Cadmium in PDB 3ao9: Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease

The structure of Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease, PDB code: 3ao9 was solved by S.Inoue, S.Fushinobu, T.Ogawa, M.Hidaka, H.Masaki, S.Yajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.78 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.710, 62.710, 100.510, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.9

The binding sites of Cadmium atom in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease (pdb code 3ao9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease, PDB code: 3ao9:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease


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 the C-Terminal Domain of Sequence-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd117 b:31.8 occ:1.00 OE2 A:GLU32 2.2 35.0 1.0 O B:HOH143 2.3 33.5 1.0 O B:GLU32 2.3 25.4 1.0 OE1 A:GLU32 2.4 28.5 1.0 O A:HOH180 2.4 22.9 1.0 O B:HOH122 2.5 21.5 1.0 CD A:GLU32 2.6 34.5 1.0 C B:GLU32 3.3 27.2 1.0 CA B:GLU32 3.7 27.7 1.0 OG1 B:THR98 3.9 29.7 1.0 O A:HOH175 4.2 27.6 1.0 CG A:GLU32 4.2 29.4 1.0 CB B:GLU32 4.2 27.3 1.0 OD2 B:ASP96 4.5 21.0 1.0 N B:ARG33 4.6 27.0 1.0 O A:HOH179 4.6 35.2 1.0 O A:HOH178 4.6 28.2 1.0 O A:GLY28 4.7 24.9 1.0 CD A:CD119 4.7 50.4 0.5 O B:PRO31 4.9 28.7 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease


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 the C-Terminal Domain of Sequence-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd118 b:69.4 occ:1.00 CG2 A:THR98 2.3 33.0 1.0 O A:HOH174 2.5 22.3 1.0 CD B:CD117 2.5 46.6 1.0 O B:HOH170 2.6 28.4 1.0 O A:HOH173 2.7 30.4 1.0 O B:HOH169 3.4 41.8 1.0 CB A:THR98 3.6 36.5 1.0 O A:THR98 4.0 37.6 1.0 OE1 B:GLU32 4.2 33.7 1.0 O A:GLU32 4.3 25.4 1.0 C A:THR98 4.3 37.2 1.0 OG1 A:THR98 4.3 37.9 1.0 OD2 A:ASP96 4.4 24.8 1.0 OE2 B:GLU32 4.5 39.2 1.0 CA A:THR98 4.6 35.3 1.0 CG B:GLN29 4.6 26.7 1.0 OD1 A:ASP96 4.6 24.9 1.0 CD B:GLU32 4.8 35.2 1.0 CG A:ASP96 4.9 23.3 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease


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 the C-Terminal Domain of Sequence-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd119 b:50.4 occ:0.50 O A:HOH138 2.7 16.4 0.5 OE2 A:GLU32 2.7 35.0 1.0 CG A:GLU32 3.5 29.4 1.0 CD A:GLU32 3.5 34.5 1.0 O A:GLY28 4.3 24.9 1.0 O A:HOH180 4.5 22.9 1.0 CD A:CD117 4.7 31.8 1.0 OE1 A:GLU32 4.8 28.5 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of the C-Terminal Domain of Sequence-Specific Ribonuclease


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 the C-Terminal Domain of Sequence-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd117 b:46.6 occ:1.00 OE2 B:GLU32 2.2 39.2 1.0 OE1 B:GLU32 2.4 33.7 1.0 CD A:CD118 2.5 69.4 1.0 O A:GLU32 2.6 25.4 1.0 O A:HOH174 2.6 22.3 1.0 CD B:GLU32 2.6 35.2 1.0 O B:HOH170 2.8 28.4 1.0 C A:GLU32 3.5 26.2 1.0 CG2 A:THR98 3.7 33.0 1.0 CA A:GLU32 3.9 27.8 1.0 CG B:GLU32 4.1 29.9 1.0 O B:HOH166 4.2 23.0 1.0 CB A:GLU32 4.4 27.3 1.0 OD2 A:ASP96 4.4 24.8 1.0 CB A:THR98 4.7 36.5 1.0 N A:ARG33 4.7 26.0 1.0 O A:HOH173 4.9 30.4 1.0 OD1 A:ASP96 5.0 24.9 1.0

S.Inoue-Ito, S.Yajima, S.Fushinobu, S.Nakamura, T.Ogawa, M.Hidaka, H.Masaki. Identification of the Catalytic Residues of Sequence-Specific and Histidine-Free Ribonuclease Colicin E5 J.Biochem. V. 152 365 2012.
ISSN: ISSN 0021-924X
PubMed: 22815490
DOI: 10.1093/JB/MVS077