Cadmium in PDB 3c4t: Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer

The structure of Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer, PDB code: 3c4t was solved by J.K.Lee, Z.Du, R.J.Tjhen, R.M.Stroud, T.L.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.80
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.126, 70.126, 132.663, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 30.4

The binding sites of Cadmium atom in the Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer (pdb code 3c4t). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer, PDB code: 3c4t:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1 b:0.1 occ:1.00 NE2 A:HIS1703 2.9 0.0 1.0 CE1 A:HIS1703 3.7 98.7 1.0 OE1 A:GLU1827 4.0 0.0 1.0 CD2 A:HIS1703 4.0 97.0 1.0 CD A:GLU1827 4.5 0.1 1.0 CG2 A:ILE1826 4.6 95.8 1.0 OH A:TYR1819 4.7 93.7 1.0 ND1 A:HIS1703 4.9 98.3 1.0 OE2 A:GLU1827 4.9 0.1 1.0 CB A:GLU1827 5.0 98.3 1.0

Cadmium binding site 2 out of 3 in the Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2 b:0.9 occ:1.00 CE1 A:HIS1645 2.6 0.9 1.0 NE2 A:HIS1645 3.1 0.9 1.0 ND1 A:HIS1645 3.8 0.7 1.0 O A:HOH1905 4.2 83.7 1.0 CD2 A:HIS1645 4.4 0.8 1.0 CG A:HIS1645 4.8 0.6 1.0

Cadmium binding site 3 out of 3 in the Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Rnaseiiib and Dsrna Binding Domains of Mouse Dicer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd3 b:0.3 occ:1.00 OE1 A:GLU1797 2.5 87.8 1.0 OE2 A:GLU1689 2.9 0.6 1.0 OD1 A:ASP1794 2.9 89.9 1.0 CD A:GLU1689 3.3 0.7 1.0 CD A:GLU1797 3.4 83.9 1.0 CG A:GLU1689 3.6 97.2 1.0 OE2 A:GLU1797 3.8 86.8 1.0 OE1 A:GLU1689 4.0 0.6 1.0 CG A:ASP1794 4.1 88.7 1.0 ND2 A:ASN1726 4.3 0.4 1.0 CA A:ASP1794 4.3 85.6 1.0 OD1 A:ASP1693 4.6 90.2 1.0 CB A:ASP1794 4.6 86.0 1.0 CG A:GLU1797 4.6 79.0 1.0 N A:ASP1794 4.9 86.8 1.0 CB A:GLU1689 4.9 94.8 1.0 CB A:GLU1797 4.9 76.1 1.0 O A:GLU1689 5.0 94.7 1.0

Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, T.L.James. Structural and Biochemical Insights Into the Dicing Mechanism of Mouse Dicer: A Conserved Lysine Is Critical For Dsrna Cleavage. Proc.Natl.Acad.Sci.Usa V. 105 2391 2008.
ISSN: ISSN 0027-8424
PubMed: 18268334
DOI: 10.1073/PNAS.0711506105