Cadmium 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:

Zinc

(Zn)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of E. Coli Oligoribonuclease (pdb code 2igi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of E. Coli Oligoribonuclease, PDB code: 2igi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:11.1 occ:1.00 O A:HOH1025 2.2 11.3 1.0 OD1 A:ASP11 2.3 8.6 1.0 O A:HOH1100 2.3 11.1 1.0 O A:HOH1058 2.3 11.9 1.0 OXT A:ACY603 2.3 16.3 1.0 O A:HOH1064 2.3 8.9 1.0 C A:ACY603 3.2 21.5 1.0 O A:ACY603 3.3 20.6 1.0 CG A:ASP11 3.3 9.5 1.0 ZN A:ZN1001 3.4 11.2 1.0 OD2 A:ASP11 3.7 9.5 1.0 O A:HOH1040 4.0 15.7 1.0 ZN A:ZN1004 4.0 14.1 1.0 O A:ACY604 4.0 20.4 1.0 O A:LEU12 4.0 8.6 1.0 OD1 A:ASP111 4.0 11.4 1.0 OD2 A:ASP111 4.2 13.6 1.0 O A:HOH1022 4.2 9.6 1.0 C A:ACY604 4.3 24.4 1.0 O A:HOH1028 4.3 10.4 1.0 OXT A:ACY604 4.4 21.7 1.0 O A:ASN106 4.4 11.2 1.0 O A:HOH1121 4.4 27.1 1.0 CH3 A:ACY603 4.5 17.9 1.0 CG A:ASP111 4.5 10.9 1.0 CB A:ASP11 4.6 8.4 1.0 OD2 A:ASP162 4.8 11.2 1.0 N A:LEU12 4.8 8.7 1.0 OE2 A:GLU13 4.9 11.0 1.0

Cadmium binding site 2 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:9.4 occ:1.00 O A:HOH1020 2.3 9.2 1.0 OXT A:ACY601 2.4 11.6 1.0 OE1 A:GLU123 2.4 8.8 1.0 O A:ACY601 2.4 11.0 1.0 OE2 A:GLU123 2.5 8.1 1.0 C A:ACY601 2.7 11.3 1.0 CD A:GLU123 2.8 7.9 1.0 CE2 A:PHE116 3.9 11.4 1.0 NH2 A:ARG112 4.0 8.5 1.0 O A:GLU123 4.0 7.7 1.0 CZ A:PHE116 4.2 10.4 1.0 CH3 A:ACY601 4.2 12.3 1.0 CG A:GLU123 4.3 8.1 1.0 CA A:ALA124 4.3 9.2 1.0 C A:GLU123 4.4 7.8 1.0 O A:HOH1023 4.6 11.1 1.0 N A:ALA124 4.6 9.3 1.0 NE A:ARG112 4.8 8.5 1.0 CD2 A:TYR128 4.8 34.5 1.0 CZ A:ARG112 4.8 8.6 1.0 O A:PHE126 4.8 10.3 1.0 O A:HOH1019 4.9 11.5 1.0 O A:HOH1157 4.9 34.3 1.0

Cadmium binding site 3 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1005 b:32.2 occ:1.00 O A:HOH1227 2.1 33.1 1.0 O A:HOH1082 2.1 19.5 1.0 NE2 A:HIS48 2.3 13.2 1.0 O A:HOH1176 2.4 36.6 1.0 O A:HOH1211 2.6 38.0 1.0 CE1 A:HIS48 3.1 16.3 1.0 CD2 A:HIS48 3.4 16.6 1.0 O A:HOH1113 4.2 28.0 1.0 O A:HOH1226 4.2 38.1 1.0 ND1 A:HIS48 4.2 16.5 1.0 CG A:HIS48 4.4 15.1 1.0 O A:HOH1107 4.4 20.8 1.0 CH3 A:ACY607 4.7 37.6 1.0 CA A:SER50 4.9 16.5 1.0 O A:GLN49 5.0 13.9 1.0

Cadmium binding site 4 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1006 b:30.4 occ:1.00 O A:THR78 2.2 19.4 1.0 O A:HOH1163 2.3 35.6 1.0 OE2 A:GLU83 2.3 24.4 1.0 OE1 A:GLU83 2.3 20.4 1.0 O A:HOH1133 2.4 28.9 1.0 OXT A:ACY607 2.5 37.5 1.0 O A:ACY607 2.5 38.2 1.0 CD A:GLU83 2.6 20.7 1.0 C A:ACY607 2.9 38.7 1.0 C A:THR78 3.2 18.6 1.0 N A:MET79 4.0 15.7 1.0 CA A:THR78 4.0 18.7 1.0 CG A:GLU83 4.1 18.3 1.0 CA A:MET79 4.2 14.8 1.0 CB A:THR78 4.3 20.8 1.0 CH3 A:ACY607 4.4 37.6 1.0 N A:GLY80 4.5 13.4 1.0 O A:HOH1182 4.7 37.8 1.0 C A:MET79 4.9 14.6 1.0 OG1 A:THR78 5.0 22.9 1.0 CB A:GLU83 5.0 14.6 1.0

Cadmium binding site 5 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1014 b:42.5 occ:1.00 CD A:CD1015 2.2 39.7 1.0 OE2 A:GLU41 2.5 27.3 1.0 OE1 A:GLU41 2.5 21.3 1.0 CD A:GLU41 2.8 23.9 1.0 NE A:ARG164 3.4 29.6 1.0 CG A:MET160 3.5 17.9 1.0 O A:HOH1092 4.0 21.1 1.0 CD A:ARG164 4.1 26.0 1.0 CG A:GLU41 4.2 21.6 1.0 CZ A:ARG164 4.3 30.2 1.0 NH2 A:ARG164 4.3 28.9 1.0 SD A:MET160 4.4 21.2 1.0 CB A:MET160 4.7 16.2 1.0 CE A:MET160 5.0 21.3 1.0

