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Cadmium in PDB 1w9h: The Structure of A Piwi Protein From Archaeoglobus Fulgidus.

Protein crystallography data

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus., PDB code: 1w9h was solved by J.S.Parker, S.M.Roe, D.Barford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.01 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.090, 137.863, 51.663, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.7

Other elements in 1w9h:

The structure of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. also contains other interesting chemical elements:

Nickel (Ni) 5 atoms
Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus. (pdb code 1w9h). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus., PDB code: 1w9h:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 1w9h

Go back to Cadmium Binding Sites List in 1w9h
Cadmium binding site 1 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1428

b:8.8
occ:1.00
OXT A:LEU427 2.4 5.2 1.0
OE1 A:GLN159 2.5 2.0 1.0
O A:HOH2080 2.5 2.0 1.0
CL A:CL1435 2.6 15.7 1.0
O A:LEU427 2.6 5.1 1.0
CL A:CL1436 2.7 13.5 1.0
C A:LEU427 2.8 5.3 1.0
CD A:GLN159 3.3 1.4 1.0
NE2 A:GLN159 3.5 2.6 1.0
NZ A:LYS163 4.1 3.2 1.0
NE2 A:GLN137 4.1 8.9 1.0
O A:HOH2238 4.2 4.2 1.0
O A:HOH2237 4.3 8.7 1.0
CA A:LEU427 4.3 3.2 1.0
NZ A:LYS127 4.4 15.6 1.0
NH2 A:ARG380 4.4 18.2 1.0
NE A:ARG380 4.4 12.6 1.0
CG A:GLN159 4.7 2.4 1.0
O A:HOH2075 4.7 21.2 1.0
CE A:LYS163 4.9 2.4 1.0
CZ A:ARG380 4.9 17.6 1.0
CB A:LEU427 5.0 3.0 1.0

Cadmium binding site 2 out of 2 in 1w9h

Go back to Cadmium Binding Sites List in 1w9h
Cadmium binding site 2 out of 2 in the The Structure of A Piwi Protein From Archaeoglobus Fulgidus.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Structure of A Piwi Protein From Archaeoglobus Fulgidus. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1429

b:14.3
occ:1.00
CL A:CL1438 2.3 17.0 1.0
OE1 A:GLN99 2.4 17.2 1.0
CL A:CL1437 2.4 15.6 1.0
CD A:GLN99 3.3 15.8 1.0
NE2 A:GLN99 3.5 18.0 1.0
O A:ILE87 4.2 17.1 1.0
ND2 A:ASN102 4.3 18.1 1.0
CD1 A:PHE86 4.5 10.5 1.0
N A:ILE87 4.6 14.6 1.0
CG A:GLN99 4.7 14.1 1.0
CB A:PHE86 4.9 10.0 1.0

Reference:

J.S.Parker, S.M.Roe, D.Barford. Crystal Structure of A Piwi Protein Suggests Mechanisms For Sirna Recognition and Slicer Activity Embo J. V. 23 4727 2004.
ISSN: ISSN 0261-4189
PubMed: 15565169
DOI: 10.1038/SJ.EMBOJ.7600488
Page generated: Sat Dec 12 08:15:17 2020

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