0 CB A:ASP882 4.4 26.2 1.0 CZ A:ARG668 4.6 42.5 1.0 N A:ASP882 4.7 28.3 1.0 NH1 A:ARG668 4.8 43.3 1.0 CG2 A:ILE709 4.9 19.4 1.0 CB A:HIS881 4.9 36.1 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