Cadmium in PDB 3ivk: Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment

The structure of Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment, PDB code: 3ivk was solved by Y.Koldobskaya, E.M.Duguid, D.M.Shechner, S.Koide, A.A.Kossiakoff, D.P.Bartel, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	207.499, 206.452, 135.926, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 22.5

The structure of Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment also contains other interesting chemical elements:

Magnesium	(Mg)	33 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Cadmium atom in the Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment (pdb code 3ivk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment, PDB code: 3ivk:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment


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 Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd214 b:83.0 occ:1.00 OD2 L:ASP2 2.2 68.8 1.0 OD1 H:ASP65 2.3 64.5 1.0 OD2 H:ASP65 2.4 64.3 1.0 CG H:ASP65 2.7 65.0 1.0 CG L:ASP2 2.9 68.3 1.0 OD1 L:ASP2 2.9 68.1 1.0 CB H:ASP65 4.2 65.8 1.0 OG L:SER1 4.2 68.8 1.0 CB L:ASP2 4.4 68.0 1.0 CG L:PRO96 4.7 63.8 1.0 CD L:PRO96 4.7 63.8 1.0 CA H:ASP65 5.0 65.9 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of the Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment


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 Catalytic Core of An Rna Polymerase Ribozyme Complexed with An Antigen Binding Antibody Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd214 b:88.0 occ:1.00 OD2 B:ASP2 2.3 69.0 1.0 OD1 A:ASP65 2.3 64.5 1.0 OD2 A:ASP65 2.5 64.3 1.0 CG A:ASP65 2.7 65.0 1.0 OD1 B:ASP2 2.9 68.1 1.0 CG B:ASP2 2.9 68.3 1.0 OG B:SER1 4.1 68.8 1.0 CB A:ASP65 4.3 65.8 1.0 CB B:ASP2 4.4 68.0 1.0 CD B:PRO96 4.7 63.8 1.0 CG B:PRO96 4.7 63.9 1.0

D.M.Shechner, R.A.Grant, S.C.Bagby, Y.Koldobskaya, J.A.Piccirilli, D.P.Bartel. Crystal Structure of the Catalytic Core of An Rna-Polymerase Ribozyme. Science V. 326 1271 2009.
ISSN: ISSN 0036-8075
PubMed: 19965478
DOI: 10.1126/SCIENCE.1174676