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Cadmium in PDB 5mik: X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)

Protein crystallography data

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data), PDB code: 5mik was solved by N.Pontillo, G.Ferraro, J.R.Helliwell, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.30 / 1.96
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.654, 180.654, 180.654, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.2

Other elements in 5mik:

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) also contains other interesting chemical elements:

Platinum (Pt) 4 atoms
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 X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) (pdb code 5mik). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data), PDB code: 5mik:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 5mik

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Cadmium binding site 1 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:49.4
occ:0.40
O A:HOH360 2.1 21.4 0.4
OE1 A:GLU11 2.6 20.8 1.0
OE2 A:GLU11 2.8 26.9 1.0
O A:HOH416 2.9 27.5 1.0
CD A:GLU11 3.1 24.6 1.0
OG1 A:THR10 4.0 24.5 1.0
CB A:SER9 4.4 15.5 1.0
OE1 A:GLN120 4.5 35.5 1.0
CG A:GLU11 4.6 22.6 1.0
NE2 A:GLN120 4.7 34.7 1.0
N A:THR10 4.7 14.8 1.0

Cadmium binding site 2 out of 13 in 5mik

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Cadmium binding site 2 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:33.8
occ:0.30
O A:HOH310 2.0 7.6 0.3
OE1 A:GLU53 2.4 25.3 0.5
OE1 A:GLU56 2.5 25.1 0.6
OE2 A:GLU53 2.5 24.3 0.5
CD A:GLU53 2.8 21.9 0.5
CD A:GLU56 3.2 22.1 0.6
OE2 A:GLU56 3.3 26.1 0.6
O A:HOH315 4.2 49.3 1.0
CG A:GLU53 4.3 20.9 0.5
CG A:GLU56 4.6 18.9 0.6
CG A:GLU53 4.8 25.1 0.5
CB A:GLU56 4.9 16.7 0.6
CG A:GLU56 4.9 18.1 0.4

Cadmium binding site 3 out of 13 in 5mik

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Cadmium binding site 3 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:51.4
occ:0.50
CD A:CD203 0.0 51.4 0.5
CD A:CD203 2.3 46.5 0.3
OE2 A:GLU60 2.4 40.5 1.0
OE2 A:GLU56 2.5 26.1 0.6
OE1 A:GLU57 2.6 16.4 0.3
OE1 A:GLU60 2.7 34.0 1.0
CD A:GLU60 2.9 32.4 1.0
CD A:GLU56 3.4 22.1 0.6
CD A:GLU57 3.6 15.7 0.3
CG A:GLU56 3.6 18.9 0.6
OE2 A:GLU57 4.0 14.7 0.3
O A:HOH315 4.1 49.3 1.0
CG A:GLU60 4.4 25.7 1.0
CL A:CL214 4.4 34.9 0.3
OE1 A:GLU56 4.5 25.1 0.6
O A:HOH310 4.8 7.6 0.3
CB A:GLU56 4.9 16.7 0.6
CG A:GLU57 5.0 15.4 0.3

Cadmium binding site 4 out of 13 in 5mik

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Cadmium binding site 4 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:46.5
occ:0.30
CD A:CD203 0.0 46.5 0.3
CL A:CL214 2.2 34.9 0.3
CD A:CD203 2.3 51.4 0.5
OE2 A:GLU57 2.4 14.7 0.3
OE1 A:GLU60 2.4 34.0 1.0
OE1 A:GLU57 2.7 16.4 0.3
CD A:GLU57 2.9 15.7 0.3
CD A:GLU60 3.5 32.4 1.0
OE2 A:GLU60 3.8 40.5 1.0
CG A:GLU57 4.4 27.7 0.7
CG A:GLU57 4.4 15.4 0.3
O A:HOH315 4.6 49.3 1.0
OE2 A:GLU56 4.8 26.1 0.6
CG A:GLU60 4.8 25.7 1.0

Cadmium binding site 5 out of 13 in 5mik

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Cadmium binding site 5 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:18.1
occ:0.50
OD2 A:ASP80 2.2 15.7 1.0
CL A:CL213 2.3 29.8 1.0
OD1 A:ASP80 2.5 15.5 1.0
CG A:ASP80 2.8 15.4 1.0
CB A:ASP80 4.2 15.9 1.0
O A:HOH342 4.5 19.1 1.0
O A:HOH413 4.5 31.4 0.2
O A:HOH353 4.5 31.9 1.0

