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Cadmium in PDB 3her: Human Prion Protein Variant F198S with V129

Protein crystallography data

The structure of Human Prion Protein Variant F198S with V129, PDB code: 3her 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) 28.81 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.611, 57.611, 163.337, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Human Prion Protein Variant F198S with V129 (pdb code 3her). 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 F198S with V129, PDB code: 3her:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3her

Go back to Cadmium Binding Sites List in 3her
Cadmium binding site 1 out of 2 in the Human Prion Protein Variant F198S 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 F198S with V129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd300

b:23.5
occ:1.00
ND1 A:HIS140 2.3 17.2 1.0
OD2 A:ASP147 2.4 21.6 1.0
OD1 A:ASP147 2.4 21.3 1.0
O A:HOH324 2.5 23.1 1.0
O A:HOH325 2.5 28.8 1.0
CG A:ASP147 2.7 22.4 1.0
CE1 A:HIS140 3.2 22.9 1.0
CG A:HIS140 3.3 19.2 1.0
CB A:HIS140 3.6 19.9 1.0
CA A:HIS140 4.0 19.9 1.0
O A:HOH306 4.2 24.4 1.0
O A:HOH326 4.2 30.3 1.0
CB A:ASP147 4.2 24.6 1.0
NH1 A:ARG151 4.3 28.9 1.0
NE2 A:HIS140 4.4 21.6 1.0
CD2 A:HIS140 4.4 18.9 1.0
N A:PHE141 4.5 24.3 1.0
O A:PHE141 4.6 28.2 1.0
O A:HOH308 4.7 42.3 1.0
C A:HIS140 4.8 22.5 1.0
O A:ILE139 4.9 22.3 1.0

Cadmium binding site 2 out of 2 in 3her

Go back to Cadmium Binding Sites List in 3her
Cadmium binding site 2 out of 2 in the Human Prion Protein Variant F198S 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 F198S with V129 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:43.5
occ:1.00
ND1 B:HIS140 2.0 36.7 1.0
OD2 B:ASP147 2.5 33.5 1.0
OD1 B:ASP147 2.6 32.0 1.0
O B:HOH438 2.6 44.6 1.0
CG B:ASP147 2.9 32.4 1.0
CE1 B:HIS140 3.0 38.7 1.0
CG B:HIS140 3.1 32.8 1.0
O B:HOH435 3.4 45.6 1.0
CB B:HIS140 3.4 32.9 1.0
CA B:HIS140 3.9 32.5 1.0
NE2 B:HIS140 4.1 32.8 1.0
CD2 B:HIS140 4.2 31.7 1.0
NH1 B:ARG151 4.3 52.4 1.0
CB B:ASP147 4.4 34.3 1.0
O B:HOH429 4.4 36.7 1.0
N B:PHE141 4.5 34.3 1.0
C B:HIS140 4.7 33.6 1.0
O B:ILE139 4.7 30.3 1.0
O B:PHE141 4.9 35.6 1.0
N B:HIS140 5.0 31.3 1.0

Reference:

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
Page generated: Wed Oct 28 10:03:23 2020
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