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Cadmium in PDB 6fx9: The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)

Protein crystallography data

The structure of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data), PDB code: 6fx9 was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.89 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.680, 181.680, 181.680, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.3

Other elements in 6fx9:

The structure of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) also contains other interesting chemical elements:

Gold (Au) 1 atom
Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) (pdb code 6fx9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data), PDB code: 6fx9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 6fx9

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Cadmium binding site 1 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:32.2
occ:0.40
O A:HOH304 1.8 21.6 0.4
O A:HOH438 2.1 37.2 0.4
O A:HOH367 2.1 27.1 0.4
OE1 A:GLU11 2.3 17.9 1.0
OE2 A:GLU11 2.4 26.8 1.0
CD A:GLU11 2.8 23.8 1.0
CL A:CL213 2.8 22.6 0.4
O A:HOH462 3.6 37.5 0.6
O A:HOH465 3.7 61.4 1.0
OG1 A:THR10 4.0 18.9 1.0
O A:HOH509 4.1 46.6 1.0
CG A:GLU11 4.3 19.2 1.0
CB A:SER9 4.5 13.9 1.0
OE1 A:GLN120 4.6 27.9 1.0
N A:THR10 4.7 13.3 1.0
NE2 A:GLN120 4.7 29.9 1.0
N A:GLU11 4.9 12.6 1.0
CD A:GLN120 5.0 29.3 1.0

Cadmium binding site 2 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 2 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:36.4
occ:0.30
O A:HOH308 2.1 16.0 0.3
OE1 A:GLU56 2.3 41.4 1.0
OE1 A:GLU53 2.3 29.3 0.5
OE2 A:GLU53 2.5 32.2 0.5
CD A:GLU53 2.7 23.9 0.5
CD A:GLU56 3.2 34.8 1.0
OE2 A:GLU56 3.4 47.8 1.0
O A:HOH316 3.8 45.0 1.0
CG A:GLU53 4.3 20.4 0.5
CG A:GLU56 4.6 23.3 1.0
CG A:GLU53 4.8 24.1 0.5
CB A:GLU56 4.9 17.1 1.0
CB A:GLU53 4.9 16.4 0.5

Cadmium binding site 3 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 3 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:27.6
occ:0.30
OE2 A:GLU60 2.2 37.1 1.0
OE2 A:GLU56 2.2 47.8 1.0
OE1 A:GLU60 2.4 33.4 1.0
O A:HOH307 2.5 29.6 1.0
CD A:GLU60 2.6 28.9 1.0
OE2 A:GLU57 2.9 29.8 0.5
CD A:GLU56 3.3 34.8 1.0
CG A:GLU56 3.7 23.3 1.0
O A:HOH316 3.9 45.0 1.0
CD A:GLU57 4.0 24.0 0.5
CG A:GLU60 4.2 22.3 1.0
OE1 A:GLU56 4.3 41.4 1.0
OE1 A:GLU57 4.4 24.1 0.5
O A:HOH308 4.7 16.0 0.3
CB A:GLU56 5.0 17.1 1.0

Cadmium binding site 4 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 4 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:16.8
occ:0.50
OD2 A:ASP80 2.1 19.9 1.0
OD1 A:ASP80 2.3 11.9 1.0
CL A:CL212 2.5 28.3 1.0
CG A:ASP80 2.7 16.9 1.0
CB A:ASP80 4.2 14.6 1.0
O A:HOH370 4.4 18.2 1.0
O A:HOH353 4.4 28.4 1.0
O A:HOH448 4.6 31.9 0.2

Cadmium binding site 5 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 5 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:51.0
occ:0.20
OE2 A:GLU88 2.2 35.3 1.0
CD A:GLU88 2.9 32.7 1.0
OE1 A:GLU88 3.0 35.9 1.0
O A:HOH441 3.1 48.0 1.0
NH2 A:ARG39 4.3 20.4 1.0
CG A:GLU88 4.4 21.3 1.0
NH1 A:ARG39 4.5 19.9 1.0
O A:HOH457 4.5 40.4 1.0
O A:HOH516 4.6 51.0 1.0
O A:HOH504 4.9 34.7 0.5
CZ A:ARG39 5.0 17.9 1.0

