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Cadmium in PDB 1i4m: Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization

Protein crystallography data

The structure of Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization, PDB code: 1i4m was solved by K.J.Knaus, M.Morillas, W.Swietnicki, M.Malone, 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) 27.10 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.441, 85.707, 40.501, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization (pdb code 1i4m). 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 the Human Prion Protein Reveals A Mechanism For Oligomerization, PDB code: 1i4m:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1i4m

Go back to Cadmium Binding Sites List in 1i4m
Cadmium binding site 1 out of 2 in the Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization


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 the Human Prion Protein Reveals A Mechanism For Oligomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd300

b:48.1
occ:1.00
O A:HOH4 1.6 26.2 1.0
OD2 A:ASP147 2.3 42.7 1.0
ND1 A:HIS140 2.5 53.7 1.0
OD1 A:ASP147 2.6 41.0 1.0
O A:HOH2 2.6 34.8 1.0
O A:HOH3 2.7 28.3 1.0
CG A:ASP147 2.8 38.8 1.0
CE1 A:HIS140 3.3 53.5 1.0
CG A:HIS140 3.4 49.1 1.0
CB A:HIS140 3.7 47.4 1.0
O A:HOH75 3.8 35.9 1.0
CA A:HIS140 4.1 47.9 1.0
O A:HOH41 4.2 52.7 1.0
CB A:ASP147 4.3 36.8 1.0
NH1 A:ARG151 4.3 34.4 1.0
NE2 A:HIS140 4.4 54.6 1.0
CD2 A:HIS140 4.4 51.9 1.0
N A:PHE141 4.9 47.1 1.0
O A:ASP147 5.0 28.4 1.0

Cadmium binding site 2 out of 2 in 1i4m

Go back to Cadmium Binding Sites List in 1i4m
Cadmium binding site 2 out of 2 in the Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization


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 the Human Prion Protein Reveals A Mechanism For Oligomerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:59.6
occ:1.00
ND1 A:HIS177 2.3 31.0 1.0
O A:HOH7 2.8 47.1 1.0
O A:HOH9 2.9 45.8 1.0
O A:HOH6 3.0 43.8 1.0
O A:HOH8 3.0 54.0 1.0
CE1 A:HIS177 3.1 27.7 1.0
CG A:HIS177 3.3 28.3 1.0
CB A:HIS177 3.7 25.5 1.0
O A:HOH10 4.0 49.3 1.0
CA A:HIS177 4.2 27.4 1.0
NE2 A:HIS177 4.3 28.1 1.0
CD2 A:HIS177 4.4 30.3 1.0
ND2 A:ASN181 4.5 26.0 1.0
O A:HOH50 4.9 38.5 1.0

Reference:

K.J.Knaus, M.Morillas, W.Swietnicki, M.Malone, W.K.Surewicz, V.C.Yee. Crystal Structure of the Human Prion Protein Reveals A Mechanism For Oligomerization. Nat.Struct.Biol. V. 8 770 2001.
ISSN: ISSN 1072-8368
PubMed: 11524679
DOI: 10.1038/NSB0901-770
Page generated: Fri Aug 28 11:56:33 2020
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