Zinc in PDB 2kfn: Klenow Fragment with Bridging-Sulfur Substrate and Manganese

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

The structure of Klenow Fragment with Bridging-Sulfur Substrate and Manganese, PDB code: 2kfn 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 (%)	21.4 / 25

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

Magnesium	(Mg)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Zinc atom in the Klenow Fragment with Bridging-Sulfur Substrate and Manganese (pdb code 2kfn). 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 Bridging-Sulfur Substrate and Manganese, PDB code: 2kfn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Klenow Fragment with Bridging-Sulfur Substrate and Manganese


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 Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:31.9 occ:1.00 OD2 A:ASP355 2.0 31.1 1.0 OP1 B:DG1007 2.1 51.7 1.0 OE2 A:GLU357 2.1 25.6 1.0 OD2 A:ASP501 2.2 30.7 1.0 CG A:ASP355 3.0 30.6 1.0 CD A:GLU357 3.1 24.2 1.0 CG A:ASP501 3.2 26.2 1.0 OD1 A:ASP355 3.4 43.9 1.0 P B:DG1007 3.4 47.0 1.0 OE1 A:GLU357 3.4 26.7 1.0 CB A:ASP501 3.6 21.3 1.0 MN B:MN2 3.9 65.8 1.0 CE1 A:TYR497 3.9 19.6 1.0 OP2 B:DG1007 4.0 49.3 1.0 O A:THR356 4.0 18.8 1.0 CB A:ASP355 4.3 21.8 1.0 OD1 A:ASP501 4.4 26.1 1.0 CG A:GLU357 4.4 21.6 1.0 O5' B:DG1007 4.5 52.6 1.0 S B:US11006 4.5 58.1 1.0 CD1 A:TYR497 4.5 18.9 1.0 CA A:ALA498 4.6 13.3 1.0 CZ A:TYR497 4.6 25.0 1.0 O A:HOH4 4.6 34.8 1.0 O A:HOH168 4.7 34.0 1.0 OH A:TYR497 4.7 21.0 1.0 O A:ALA498 4.8 19.0 1.0 C5' B:DG1007 4.9 44.4 1.0 C A:THR356 4.9 16.5 1.0

Zinc binding site 2 out of 3 in the Klenow Fragment with Bridging-Sulfur Substrate and Manganese


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 Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:73.3 occ:1.00 OE2 A:GLU905 2.1 51.6 1.0 O A:HOH293 2.2 57.0 1.0 NE2 A:HIS901 2.3 48.1 1.0 CD A:GLU905 2.9 50.4 1.0 CD2 A:HIS901 3.2 42.9 1.0 CE1 A:HIS901 3.4 45.2 1.0 OE1 A:GLU905 3.4 47.6 1.0 CG A:GLU905 4.0 46.9 1.0 CG A:HIS901 4.4 39.0 1.0 ND1 A:HIS901 4.5 43.0 1.0

Zinc binding site 3 out of 3 in the Klenow Fragment with Bridging-Sulfur Substrate and Manganese


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 Manganese 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 3.0 33.9 1.0 CD A:GLU710 3.1 66.4 1.0 OD1 A:ASP882 3.1 33.5 1.0 O A:HOH206 3.3 47.9 1.0 OE1 A:GLU710 3.5 68.9 1.0 NH2 A:ARG668 3.7 42.8 1.0 CB A:ASP882 4.3 26.2 1.0 CG A:GLU710 4.3 53.1 1.0 CZ A:ARG668 4.4 42.5 1.0 NH1 A:ARG668 4.6 43.3 1.0 N A:ASP882 4.7 28.3 1.0 CB A:HIS881 4.9 36.1 1.0 CG2 A:ILE709 4.9 19.4 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