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Cadmium in PDB 7bd7: X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin

Protein crystallography data

The structure of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin, PDB code: 7bd7 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.54 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.91, 180.91, 180.91, 90, 90, 90
R / Rfree (%) 16.6 / 18.5

Other elements in 7bd7:

The structure of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin also contains other interesting chemical elements:

Arsenic (As) 1 atom
Sodium (Na) 3 atoms
Chlorine (Cl) 1 atom
Platinum (Pt) 1 atom

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin (pdb code 7bd7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin, PDB code: 7bd7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in 7bd7

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Cadmium binding site 1 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:24.1
occ:0.40
O A:HOH304 1.6 19.9 0.4
O A:HOH375 1.9 22.1 0.5
OE1 A:GLU11 2.4 18.3 1.0
OE2 A:GLU11 2.6 26.5 1.0
CL A:CL222 2.7 42.6 1.0
CD A:GLU11 2.8 23.3 1.0
O A:HOH441 3.7 52.4 1.0
OG1 A:THR10 3.9 18.2 1.0
CG A:GLU11 4.4 18.6 1.0
OE1 A:GLN120 4.4 28.5 1.0
CB A:SER9 4.5 12.2 1.0
N A:THR10 4.6 11.9 1.0
NE2 A:GLN120 4.7 28.0 1.0
CD A:GLN120 4.9 23.5 1.0
N A:GLU11 4.9 12.5 1.0

Cadmium binding site 2 out of 15 in 7bd7

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Cadmium binding site 2 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:13.3
occ:0.50
OD1 A:ASP80 2.3 10.9 1.0
OD2 A:ASP80 2.4 13.3 1.0
O A:HOH462 2.5 9.4 1.0
CG A:ASP80 2.7 12.7 1.0
CB A:ASP80 4.2 11.6 1.0
O A:HOH322 4.6 26.5 1.0

Cadmium binding site 3 out of 15 in 7bd7

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Cadmium binding site 3 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:38.9
occ:0.40
OE2 A:GLU60 2.2 37.9 1.0
OE2 A:GLU56 2.3 43.4 1.0
CD A:CD215 2.6 66.6 0.5
O A:HOH443 2.7 33.1 0.5
CD A:GLU60 2.8 31.4 1.0
OE1 A:GLU60 2.8 32.9 1.0
OE2 A:GLU57 3.3 51.3 1.0
CD A:GLU56 3.3 33.2 1.0
CG A:GLU56 3.7 23.3 1.0
O A:HOH348 4.1 56.9 1.0
CG A:GLU60 4.3 22.9 1.0
O A:HOH309 4.4 18.1 0.5
OE1 A:GLU56 4.4 36.3 1.0
CD A:GLU57 4.5 36.1 1.0
O A:HOH509 4.7 63.1 1.0

Cadmium binding site 4 out of 15 in 7bd7

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Cadmium binding site 4 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:72.6
occ:0.50
ND1 A:HIS132 2.3 44.1 1.0
CE1 A:HIS132 3.2 46.6 1.0
CG A:HIS132 3.3 34.5 1.0
CB A:HIS132 3.5 27.3 1.0
NE A:ARG64 3.5 45.8 1.0
OE2 A:GLU136 3.6 77.0 1.0
NH2 A:ARG64 3.6 58.0 1.0
CZ A:ARG64 3.6 50.9 1.0
CA A:HIS132 3.6 23.3 1.0
O A:SER131 4.3 29.3 1.0
O A:HIS132 4.3 22.7 1.0
CD A:ARG64 4.3 35.5 1.0
NH1 A:ARG64 4.4 54.2 1.0
NE2 A:HIS132 4.4 44.8 1.0
CD2 A:HIS132 4.4 39.5 1.0
C A:HIS132 4.5 20.5 1.0
CD A:GLU136 4.5 62.3 1.0
OE1 A:GLU136 4.6 75.2 1.0
N A:HIS132 4.7 20.1 1.0
C A:SER131 4.8 28.7 1.0

