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Cadmium in PDB 2z5p: Apo-Fr with Low Content of Pd Ions

Protein crystallography data

The structure of Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p was solved by T.Ueno, K.Hirata, M.Abe, M.Suzuki, S.Abe, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.79 / 1.65
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.790, 180.790, 180.790, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.8

Other elements in 2z5p:

The structure of Apo-Fr with Low Content of Pd Ions also contains other interesting chemical elements:

Palladium (Pd) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apo-Fr with Low Content of Pd Ions (pdb code 2z5p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 2z5p

Go back to Cadmium Binding Sites List in 2z5p
Cadmium binding site 1 out of 2 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:13.6
occ:0.50
OD1 A:ASP80 2.4 10.6 1.0
OD2 A:ASP80 2.4 12.9 1.0
CG A:ASP80 2.8 11.0 1.0
CB A:ASP80 4.3 11.1 1.0
O A:HOH1020 4.3 14.1 1.0
O A:HOH1028 4.6 20.1 1.0

Cadmium binding site 2 out of 2 in 2z5p

Go back to Cadmium Binding Sites List in 2z5p
Cadmium binding site 2 out of 2 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apo-Fr with Low Content of Pd Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:0.6
occ:0.10
NE2 A:HIS132 2.7 27.0 0.5
CD2 A:HIS132 3.1 26.5 0.5
OG A:SER131 3.7 26.5 0.5
OD2 A:ASP127 3.9 27.3 0.3
CE1 A:HIS132 4.0 26.9 0.5
CG A:HIS132 4.4 25.0 0.5
CA A:PHE128 4.5 24.6 0.8
O A:ASP127 4.7 26.2 0.6
ND1 A:HIS132 4.8 26.6 0.5
CG A:ASP127 4.9 27.0 0.3
N A:PHE128 4.9 25.4 0.8
C A:ASP127 5.0 26.2 1.0

Reference:

T.Ueno, M.Abe, K.Hirata, S.Abe, M.Suzuki, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe. Process of Accumulation of Metal Ions on the Interior Surface of Apo-Ferritin: Crystal Structures of A Series of Apo-Ferritins Containing Variable Quantities of Pd(II) Ions. J.Am.Chem.Soc. V. 131 5094 2009.
ISSN: ISSN 0002-7863
PubMed: 19317403
DOI: 10.1021/JA806688S
Page generated: Sat Dec 12 08:18:47 2020

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