Zinc in PDB 2igi: Crystal Structure of E. Coli Oligoribonuclease

The structure of Crystal Structure of E. Coli Oligoribonuclease, PDB code: 2igi was solved by Y.Zuo, A.Malhotra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.97 / 1.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	91.550, 91.550, 111.180, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20

The structure of Crystal Structure of E. Coli Oligoribonuclease also contains other interesting chemical elements:

Cadmium

(Cd)

13 atoms

The binding sites of Zinc atom in the Crystal Structure of E. Coli Oligoribonuclease (pdb code 2igi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of E. Coli Oligoribonuclease, PDB code: 2igi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli Oligoribonuclease


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 E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:11.2 occ:1.00 OE2 A:GLU13 1.9 11.0 1.0 O A:HOH1064 1.9 8.9 1.0 OD2 A:ASP162 2.0 11.2 1.0 OD2 A:ASP11 2.0 9.5 1.0 CD A:GLU13 2.9 12.7 1.0 CG A:ASP11 3.0 9.5 1.0 CG A:ASP162 3.0 13.0 1.0 OD1 A:ASP11 3.2 8.6 1.0 ZN A:ZN1004 3.3 14.1 1.0 CB A:ASP162 3.3 10.7 1.0 CD A:CD1002 3.4 11.1 1.0 OE1 A:GLU13 3.4 11.5 1.0 OXT A:ACY603 3.6 16.3 1.0 O A:LEU12 3.6 8.6 1.0 O A:ACY603 3.7 20.6 1.0 C A:ACY603 3.9 21.5 1.0 CA A:HIS157 4.1 14.8 1.0 OD1 A:ASP162 4.1 13.8 1.0 CG A:GLU13 4.2 11.2 1.0 C A:HIS157 4.2 14.6 1.0 CA A:ALA159 4.3 12.3 1.0 ND1 A:HIS157 4.3 12.6 1.0 CB A:ASP11 4.3 8.4 1.0 O A:HOH1100 4.3 11.1 1.0 O A:GLN158 4.4 11.8 1.0 N A:ALA159 4.4 11.9 1.0 C A:GLN158 4.4 13.4 1.0 N A:GLN158 4.4 14.3 1.0 C A:LEU12 4.6 8.8 1.0 O A:HIS157 4.7 13.8 1.0 CB A:HIS157 4.7 14.7 1.0 OXT A:ACY604 4.7 21.7 1.0 O A:HOH1062 4.8 16.8 1.0 CA A:ASP162 4.9 9.8 1.0 CG A:HIS157 4.9 15.2 1.0 N A:LEU12 5.0 8.7 1.0 O A:ALA159 5.0 10.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli Oligoribonuclease


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 E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:14.1 occ:1.00 OXT A:ACY604 1.9 21.7 1.0 O A:HOH1064 2.1 8.9 1.0 ND1 A:HIS157 2.1 12.6 1.0 OE1 A:GLU13 2.3 11.5 1.0 C A:ACY604 2.6 24.4 1.0 O A:ACY604 2.8 20.4 1.0 CE1 A:HIS157 2.9 14.2 1.0 CD A:GLU13 3.2 12.7 1.0 CG A:HIS157 3.2 15.2 1.0 ZN A:ZN1001 3.3 11.2 1.0 OE2 A:GLU13 3.3 11.0 1.0 O A:HOH1032 3.7 16.3 1.0 CB A:HIS157 3.7 14.7 1.0 O A:HOH1100 4.0 11.1 1.0 CD A:CD1002 4.0 11.1 1.0 O A:LEU12 4.0 8.6 1.0 O A:ACY603 4.0 20.6 1.0 CH3 A:ACY604 4.1 24.2 1.0 NE2 A:HIS157 4.1 15.2 1.0 OD2 A:ASP162 4.3 11.2 1.0 CA A:HIS157 4.3 14.8 1.0 CD2 A:HIS157 4.3 14.3 1.0 O A:HOH1058 4.3 11.9 1.0 CG A:GLU13 4.6 11.2 1.0 CA A:GLU13 4.7 10.2 1.0 C A:HIS157 4.9 14.6 1.0 C A:ACY603 5.0 21.5 1.0 O A:HIS157 5.0 13.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli Oligoribonuclease