Cadmium binding site 6 out of 13 in 5mik

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Cadmium binding site 6 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:62.0
occ:0.20
OE2 A:GLU88 2.6 40.1 1.0
OE1 A:GLU88 2.9 40.7 1.0
CD A:GLU88 3.1 33.8 1.0
O A:HOH309 4.2 48.2 1.0
O A:HOH423 4.5 48.1 1.0
CG A:GLU88 4.7 26.5 1.0

Cadmium binding site 7 out of 13 in 5mik

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Cadmium binding site 7 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:39.8
occ:0.20
CL A:CL212 1.7 22.8 0.4
OE1 A:GLU130 2.5 40.5 1.0
CD A:GLU130 3.3 31.4 1.0
OE2 A:GLU130 3.4 31.7 1.0
CD A:CD210 4.7 46.8 0.2
CG A:GLU130 4.8 30.3 1.0

Cadmium binding site 8 out of 13 in 5mik

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Cadmium binding site 8 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:43.6
occ:0.20
CD A:CD207 0.0 43.6 0.2
SG A:CYS126 2.2 32.8 1.0
CD A:CD207 2.7 50.5 0.2
CB A:CYS126 3.1 26.2 1.0
CA A:SER118 3.7 23.1 1.0
CB A:SER118 4.0 29.5 1.0
N A:SER118 4.0 21.2 1.0
O A:ASP122 4.1 18.1 1.0
CA A:PRO123 4.2 16.9 1.0
O A:GLY117 4.4 18.9 1.0
C A:GLY117 4.4 19.9 1.0
C A:ASP122 4.5 18.2 1.0
OG A:SER118 4.5 31.9 1.0
CA A:CYS126 4.5 22.7 1.0
N A:PRO123 4.6 17.7 1.0
NE2 A:HIS114 4.7 26.1 1.0
CB A:PRO123 4.8 18.1 1.0
N A:CYS126 4.9 20.5 1.0
N A:ASP122 4.9 16.9 1.0

Cadmium binding site 9 out of 13 in 5mik

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Cadmium binding site 9 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:50.5
occ:0.20
CD A:CD207 0.0 50.5 0.2
CD A:CD207 2.7 43.6 0.2
NE2 A:HIS114 2.9 26.1 1.0
SG A:CYS126 3.2 32.8 1.0
CB A:CYS126 3.4 26.2 1.0
CE1 A:HIS114 3.6 24.0 1.0
OE2 A:GLU130 3.7 31.7 1.0
CD2 A:HIS114 4.0 23.0 1.0
CL A:CL212 4.5 22.8 0.4
CB A:SER118 4.6 29.5 1.0
ND1 A:HIS114 4.7 25.4 1.0
CA A:CYS126 4.8 22.7 1.0
CD A:GLU130 4.9 31.4 1.0
CG A:HIS114 4.9 22.3 1.0
OG A:SER118 4.9 31.9 1.0

Cadmium binding site 10 out of 13 in 5mik

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Cadmium binding site 10 out of 13 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


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 Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:32.9
occ:0.45
O A:HOH468 2.0 10.9 0.5
SG A:CYS48 2.1 17.1 1.0
CB A:CYS48 3.0 14.7 1.0
ND1 A:HIS49 3.4 20.9 0.5
C A:CYS48 3.5 15.0 1.0
N A:HIS49 3.5 14.4 0.5
N A:HIS49 3.5 14.8 0.5
CE1 A:HIS49 3.5 20.4 0.5
NH1 A:ARG52 3.7 35.1 1.0
CD A:ARG52 3.7 26.9 1.0
CA A:CYS48 3.8 14.7 1.0
CG A:HIS49 3.9 19.6 0.5
O A:HOH384 3.9 24.5 0.5
O A:CYS48 3.9 14.2 1.0
CA A:HIS49 4.0 17.3 0.5
CA A:HIS49 4.0 16.1 0.5
NE2 A:HIS49 4.1 19.9 0.5
O A:GLU45 4.2 14.7 1.0
CD2 A:HIS49 4.3 20.2 0.5
CG A:ARG52 4.5 22.7 1.0
CB A:HIS49 4.5 17.4 0.5
CZ A:ARG52 4.6 36.2 1.0
CB A:HIS49 4.6 19.8 0.5
NE A:ARG52 4.6 28.8 1.0
N A:CYS48 4.9 12.9 1.0
O A:HOH399 4.9 29.9 1.0
CB A:ARG52 5.0 18.8 1.0

Reference:

N.Pontillo, G.Ferraro, J.R.Helliwell, A.Amoresano, A.Merlino. X-Ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage. Acs Med Chem Lett V. 8 433 2017.
ISSN: ISSN 1948-5875
PubMed: 28435532
DOI: 10.1021/ACSMEDCHEMLETT.7B00025
Page generated: Sat Dec 12 08:27:02 2020

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