Zinc in PDB 4lef: Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site

The structure of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site, PDB code: 4lef was solved by A.A.Fedorov, E.V.Fedorov, D.F.Xiang, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.57 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.048, 100.308, 168.037, 90.00, 104.48, 90.00
R / Rfree (%)	17.5 / 20.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site (pdb code 4lef). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site, PDB code: 4lef:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:11.3 occ:1.00 O1 C:PO4303 1.9 16.1 1.0 NE2 C:HIS12 2.0 9.0 1.0 OE2 C:GLU125 2.1 13.5 1.0 NE2 C:HIS14 2.1 12.0 1.0 OD1 C:ASP243 2.5 13.5 1.0 CD2 C:HIS12 3.0 8.7 1.0 CE1 C:HIS12 3.0 10.2 1.0 CE1 C:HIS14 3.0 11.7 1.0 CD2 C:HIS14 3.0 8.4 1.0 CD C:GLU125 3.1 10.3 1.0 P C:PO4303 3.2 14.6 1.0 CG C:ASP243 3.3 9.6 1.0 O2 C:PO4303 3.5 18.5 1.0 OE1 C:GLU125 3.5 9.7 1.0 OD2 C:ASP243 3.6 11.5 1.0 ZN C:ZN302 3.8 12.2 1.0 O3 C:PO4303 3.9 8.6 1.0 ND1 C:HIS12 4.1 11.4 1.0 ND1 C:HIS14 4.1 11.2 1.0 CB C:MET54 4.2 9.8 1.0 CE1 C:HIS186 4.2 14.6 1.0 CG C:HIS12 4.2 8.6 1.0 CG C:HIS14 4.2 12.3 1.0 O4 C:PO4303 4.2 13.8 1.0 CG C:GLU125 4.4 7.2 1.0 NE2 C:HIS186 4.4 9.8 1.0 CG2 C:THR245 4.4 17.6 1.0 CB C:ASP243 4.6 7.5 1.0 CG C:MET54 4.6 9.6 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:12.2 occ:1.00 OE1 C:GLU125 2.0 9.7 1.0 O3 C:PO4303 2.0 8.6 1.0 NE2 C:HIS186 2.0 9.8 1.0 ND1 C:HIS158 2.1 8.6 1.0 O1 C:PO4303 2.8 16.1 1.0 P C:PO4303 2.9 14.6 1.0 CD2 C:HIS186 2.9 11.5 1.0 CD C:GLU125 3.0 10.3 1.0 CE1 C:HIS158 3.0 13.4 1.0 CE1 C:HIS186 3.0 14.6 1.0 CG C:HIS158 3.1 11.5 1.0 OE2 C:GLU125 3.4 13.5 1.0 CB C:HIS158 3.5 8.8 1.0 ZN C:ZN301 3.8 11.3 1.0 O4 C:PO4303 3.8 13.8 1.0 CE1 C:TYR84 4.0 9.5 1.0 OH C:TYR84 4.1 12.6 1.0 O2 C:PO4303 4.1 18.5 1.0 CE1 C:HIS12 4.1 10.2 1.0 CG C:HIS186 4.1 10.8 1.0 ND1 C:HIS186 4.1 11.3 1.0 NE2 C:HIS158 4.2 12.0 1.0 CD2 C:HIS158 4.2 13.7 1.0 NE2 C:HIS12 4.3 9.0 1.0 CG C:GLU125 4.3 7.2 1.0 CA C:HIS158 4.3 10.9 1.0 CZ C:TYR84 4.5 14.3 1.0 O C:HOH518 4.7 28.0 1.0 CB C:GLU125 4.9 10.1 1.0 OD2 C:ASP243 4.9 11.5 1.0 O C:HOH585 5.0 43.0 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:15.7 