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 E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:11.7 occ:1.00 OE2 B:GLU13 1.9 11.2 1.0 O B:HOH1063 1.9 10.6 1.0 OD2 B:ASP162 2.0 12.2 1.0 OD2 B:ASP11 2.0 9.4 1.0 CD B:GLU13 2.9 12.3 1.0 CG B:ASP162 3.0 13.5 1.0 CG B:ASP11 3.0 10.1 1.0 OD1 B:ASP11 3.2 10.8 1.0 ZN B:ZN1010 3.3 13.8 1.0 CB B:ASP162 3.3 11.0 1.0 OE1 B:GLU13 3.4 10.7 1.0 CD B:CD1008 3.4 11.4 1.0 OXT B:ACY605 3.6 21.8 1.0 O B:ACY605 3.7 17.4 1.0 O B:LEU12 3.7 11.1 1.0 C B:ACY605 4.0 23.1 1.0 CA B:HIS157 4.1 12.8 1.0 OD1 B:ASP162 4.1 13.4 1.0 C B:HIS157 4.2 13.7 1.0 CG B:GLU13 4.2 10.9 1.0 CA B:ALA159 4.3 13.6 1.0 N B:ALA159 4.3 14.0 1.0 ND1 B:HIS157 4.3 13.9 1.0 CB B:ASP11 4.4 10.0 1.0 O B:HOH1079 4.4 10.0 1.0 N B:GLN158 4.4 13.3 1.0 C B:GLN158 4.4 14.0 1.0 O B:GLN158 4.4 13.1 1.0 C B:LEU12 4.6 10.5 1.0 O B:HIS157 4.6 12.8 1.0 OXT B:ACY606 4.6 20.8 1.0 CB B:HIS157 4.7 13.6 1.0 O B:HOH1037 4.7 16.4 1.0 CA B:ASP162 4.8 11.9 1.0 CG B:HIS157 4.9 14.6 1.0 O B:ALA159 4.9 13.1 1.0 N B:LEU12 5.0 11.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli Oligoribonuclease


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 E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1010 b:13.8 occ:1.00 OXT B:ACY606 1.9 20.8 1.0 ND1 B:HIS157 2.1 13.9 1.0 O B:HOH1063 2.1 10.6 1.0 OE1 B:GLU13 2.2 10.7 1.0 C B:ACY606 2.7 22.5 1.0 O B:ACY606 2.8 19.5 1.0 CE1 B:HIS157 2.9 15.0 1.0 CD B:GLU13 3.1 12.3 1.0 CG B:HIS157 3.2 14.6 1.0 ZN B:ZN1007 3.3 11.7 1.0 OE2 B:GLU13 3.3 11.2 1.0 CB B:HIS157 3.7 13.6 1.0 O B:HOH1042 3.7 16.5 1.0 O B:LEU12 4.0 11.1 1.0 CD B:CD1008 4.0 11.4 1.0 O B:HOH1079 4.0 10.0 1.0 OXT B:ACY605 4.0 21.8 1.0 NE2 B:HIS157 4.1 15.3 1.0 CH3 B:ACY606 4.1 22.5 1.0 CA B:HIS157 4.2 12.8 1.0 OD2 B:ASP162 4.2 12.2 1.0 CD2 B:HIS157 4.3 12.8 1.0 O B:HOH1089 4.3 14.8 1.0 CG B:GLU13 4.5 10.9 1.0 CA B:GLU13 4.7 9.9 1.0 C B:HIS157 4.9 13.7 1.0 O B:HIS157 5.0 12.8 1.0 C B:ACY605 5.0 23.1 1.0 CB B:GLU13 5.0 11.4 1.0

T.J.Fiedler, Y.Zuo, A.Malhotra. Crystal Structure of Oligoribonuclease, the Lone Essential Exoribonuclease in Escherichia Coli To Be Published.