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Cadmium in PDB 3af9: Crystal Structure of Pd(Allyl)/Apo-C48AFR

Protein crystallography data

The structure of Crystal Structure of Pd(Allyl)/Apo-C48AFR, PDB code: 3af9 was solved by S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.55 / 1.85
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.433, 182.433, 182.433, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Pd(Allyl)/Apo-C48AFR (pdb code 3af9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Pd(Allyl)/Apo-C48AFR, PDB code: 3af9:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 3af9

Go back to Cadmium Binding Sites List in 3af9
Cadmium binding site 1 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-C48AFR


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-C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd176

b:27.3
occ:0.50
OD2 X:ASP80 2.2 25.0 1.0
OD1 X:ASP80 2.7 18.7 1.0
CG X:ASP80 2.8 20.6 1.0
CB X:ASP80 4.3 18.2 1.0
O X:HOH283 4.7 21.5 1.0

Cadmium binding site 2 out of 3 in 3af9

Go back to Cadmium Binding Sites List in 3af9
Cadmium binding site 2 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-C48AFR


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-C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd177

b:44.8
occ:0.20
NE2 X:HIS49 2.4 14.7 0.5
CE1 X:HIS49 3.2 14.6 0.5
CD2 X:HIS49 3.4 14.4 0.5
ND1 X:HIS49 4.3 14.8 0.5
CG X:HIS49 4.5 12.0 0.5

Cadmium binding site 3 out of 3 in 3af9

Go back to Cadmium Binding Sites List in 3af9
Cadmium binding site 3 out of 3 in the Crystal Structure of Pd(Allyl)/Apo-C48AFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Pd(Allyl)/Apo-C48AFR within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd178

b:28.3
occ:0.20
OD2 X:ASP135 2.1 25.0 1.0
CG X:ASP135 3.1 21.5 1.0
OD1 X:ASP135 3.5 25.3 1.0
CG X:GLU130 4.4 24.1 1.0
CB X:ASP135 4.5 16.9 1.0
O X:GLU130 4.7 22.9 1.0
CA X:SER131 4.7 24.2 1.0
OE2 X:GLU130 4.9 28.8 1.0
C X:GLU130 4.9 22.9 1.0

Reference:

S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes Into the Protein Nanocage of Apo-Ferritin. Inorg.Chem. V. 49 6967 2010.
ISSN: ISSN 0020-1669
PubMed: 20586408
DOI: 10.1021/IC1003758
Page generated: Fri Aug 28 13:21:11 2020
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