occ:1.00 O3 D:PO4303 1.9 15.2 1.0 NE2 D:HIS14 2.1 18.0 1.0 NE2 D:HIS12 2.1 14.9 1.0 OE2 D:GLU125 2.1 18.0 1.0 OD1 D:ASP243 2.6 19.0 1.0 CD2 D:HIS14 3.0 16.5 1.0 CD2 D:HIS12 3.0 18.1 1.0 CE1 D:HIS14 3.1 22.4 1.0 CE1 D:HIS12 3.1 15.5 1.0 P D:PO4303 3.1 17.9 1.0 CD D:GLU125 3.2 17.3 1.0 O4 D:PO4303 3.3 17.7 1.0 CG D:ASP243 3.4 18.0 1.0 OE1 D:GLU125 3.6 15.8 1.0 OD2 D:ASP243 3.6 20.5 1.0 ZN D:ZN302 3.8 14.4 1.0 O1 D:PO4303 3.9 14.0 1.0 CE1 D:HIS186 4.1 19.2 1.0 CG D:HIS14 4.1 17.4 1.0 ND1 D:HIS14 4.2 16.9 1.0 CG D:HIS12 4.2 16.7 1.0 ND1 D:HIS12 4.2 17.2 1.0 CB D:MET54 4.2 18.4 1.0 O2 D:PO4303 4.3 21.2 1.0 NE2 D:HIS186 4.3 17.9 1.0 CG2 D:THR245 4.3 18.1 1.0 CG D:GLU125 4.5 16.6 1.0 CB D:ASP243 4.7 16.6 1.0 CG D:MET54 4.7 18.1 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:14.4 occ:1.00 OE1 D:GLU125 1.9 15.8 1.0 O1 D:PO4303 2.0 14.0 1.0 NE2 D:HIS186 2.0 17.9 1.0 ND1 D:HIS158 2.1 11.3 1.0 O3 D:PO4303 2.8 15.2 1.0 CD2 D:HIS186 2.9 15.8 1.0 P D:PO4303 2.9 17.9 1.0 CE1 D:HIS158 3.0 11.0 1.0 CD D:GLU125 3.0 17.3 1.0 CG D:HIS158 3.1 13.4 1.0 CE1 D:HIS186 3.2 19.2 1.0 OE2 D:GLU125 3.4 18.0 1.0 CB D:HIS158 3.5 12.8 1.0 ZN D:ZN301 3.8 15.7 1.0 O2 D:PO4303 3.9 21.2 1.0 CE1 D:TYR84 4.0 15.4 1.0 O4 D:PO4303 4.0 17.7 1.0 CE1 D:HIS12 4.1 15.5 1.0 CG D:HIS186 4.1 14.0 1.0 OH D:TYR84 4.1 11.8 1.0 NE2 D:HIS158 4.1 10.7 1.0 ND1 D:HIS186 4.2 13.5 1.0 CD2 D:HIS158 4.2 10.5 1.0 NE2 D:HIS12 4.3 14.9 1.0 CA D:HIS158 4.3 13.0 1.0 CG D:GLU125 4.3 16.6 1.0 O D:HOH590 4.4 27.0 1.0 CZ D:TYR84 4.5 15.5 1.0 O D:HOH593 4.6 37.8 1.0 O D:HOH559 4.7 28.7 1.0 OD2 D:ASP243 4.9 20.5 1.0 CB D:GLU125 5.0 13.8 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.2 occ:1.00 O1 A:PO4303 1.9 15.0 1.0 NE2 A:HIS12 2.0 9.2 1.0 NE2 A:HIS14 2.1 6.6 1.0 OE2 A:GLU125 2.1 9.6 1.0 OD1 A:ASP243 2.4 8.8 1.0 CE1 A:HIS12 3.0 11.3 1.0 CE1 A:HIS14 3.0 6.9 1.0 CD2 A:HIS12 3.0 11.8 1.0 CD2 A:HIS14 3.1 6.1 1.0 CD A:GLU125 3.1 8.4 1.0 P A:PO4303 3.2 13.3 1.0 CG A:ASP243 3.3 8.9 1.0 O4 A:PO4303 3.5 18.5 1.0 OE1 A:GLU125 3.5 11.5 1.0 OD2 A:ASP243 3.6 8.8 1.0 ZN A:ZN302 3.8 10.6 1.0 O2 A:PO4303 3.9 11.8 1.0 ND1 A:HIS12 4.1 8.0 1.0 ND1 A:HIS14 4.1 8.2 1.0 CG A:HIS12 4.2 7.3 1.0 CG A:HIS14 4.2 7.1 1.0 CE1 A:HIS186 4.2 12.4 1.0 