Cadmium binding site 6 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 6 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:29.8
occ:0.40
O A:HOH303 2.0 6.2 0.4
O A:HOH405 2.1 31.8 0.8
NE2 A:HIS132 2.4 42.8 1.0
CE1 A:HIS132 3.4 40.7 1.0
CD2 A:HIS132 3.5 34.9 1.0
OD2 A:ASP127 4.4 29.8 1.0
O A:HOH331 4.4 19.7 1.0
ND1 A:HIS132 4.5 41.0 1.0
CG A:HIS132 4.6 31.3 1.0
O A:HOH321 4.7 46.6 1.0
CB A:SER131 4.8 23.3 1.0
CD1 A:PHE128 5.0 15.1 1.0

Cadmium binding site 7 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 7 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:31.8
occ:0.20
CL A:CL211 1.7 11.0 0.4
OE1 A:GLU130 2.2 30.7 1.0
CD A:GLU130 3.0 27.1 1.0
OE2 A:GLU130 3.2 26.6 1.0
O A:HOH302 3.8 31.9 1.0
CG A:GLU130 4.5 22.0 1.0
CD A:CD217 4.6 25.1 0.2
CB A:GLU130 4.9 19.6 1.0

Cadmium binding site 8 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 8 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:47.3
occ:0.20
OE1 A:GLU63 2.2 34.8 1.0
NH1 A:ARG59 2.2 30.1 0.5
CD A:GLU63 3.0 33.2 1.0
OE2 A:GLU63 3.1 36.9 1.0
CZ A:ARG59 3.4 29.7 0.5
O A:HOH354 3.6 48.2 1.0
NH2 A:ARG59 4.1 31.1 0.5
NE A:ARG59 4.4 26.2 0.5
CG A:GLU63 4.5 19.5 1.0
CD A:ARG59 4.7 24.1 0.5

Cadmium binding site 9 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 9 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:31.9
occ:0.30
O A:HOH498 2.2 25.3 0.3
SG A:CYS48 2.2 19.1 1.0
CB A:CYS48 3.1 13.8 1.0
ND1 A:HIS49 3.2 31.6 0.5
C A:CYS48 3.5 11.6 1.0
CE1 A:HIS49 3.5 31.4 0.5
N A:HIS49 3.5 12.3 1.0
CD A:ARG52 3.6 26.4 1.0
O A:CYS48 3.8 12.8 1.0
O A:HOH387 3.9 55.3 1.0
CG A:HIS49 3.9 24.4 0.5
CA A:CYS48 3.9 11.6 1.0
CA A:HIS49 3.9 14.3 1.0
NH1 A:ARG52 3.9 38.0 1.0
NE2 A:HIS49 4.3 27.8 0.5
CG A:ARG52 4.3 19.8 1.0
O A:GLU45 4.4 12.1 1.0
O A:HOH313 4.4 31.4 1.0
CD2 A:HIS49 4.5 30.9 0.5
CB A:HIS49 4.5 18.2 0.5
CB A:HIS49 4.6 15.5 0.5
NE A:ARG52 4.7 28.5 1.0
CB A:ARG52 4.8 16.1 1.0
CZ A:ARG52 4.8 37.1 1.0
N A:CYS48 5.0 10.9 1.0

Cadmium binding site 10 out of 13 in 6fx9

Go back to Cadmium Binding Sites List in 6fx9
Cadmium binding site 10 out of 13 in the The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of The X-Ray Structure of the Ferritin Nanocage Containing Au and Pt, Obtained Upon Encapsulation of A Single Heterobimetallic Compound Within the Protein Cage (Synchrtron Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:54.5
occ:0.30
O A:HOH454 2.2 51.3 1.0
OE1 A:GLU45 2.3 36.3 1.0
O A:HOH325 2.4 39.2 1.0
CD A:GLU45 3.1 39.1 1.0
OE2 A:GLU45 3.3 55.3 1.0
O A:HOH411 3.4 33.4 1.0
CE A:LYS172 3.8 70.4 1.0
NZ A:LYS172 4.2 74.2 1.0
CG A:GLU45 4.6 25.1 1.0
NH1 A:ARG168 4.6 15.4 1.0
CB A:GLU45 4.9 17.4 1.0

Reference:

G.Ferraro, G.Petruk, L.Maiore, F.Pane, A.Amoresano, M.A.Cinellu, D.M.Monti, A.Merlino. Caged Noble Metals: Encapsulation of A Cytotoxic Platinum(II)-Gold(I) Compound Within the Ferritin Nanocage. Int. J. Biol. Macromol. V. 115 1116 2018.
ISSN: ISSN 1879-0003
PubMed: 29709536
DOI: 10.1016/J.IJBIOMAC.2018.04.142
Page generated: Sat Dec 12 08:28:26 2020

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