Cadmium in PDB 3hjx: Human Prion Protein Variant D178N with V129

The structure of Human Prion Protein Variant D178N with V129, PDB code: 3hjx 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)	27.38 / 2.00
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.159, 57.656, 93.315, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.6

The structure of Human Prion Protein Variant D178N with V129 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Human Prion Protein Variant D178N with V129 (pdb code 3hjx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Human Prion Protein Variant D178N with V129, PDB code: 3hjx:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Human Prion Protein Variant D178N with V129


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 D178N with V129 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:16.3 occ:0.65 CD A:CD300 0.0 16.3 0.7 CD A:CD300 1.4 15.7 0.3 OD2 A:ASP147 2.3 20.6 1.0 OD1 A:ASP147 2.4 26.4 1.0 ND1 A:HIS140 2.4 18.7 1.0 O A:HOH350 2.4 32.0 1.0 CG A:ASP147 2.7 23.0 1.0 CG A:HIS140 3.3 19.2 1.0 CE1 A:HIS140 3.4 19.7 1.0 CB A:HIS140 3.5 18.2 1.0 O A:HOH354 3.6 9.0 0.3 CA A:HIS140 4.0 18.9 1.0 O A:HOH302 4.1 16.9 1.0 CB A:ASP147 4.2 20.1 1.0 N A:PHE141 4.4 20.8 1.0 CD2 A:HIS140 4.5 17.9 1.0 NE2 A:HIS140 4.5 18.3 1.0 O A:HOH354 4.7 10.8 0.7 O A:PHE141 4.7 22.5 1.0 C A:HIS140 4.7 19.8 1.0 O A:ILE139 4.8 16.7 1.0

Cadmium binding site 2 out of 2 in the Human Prion Protein Variant D178N with V129


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Human Prion Protein Variant D178N with V129 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:15.7 occ:0.35 CD A:CD300 0.0 15.7 0.3 CD A:CD300 1.4 16.3 0.7 O A:HOH354 2.4 9.0 0.3 OD1 A:ASP147 2.5 26.4 1.0 ND1 A:HIS140 2.5 18.7 1.0 OD2 A:ASP147 2.7 20.6 1.0 CG A:ASP147 2.9 23.0 1.0 O A:HOH302 3.1 16.9 1.0 CE1 A:HIS140 3.1 19.7 1.0 CG A:HIS140 3.7 19.2 1.0 O A:HOH354 3.7 10.8 0.7 O A:HOH350 3.8 32.0 1.0 NE A:ARG151 4.0 35.1 1.0 CB A:HIS140 4.2 18.2 1.0 CB A:ASP147 4.3 20.1 1.0 NE2 A:HIS140 4.4 18.3 1.0 CA A:HIS140 4.4 18.9 1.0 O A:ILE139 4.4 16.7 1.0 CG2 A:ILE138 4.5 21.8 1.0 O A:ASP147 4.6 19.5 1.0 CD A:ARG151 4.6 31.9 1.0 CD2 A:HIS140 4.7 17.9 1.0 NH1 A:ARG151 4.7 30.6 1.0 CZ A:ARG151 4.8 32.7 1.0 CA A:ASP147 4.9 20.6 1.0 C A:ASP147 5.0 20.6 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