Cadmium binding site 5 out of 15 in 7bd7

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Cadmium binding site 5 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:40.6
occ:0.20
OE1 A:GLU130 2.5 30.7 1.0
CD A:GLU130 3.4 29.5 1.0
OE2 A:GLU130 3.6 35.2 1.0
O A:HOH301 3.7 7.3 0.2
O A:HOH463 4.2 42.2 1.0
CD A:CD209 4.3 32.5 0.2
CG A:GLU130 4.8 25.0 1.0

Cadmium binding site 6 out of 15 in 7bd7

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Cadmium binding site 6 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:32.5
occ:0.20
O A:HOH301 2.3 7.3 0.2
OD1 A:ASP127 3.7 26.7 1.0
O A:HOH335 4.0 50.8 1.0
OE1 A:GLU130 4.2 30.7 1.0
CD A:CD208 4.3 40.6 0.2
OG A:SER131 4.4 38.1 1.0
CG A:ASP127 4.9 28.9 1.0
CB A:GLU130 5.0 22.7 1.0

Cadmium binding site 7 out of 15 in 7bd7

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Cadmium binding site 7 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:39.6
occ:0.50
O A:HOH309 2.1 18.1 0.5
OE1 A:GLU53 2.4 39.7 1.0
OE2 A:GLU53 2.5 41.0 1.0
OE1 A:GLU56 2.5 36.3 1.0
CD A:GLU53 2.8 30.4 1.0
CD A:GLU56 3.4 33.2 1.0
OE2 A:GLU56 3.5 43.4 1.0
O A:HOH348 4.2 56.9 1.0
O A:HOH320 4.2 19.5 0.5
CG A:GLU53 4.3 23.4 1.0
C4 A:A6R223 4.5 29.9 0.4
CG A:GLU56 4.7 23.3 1.0

Cadmium binding site 8 out of 15 in 7bd7

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Cadmium binding site 8 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:40.9
occ:0.50
NE2 A:HIS114 2.6 21.2 1.0
CE1 A:HIS114 2.8 20.4 1.0
O A:HOH463 3.0 42.2 1.0
CB A:CYS126 3.2 23.1 1.0
SG A:CYS126 3.4 34.0 1.0
OE2 A:GLU130 3.4 35.2 1.0
CD2 A:HIS114 3.8 19.1 1.0
ND1 A:HIS114 4.0 23.8 1.0
CA A:CYS126 4.5 19.4 1.0
CD A:GLU130 4.5 29.5 1.0
CG A:HIS114 4.5 18.3 1.0

Cadmium binding site 9 out of 15 in 7bd7

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Cadmium binding site 9 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:48.9
occ:0.40
O A:HOH410 2.4 48.2 1.0
OE2 A:GLU45 2.5 38.1 1.0
OE1 A:GLU45 2.9 35.6 1.0
CD A:GLU45 3.0 33.7 1.0
O A:HOH431 3.5 45.4 1.0
CG A:GLU45 4.5 29.2 1.0
NH1 A:ARG168 4.6 16.0 1.0

Cadmium binding site 10 out of 15 in 7bd7

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Cadmium binding site 10 out of 15 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd213

b:35.1
occ:0.40
CD A:CD214 2.6 65.2 0.4
NE2 A:HIS132 2.6 44.8 1.0
CE1 A:HIS132 3.6 46.6 1.0
CD2 A:HIS132 3.6 39.5 1.0
O A:HOH329 4.6 28.1 1.0
OD2 A:ASP127 4.7 31.4 1.0
ND1 A:HIS132 4.7 44.1 1.0
CG A:HIS132 4.7 34.5 1.0
CB A:SER131 4.8 30.6 1.0
O A:HOH303 4.9 28.3 1.0
CD1 A:PHE128 4.9 17.7 1.0

Reference:

G.Ferraro, A.Pratesi, D.Cirri, P.Imbimbo, D.Maria Monti, L.Messori, A.Merlino. Arsenoplatin-Ferritin Nanocage: Structure and Cytotoxicity. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 33668605
DOI: 10.3390/IJMS22041874
Page generated: Sat Apr 17 14:38:34 2021

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