Cadmium in PDB 4uto: Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State

The structure of Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State, PDB code: 4uto was solved by Z.Luo, R.M.Counago, M.Maher, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.737, 59.292, 62.468, 106.86, 104.90, 93.37
R / Rfree (%)	18.1 / 21.4

The binding sites of Cadmium atom in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State (pdb code 4uto). 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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State, PDB code: 4uto:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State


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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1310 b:13.2 occ:0.21 NE2 A:HIS139 2.6 9.7 1.0 OE2 A:GLU205 2.6 20.1 1.0 OE1 A:GLU205 2.6 21.5 1.0 O A:HOH2037 2.7 45.1 1.0 CD A:GLU205 2.9 23.0 1.0 HE1 A:HIS67 3.0 24.1 0.6 HE1 A:HIS139 3.1 10.9 1.0 CE1 A:HIS139 3.2 10.0 1.0 CE1 A:HIS67 3.4 22.1 0.6 NE2 A:HIS67 3.4 22.1 0.6 HB3 A:ALA207 3.6 10.4 1.0 CD2 A:HIS139 3.7 8.8 1.0 HG12 A:ILE225 3.8 21.0 1.0 HD2 A:HIS139 4.0 11.8 1.0 HB2 A:ALA207 4.1 8.8 1.0 HG21 A:ILE225 4.3 21.9 1.0 CB A:ALA207 4.3 9.3 1.0 CG A:GLU205 4.3 13.7 1.0 ND1 A:HIS139 4.4 8.9 1.0 ND1 A:HIS67 4.4 22.9 0.6 HD21 A:ASN280 4.5 41.7 1.0 HG2 A:GLU205 4.5 15.2 1.0 CD2 A:HIS67 4.5 22.4 0.6 O A:HOH2188 4.6 19.2 1.0 CG A:HIS139 4.7 7.3 1.0 O A:HOH2187 4.7 37.1 1.0 HA A:ILE225 4.8 13.9 1.0 CG1 A:ILE225 4.8 20.1 1.0 HG3 A:GLU205 4.9 16.9 1.0 HB3 A:GLU205 4.9 9.7 1.0 HD1 A:HIS67 4.9 26.0 0.6 HB1 A:ALA207 4.9 6.0 1.0 HA A:ALA207 5.0 8.1 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State


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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1310 b:17.2 occ:0.18 NE2 B:HIS139 2.5 10.2 1.0 HE1 B:HIS67 2.6 24.1 0.5 OE1 B:GLU205 2.7 21.9 1.0 OE2 B:GLU205 2.8 27.6 1.0 CE1 B:HIS67 3.0 23.1 0.5 CD B:GLU205 3.1 28.5 1.0 HE1 B:HIS139 3.2 13.4 1.0 NE2 B:HIS67 3.2 23.8 0.5 CE1 B:HIS139 3.2 9.6 1.0 CD2 B:HIS139 3.7 9.3 1.0 HB3 B:ALA207 3.7 11.4 1.0 HD2 B:HIS139 3.9 11.4 1.0 ND1 B:HIS67 4.1 23.8 0.5 HG12 B:ILE225 4.1 20.4 1.0 HD21 B:ASN280 4.1 28.8 1.0 HG21 B:ILE225 4.2 24.3 1.0 HB2 B:ALA207 4.2 11.2 1.0 CD2 B:HIS67 4.3 24.6 0.5 CB B:ALA207 4.4 10.9 1.0 ND1 B:HIS139 4.4 8.3 1.0 HD1 B:HIS67 4.5 26.1 0.5 CG B:GLU205 4.5 11.9 1.0 O B:HOH2174 4.7 20.3 1.0 CG B:HIS139 4.7 8.2 1.0 HG2 B:GLU205 4.7 10.8 1.0 O B:HOH2204 4.7 27.3 1.0 CG B:HIS67 4.8 23.5 0.5 ND2 B:ASN280 4.8 23.5 1.0 HD2 B:HIS67 4.9 26.3 0.5 HB3 B:GLU205 5.0 7.0 1.0

S.L.Begg, B.A.Eijkelkamp, Z.Luo, R.M.Counago, J.R.Morey, M.J.Maher, C.Y.Ong, A.G.Mcewan, B.Kobe, M.L.O'mara, J.C.Paton, C.A.Mcdevitt. Dysregulation of Transition Metal Ion Homeostasis Is the Molecular Basis For Cadmium Toxicity in Streptococcus Pneumoniae. Nat.Commun. V. 6 6418 2015.
ISSN: ISSN 2041-1723
PubMed: 25731976
DOI: 10.1038/NCOMMS7418