Cadmium binding site 6 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1015 b:39.7 occ:1.00 CD A:CD1014 2.2 42.5 1.0 NE A:ARG164 3.5 29.6 1.0 CD A:ARG164 3.8 26.0 1.0 OE1 A:GLU41 4.0 21.3 1.0 O A:HOH1179 4.1 30.8 1.0 CZ A:ARG164 4.4 30.2 1.0 OE2 A:GLU41 4.6 27.3 1.0 CD A:GLU41 4.7 23.9 1.0 NH2 A:ARG164 4.8 28.9 1.0 CG A:MET160 4.8 17.9 1.0

Cadmium binding site 7 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1016 b:63.5 occ:1.00 NE2 A:HIS176 2.4 25.1 1.0 O A:HOH1103 2.5 28.0 1.0 O A:HOH1229 2.7 36.3 1.0 O A:HOH1191 2.7 38.1 1.0 CE1 A:HIS176 3.2 24.1 1.0 CD2 A:HIS176 3.5 22.7 1.0 CG A:GLU175 4.3 27.0 1.0 O A:HOH1230 4.3 38.4 1.0 ND1 A:HIS176 4.4 25.0 1.0 CD1 A:TYR172 4.5 17.5 1.0 CG A:HIS176 4.6 23.8 1.0 CE1 A:TYR172 4.7 19.0 1.0 CB A:GLU175 5.0 23.1 1.0

Cadmium binding site 8 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1017 b:73.4 occ:1.00 ND1 A:HIS176 2.4 25.0 1.0 O B:HOH1207 2.4 38.6 1.0 O A:HOH1222 2.5 37.1 1.0 CE1 A:HIS176 3.2 24.1 1.0 CG A:HIS176 3.4 23.8 1.0 CB A:HIS176 3.8 21.4 1.0 CA A:HIS176 4.1 20.8 1.0 NE2 A:HIS176 4.4 25.1 1.0 CD2 A:HIS176 4.5 22.7 1.0 O A:HIS176 4.7 20.0 1.0 O A:HOH1230 4.7 38.4 1.0 O A:HOH1209 4.7 40.0 1.0 O A:GLU175 4.8 22.7 1.0 C A:HIS176 4.9 20.8 1.0

Cadmium binding site 9 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1008 b:11.4 occ:1.00 O B:HOH1089 2.2 14.8 1.0 OD1 B:ASP11 2.2 10.8 1.0 O B:HOH1079 2.3 10.0 1.0 O B:HOH1016 2.3 12.6 1.0 O B:ACY605 2.3 17.4 1.0 O B:HOH1063 2.3 10.6 1.0 C B:ACY605 3.2 23.1 1.0 CG B:ASP11 3.3 10.1 1.0 ZN B:ZN1007 3.4 11.7 1.0 OXT B:ACY605 3.4 21.8 1.0 OD2 B:ASP11 3.7 9.4 1.0 O B:ACY606 3.9 19.5 1.0 O B:LEU12 4.0 11.1 1.0 ZN B:ZN1010 4.0 13.8 1.0 OD2 B:ASP111 4.0 11.9 1.0 O B:HOH1048 4.1 15.4 1.0 O B:HOH1017 4.2 9.8 1.0 OD1 B:ASP111 4.2 11.2 1.0 OXT B:ACY606 4.2 20.8 1.0 C B:ACY606 4.3 22.5 1.0 O B:HOH1091 4.4 25.7 1.0 O B:HOH1021 4.4 12.6 1.0 O B:ASN106 4.4 13.3 1.0 CH3 B:ACY605 4.5 20.8 1.0 CG B:ASP111 4.6 12.5 1.0 CB B:ASP11 4.6 10.0 1.0 OD2 B:ASP162 4.8 12.2 1.0 N B:LEU12 4.8 11.3 1.0 OE2 B:GLU13 4.9 11.2 1.0

Cadmium binding site 10 out of 13 in the Crystal Structure of E. Coli Oligoribonuclease


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of E. Coli Oligoribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1009 b:11.3 occ:1.00 O B:HOH1015 2.3 10.3 1.0 OE1 B:GLU123 2.4 12.3 1.0 OXT B:ACY602 2.4 11.7 1.0 O B:ACY602 2.4 12.8 1.0 OE2 B:GLU123 2.5 10.1 1.0 C B:ACY602 2.7 11.4 1.0 CD B:GLU123 2.7 11.8 1.0 CE2 B:PHE116 3.9 11.9 1.0 O B:GLU123 4.0 10.6 1.0 NH2 B:ARG112 4.0 9.4 1.0 CZ B:PHE116 4.1 11.1 1.0 CH3 B:ACY602 4.3 13.0 1.0 CG B:GLU123 4.3 10.4 1.0 CA B:ALA124 4.3 11.3 1.0 C B:GLU123 4.4 11.0 1.0 O B:HOH1034 4.5 14.6 1.0 N B:ALA124 4.6 11.2 1.0 CD2 B:TYR128 4.8 35.5 1.0 NE B:ARG112 4.8 9.8 1.0 CZ B:ARG112 4.8 11.0 1.0 O B:PHE126 4.8 11.6 1.0 O B:HOH1014 4.9 11.9 1.0

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