CB A:MET54 4.2 9.1 1.0 O3 A:PO4303 4.3 19.1 1.0 NE2 A:HIS186 4.4 9.6 1.0 CG A:GLU125 4.4 8.3 1.0 CG2 A:THR245 4.5 16.1 1.0 CB A:ASP243 4.6 6.2 1.0 CG A:MET54 4.7 9.8 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.6 occ:1.00 OE1 A:GLU125 2.0 11.5 1.0 O2 A:PO4303 2.0 11.8 1.0 ND1 A:HIS158 2.0 9.2 1.0 NE2 A:HIS186 2.1 9.6 1.0 O1 A:PO4303 2.8 15.0 1.0 P A:PO4303 2.9 13.3 1.0 CE1 A:HIS158 3.0 11.8 1.0 CD2 A:HIS186 3.0 9.3 1.0 CD A:GLU125 3.0 8.4 1.0 CG A:HIS158 3.1 13.7 1.0 CE1 A:HIS186 3.1 12.4 1.0 OE2 A:GLU125 3.4 9.6 1.0 CB A:HIS158 3.5 9.9 1.0 ZN A:ZN301 3.8 10.2 1.0 O3 A:PO4303 3.8 19.1 1.0 CE1 A:TYR84 4.1 12.2 1.0 O4 A:PO4303 4.1 18.5 1.0 CE1 A:HIS12 4.1 11.3 1.0 NE2 A:HIS158 4.1 10.3 1.0 OH A:TYR84 4.1 11.5 1.0 CG A:HIS186 4.2 12.2 1.0 CD2 A:HIS158 4.2 12.2 1.0 ND1 A:HIS186 4.2 9.9 1.0 O A:HOH554 4.2 34.2 1.0 NE2 A:HIS12 4.3 9.2 1.0 CA A:HIS158 4.3 8.4 1.0 CG A:GLU125 4.3 8.3 1.0 CZ A:TYR84 4.6 13.6 1.0 O A:HOH466 4.8 23.2 1.0 OD2 A:ASP243 4.9 8.8 1.0 CB A:GLU125 4.9 9.5 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:10.6 occ:1.00 O3 B:PO4303 1.9 11.8 1.0 NE2 B:HIS14 2.0 6.8 1.0 NE2 B:HIS12 2.1 11.2 1.0 OE2 B:GLU125 2.2 8.7 1.0 OD1 B:ASP243 2.5 8.4 1.0 CD2 B:HIS14 3.0 10.9 1.0 CE1 B:HIS14 3.0 8.5 1.0 CE1 B:HIS12 3.1 10.8 1.0 CD2 B:HIS12 3.1 7.9 1.0 P B:PO4303 3.1 15.8 1.0 CD B:GLU125 3.2 11.2 1.0 CG B:ASP243 3.3 9.2 1.0 O2 B:PO4303 3.4 19.0 1.0 OE1 B:GLU125 3.6 10.8 1.0 OD2 B:ASP243 3.6 10.2 1.0 ZN B:ZN302 3.7 12.8 1.0 O4 B:PO4303 3.9 14.7 1.0 ND1 B:HIS14 4.1 10.4 1.0 CG B:HIS14 4.1 12.8 1.0 CE1 B:HIS186 4.2 12.1 1.0 ND1 B:HIS12 4.2 7.4 1.0 CB B:MET54 4.2 8.0 1.0 CG B:HIS12 4.2 6.1 1.0 O1 B:PO4303 4.3 19.9 1.0 NE2 B:HIS186 4.4 11.8 1.0 CG2 B:THR245 4.4 11.1 1.0 CG B:GLU125 4.5 6.4 1.0 CB B:ASP243 4.6 8.8 1.0 CG B:MET54 4.7 8.7 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.8 occ:1.00 O4 B:PO4303 2.0 14.7 1.0 OE1 B:GLU125 2.0 10.8 1.0 ND1 B:HIS158 2.0 8.1 1.0 NE2 B:HIS186 2.1 11.8 1.0 O3 B:PO4303 2.8 11.8 1.0 P B:PO4303 2.9 15.8 1.0 CE1 B:HIS158 2.9 10.2 1.0 CD2 B:HIS186 3.0 9.9 1.0 CD B:GLU125 3.0 11.2 1.0 CG B:HIS158 3.1 12.5 1.0 CE1 B:HIS186 3.1 12.1 1.0 OE2 B:GLU125 3.4 8.7 1.0 CB B:HIS158 3.5 9.0 1.0 ZN B:ZN301 3.7 10.6 1.0 O1 B:PO4303 3.9 