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Cadmium in PDB 3np2: Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr, PDB code: 3np2 was solved by Z.Wang, T.Ueno, S.Abe, Y.Takezawa, H.Aoyagi, T.Hikage, Y.Watanabe, S.Kitagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.36 / 1.86
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.296, 182.296, 182.296, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr (pdb code 3np2). 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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr, PDB code: 3np2:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3np2

Go back to Cadmium Binding Sites List in 3np2
Cadmium binding site 1 out of 2 in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr


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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd180

b:24.0
occ:0.50
OD2 X:ASP80 1.9 15.9 1.0
CG X:ASP80 2.7 19.7 1.0
OD1 X:ASP80 2.8 14.9 1.0
CB X:ASP80 4.1 19.2 1.0
O X:HOH262 4.5 22.7 1.0
O X:HOH263 4.6 30.9 1.0

Cadmium binding site 2 out of 2 in 3np2

Go back to Cadmium Binding Sites List in 3np2
Cadmium binding site 2 out of 2 in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr


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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd181

b:82.3
occ:0.50
OE2 X:GLU60 2.5 31.6 1.0
OE1 X:GLU60 2.6 28.6 1.0
OE2 X:GLU56 2.8 35.5 1.0
CD X:GLU60 2.9 27.2 1.0
CD X:GLU56 3.7 31.7 1.0
CG X:GLU56 3.9 23.2 1.0
CG X:GLU60 4.4 21.0 1.0
OE2 X:GLU53 4.7 25.1 0.5
OE1 X:GLU56 4.8 32.4 1.0

Reference:

Z.Wang, Y.Takezawa, H.Aoyagi, S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Definite Coordination Arrangement of Organometallic Palladium Complexes Accumulated on the Designed Interior Surface of Apo-Ferritin. Chem.Commun.(Camb.) V. 47 170 2011.
ISSN: ISSN 1359-7345
PubMed: 20730233
DOI: 10.1039/C0CC02221G
Page generated: Fri Aug 28 13:49:50 2020
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