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Cadmium in PDB 3heq: Human Prion Protein Variant D178N with M129

Protein crystallography data

The structure of Human Prion Protein Variant D178N with M129, PDB code: 3heq 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) 40.12 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.489, 57.489, 168.013, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Human Prion Protein Variant D178N with M129 (pdb code 3heq). 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 M129, PDB code: 3heq:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3heq

Go back to Cadmium Binding Sites List in 3heq
Cadmium binding site 1 out of 2 in the Human Prion Protein Variant D178N with M129


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 M129 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd300

b:15.2
occ:1.00
ND1 A:HIS140 2.3 14.7 1.0
O A:HOH361 2.4 16.8 1.0
O A:HOH327 2.4 14.8 1.0
OD2 A:ASP147 2.4 13.6 1.0
OD1 A:ASP147 2.5 9.6 1.0
CG A:ASP147 2.8 12.0 1.0
CE1 A:HIS140 3.2 16.7 1.0
CG A:HIS140 3.3 13.3 1.0
CB A:HIS140 3.6 12.1 1.0
CA A:HIS140 3.9 12.7 1.0
O A:HOH366 4.1 12.2 1.0
NH1 A:ARG151 4.1 23.6 1.0
O A:HOH388 4.2 33.6 1.0
CB A:ASP147 4.3 11.2 1.0
NE2 A:HIS140 4.3 17.3 1.0
CD2 A:HIS140 4.4 14.7 1.0
O A:HOH390 4.6 55.8 1.0
O A:ILE139 4.6 13.6 1.0
N A:PHE141 4.8 13.0 1.0
N A:HIS140 4.9 12.2 1.0
C A:HIS140 4.9 12.3 1.0
O A:HOH360 5.0 23.5 1.0

Cadmium binding site 2 out of 2 in 3heq

Go back to Cadmium Binding Sites List in 3heq
Cadmium binding site 2 out of 2 in the Human Prion Protein Variant D178N with M129


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 M129 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:14.4
occ:1.00
ND1 B:HIS140 2.3 13.0 1.0
OD2 B:ASP147 2.4 11.8 1.0
O B:HOH430 2.4 17.4 1.0
OD1 B:ASP147 2.4 13.2 1.0
CG B:ASP147 2.8 11.7 1.0
CE1 B:HIS140 3.2 14.7 1.0
CG B:HIS140 3.3 16.1 1.0
CB B:HIS140 3.6 14.8 1.0
CA B:HIS140 4.1 16.4 1.0
O B:HOH511 4.2 12.7 1.0
NH1 B:ARG151 4.2 15.3 1.0
CB B:ASP147 4.3 12.3 1.0
NE2 B:HIS140 4.4 17.1 1.0
CD2 B:HIS140 4.5 14.4 1.0
N B:PHE141 4.7 16.9 1.0
C B:HIS140 4.9 17.2 1.0
O B:PHE141 5.0 17.4 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: Fri Aug 28 13:42:40 2020
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