Cadmium in PDB 3b40: Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa

The structure of Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa, PDB code: 3b40 was solved by J.B.Bonanno, Y.Patskovsky, M.Dickey, K.T.Bain, M.Mendoza, R.Fong, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	147.123, 147.123, 147.123, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.3

The structure of Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Cadmium atom in the Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa (pdb code 3b40). 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 Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa, PDB code: 3b40:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa


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 Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:17.8 occ:1.00 OE2 A:GLU48 2.3 16.4 1.0 OE1 A:GLU51 2.4 13.2 1.0 OE1 A:GLU48 2.4 16.9 1.0 OE2 A:GLU51 2.5 12.8 1.0 CD A:GLU48 2.7 17.2 1.0 CD A:GLU51 2.8 12.4 1.0 CG A:GLU48 4.3 16.5 1.0 CG A:GLU51 4.3 12.4 1.0 NH2 A:ARG52 4.3 16.4 1.0 NH1 A:ARG52 4.5 17.1 1.0 O A:HOH702 4.6 41.3 1.0 O A:HOH564 4.9 20.2 1.0 CZ A:ARG52 4.9 17.6 1.0 CA A:GLU48 5.0 17.0 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa


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 Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2 b:34.2 occ:1.00 NE2 A:HIS384 2.3 13.2 1.0 O A:HOH793 2.3 27.2 1.0 O A:HOH792 2.4 16.4 1.0 O A:HOH530 2.5 24.9 1.0 O A:HOH794 2.7 28.2 1.0 CE1 A:HIS384 3.2 15.9 1.0 CD2 A:HIS384 3.3 11.9 1.0 O A:HOH612 4.0 29.2 1.0 NZ A:LYS287 4.2 30.2 1.0 ND1 A:HIS384 4.3 13.7 1.0 CG A:HIS384 4.4 12.4 1.0 CB A:ASP383 4.6 14.2 1.0 OD2 A:ASP383 4.6 23.9 1.0 O A:HOH791 4.7 14.9 1.0

J.B.Bonanno, Y.Patskovsky, M.Dickey, K.T.Bain, M.Mendoza, R.Fong, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of the Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa. To Be Published.