19.9 1.0 CE1 B:TYR84 4.0 9.7 1.0 O2 B:PO4303 4.0 19.0 1.0 CE1 B:HIS12 4.0 10.8 1.0 NE2 B:HIS158 4.1 9.8 1.0 OH B:TYR84 4.2 13.5 1.0 CG B:HIS186 4.2 11.6 1.0 CD2 B:HIS158 4.2 11.8 1.0 ND1 B:HIS186 4.2 12.5 1.0 O B:HOH542 4.2 32.7 1.0 NE2 B:HIS12 4.2 11.2 1.0 CA B:HIS158 4.3 10.6 1.0 CG B:GLU125 4.3 6.4 1.0 CZ B:TYR84 4.6 10.9 1.0 O B:HOH524 4.8 25.4 1.0 OD2 B:ASP243 4.8 10.2 1.0 CB B:GLU125 4.9 6.1 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:17.9 occ:1.00 NE2 E:HIS12 2.0 14.2 1.0 NE2 E:HIS14 2.0 17.9 1.0 O4 E:PO4303 2.1 12.9 1.0 OE2 E:GLU125 2.1 17.0 1.0 OD1 E:ASP243 2.6 14.6 1.0 CE1 E:HIS12 3.0 21.5 1.0 CD2 E:HIS14 3.0 15.2 1.0 CD2 E:HIS12 3.0 16.5 1.0 CE1 E:HIS14 3.1 14.9 1.0 CD E:GLU125 3.1 18.2 1.0 P E:PO4303 3.1 20.7 1.0 O1 E:PO4303 3.3 25.4 1.0 CG E:ASP243 3.4 22.0 1.0 OE1 E:GLU125 3.5 21.8 1.0 OD2 E:ASP243 3.6 20.5 1.0 ZN E:ZN302 3.8 16.5 1.0 O3 E:PO4303 3.8 21.7 1.0 ND1 E:HIS12 4.1 14.0 1.0 CG E:HIS14 4.1 15.6 1.0 CG E:HIS12 4.1 16.3 1.0 ND1 E:HIS14 4.1 15.5 1.0 CE1 E:HIS186 4.2 20.4 1.0 CB E:MET54 4.2 19.6 1.0 O2 E:PO4303 4.3 23.0 1.0 NE2 E:HIS186 4.4 13.3 1.0 CG E:GLU125 4.4 16.1 1.0 CG2 E:THR245 4.5 23.7 1.0 CG E:MET54 4.6 17.5 1.0 CB E:ASP243 4.7 16.6 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:16.5 occ:1.00 O3 E:PO4303 1.9 21.7 1.0 NE2 E:HIS186 2.0 13.3 1.0 OE1 E:GLU125 2.1 21.8 1.0 ND1 E:HIS158 2.1 13.0 1.0 O4 E:PO4303 2.8 12.9 1.0 P E:PO4303 2.9 20.7 1.0 CD2 E:HIS186 2.9 14.4 1.0 CE1 E:HIS186 3.0 20.4 1.0 CD E:GLU125 3.0 18.2 1.0 CE1 E:HIS158 3.1 13.2 1.0 CG E:HIS158 3.1 16.1 1.0 OE2 E:GLU125 3.4 17.0 1.0 CB E:HIS158 3.5 17.0 1.0 ZN E:ZN301 3.8 17.9 1.0 O2 E:PO4303 3.8 23.0 1.0 CE1 E:HIS12 4.0 21.5 1.0 O1 E:PO4303 4.0 25.4 1.0 OH E:TYR84 4.0 20.5 1.0 ND1 E:HIS186 4.1 15.8 1.0 CG E:HIS186 4.1 14.8 1.0 CE1 E:TYR84 4.1 13.9 1.0 NE2 E:HIS158 4.2 16.5 1.0 NE2 E:HIS12 4.2 14.2 1.0 CD2 E:HIS158 4.3 13.9 1.0 CA E:HIS158 4.3 17.7 1.0 CG E:GLU125 4.3 16.1 1.0 CZ E:TYR84 4.6 21.0 1.0 O E:HOH480 4.6 36.3 1.0 OD2 E:ASP243 4.9 20.5 1.0 CB E:GLU125 4.9 13.4 1.0

A.A.Fedorov, E.V.Fedorov, D.F.Xiang, F.M.Raushel, S.C.Almo. Crystal Structure of Phosphotriesterase Homology Protein From Escherichia Coli Complexed with Phosphate in Active Site To Be Published.