Cadmium in PDB 3haf: Human Prion Protein Variant V129 Domain Swapped Dimer

The structure of Human Prion Protein Variant V129 Domain Swapped Dimer, PDB code: 3haf was solved by S.Lee, L.Antony, R.Hartmann, K.J.Knaus, K.Surewicz, W.K.Surewicz, V.C.Yee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.27 / 2.26
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	85.287, 86.358, 40.736, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 27.8

The structure of Human Prion Protein Variant V129 Domain Swapped Dimer also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Human Prion Protein Variant V129 Domain Swapped Dimer (pdb code 3haf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Human Prion Protein Variant V129 Domain Swapped Dimer, PDB code: 3haf:

Cadmium binding site 1 out of 1 in the Human Prion Protein Variant V129 Domain Swapped Dimer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Human Prion Protein Variant V129 Domain Swapped Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:92.3 occ:0.50 ND1 A:HIS140 2.8 59.5 0.5 CE1 A:HIS140 3.3 59.2 0.5 OD2 A:ASP147 3.4 52.4 1.0 CG A:ASP147 3.5 46.9 1.0 O A:HOH352 3.5 63.7 1.0 ND1 A:HIS140 3.5 59.7 0.5 OD1 A:ASP147 3.7 52.1 1.0 CB A:ASP147 4.0 43.2 1.0 CG A:HIS140 4.0 59.5 0.5 O A:HOH334 4.1 49.6 1.0 CE1 A:HIS140 4.4 60.0 0.5 NH1 A:ARG151 4.4 45.3 1.0 CG A:HIS140 4.4 59.7 0.5 CB A:HIS140 4.5 59.6 0.5 O A:ILE139 4.5 59.1 1.0 CB A:HIS140 4.6 59.5 0.5 NE2 A:HIS140 4.6 60.1 0.5 CA A:HIS140 4.7 59.6 0.5 CA A:HIS140 4.7 59.7 0.5 CD2 A:HIS140 5.0 59.8 0.5 CA A:ASP147 5.0 42.2 1.0

S.Lee, L.Antony, R.Hartmann, K.J.Knaus, K.Surewicz, W.K.Surewicz, V.C.Yee. Conformational Diversity in Prion Protein Variants Influences Intermolecular Beta-Sheet Formation. Embo J. V. 29 251 2010.
ISSN: ISSN 0261-4189
PubMed: 19927125
DOI: 10.1038/EMBOJ.2009.333