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Cadmium in PDB 5mij: X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin, PDB code: 5mij 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) 104.89 / 1.49
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.670, 181.670, 181.670, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.1

Other elements in 5mij:

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Platinum (Pt) 4 atoms
Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (pdb code 5mij). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin, PDB code: 5mij:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 5mij

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Cadmium binding site 1 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:39.2
occ:0.40
O A:HOH311 2.0 38.2 1.0
O A:HOH384 2.1 23.7 0.4
OE1 A:GLU11 2.3 17.8 1.0
OE2 A:GLU11 2.4 24.2 1.0
CD A:GLU11 2.7 21.2 1.0
CL A:CL213 2.8 22.9 0.4
O A:HOH479 3.3 54.9 1.0
O A:HOH540 3.7 38.6 1.0
OG1 A:THR10 3.7 19.0 1.0
O A:HOH474 4.1 52.6 1.0
CG A:GLU11 4.2 16.3 1.0
CB A:SER9 4.5 11.7 1.0
N A:THR10 4.6 12.4 1.0
OE1 A:GLN120 4.7 23.4 1.0
N A:GLU11 4.8 11.9 1.0
NE2 A:GLN120 4.8 27.8 1.0
CB A:THR10 5.0 16.1 1.0

Cadmium binding site 2 out of 12 in 5mij

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Cadmium binding site 2 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:33.8
occ:0.30
O A:HOH315 2.1 17.3 0.3
OE1 A:GLU53 2.2 24.1 0.6
OE1 A:GLU56 2.3 37.8 1.0
OE2 A:GLU53 2.8 30.8 0.6
CD A:GLU53 2.9 19.5 0.6
CD A:GLU56 3.2 26.4 1.0
OE2 A:GLU56 3.3 32.0 1.0
O A:HOH316 3.9 20.8 0.5
CG A:GLU53 4.4 15.2 0.6
CG A:GLU56 4.6 20.5 1.0
CB A:GLU56 4.9 14.7 1.0

Cadmium binding site 3 out of 12 in 5mij

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Cadmium binding site 3 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:30.7
occ:0.50
CD A:CD203 0.0 30.7 0.5
CD A:CD203 1.6 24.5 0.3
OE2 A:GLU56 2.2 32.0 1.0
OE2 A:GLU60 2.3 32.2 1.0
OE1 A:GLU60 2.5 27.9 1.0
CD A:GLU60 2.8 23.0 1.0
CD A:GLU56 3.2 26.4 1.0
OE2 A:GLU57 3.2 33.7 1.0
CL A:CL218 3.3 17.4 0.3
CG A:GLU56 3.5 20.5 1.0
O A:HOH316 4.2 20.8 0.5
OE1 A:GLU56 4.3 37.8 1.0
O A:HOH315 4.3 17.3 0.3
CG A:GLU60 4.3 15.7 1.0
CD A:GLU57 4.4 31.4 1.0
CB A:GLU56 4.9 14.7 1.0
OE1 A:GLU57 4.9 32.8 1.0

Cadmium binding site 4 out of 12 in 5mij

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Cadmium binding site 4 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:24.5
occ:0.30
CD A:CD203 0.0 24.5 0.3
CD A:CD203 1.6 30.7 0.5
CL A:CL218 1.8 17.4 0.3
OE2 A:GLU57 2.1 33.7 1.0
OE1 A:GLU60 2.1 27.9 1.0
CD A:GLU60 3.1 23.0 1.0
CD A:GLU57 3.1 31.4 1.0
OE2 A:GLU60 3.2 32.2 1.0
OE1 A:GLU57 3.4 32.8 1.0
OE2 A:GLU56 3.5 32.0 1.0
O A:HOH316 3.9 20.8 0.5
CD A:GLU56 4.2 26.4 1.0
CG A:GLU56 4.3 20.5 1.0
CG A:GLU60 4.5 15.7 1.0
CG A:GLU57 4.5 22.8 1.0
O A:HOH316 4.7 29.4 0.5

Cadmium binding site 5 out of 12 in 5mij

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Cadmium binding site 5 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:9.3
occ:0.50
CL A:CL212 2.3 14.3 1.0
OD1 A:ASP80 2.4 9.6 1.0
OD2 A:ASP80 2.5 11.2 1.0
CG A:ASP80 2.8 10.2 1.0
CB A:ASP80 4.3 9.7 1.0
O A:HOH363 4.5 13.0 1.0
O A:HOH383 4.8 16.6 1.0

Cadmium binding site 6 out of 12 in 5mij

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Cadmium binding site 6 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:37.5
occ:0.20
O A:HOH420 2.1 7.1 0.2
O A:HOH307 2.2 54.7 1.0
OE2 A:GLU88 2.2 35.9 1.0
O A:HOH428 2.7 41.3 1.0
OE1 A:GLU88 2.8 33.1 1.0
CD A:GLU88 2.9 29.7 1.0
CG A:GLU88 4.3 18.8 1.0
NH2 A:ARG39 4.3 21.9 1.0
NH1 A:ARG39 4.5 20.1 1.0
O A:HOH551 4.7 36.8 1.0
O A:HOH557 4.8 42.5 1.0

Cadmium binding site 7 out of 12 in 5mij

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Cadmium binding site 7 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:22.3
occ:0.20
CL A:CL211 1.6 6.0 0.2
OE1 A:GLU130 2.2 32.0 1.0
CD A:GLU130 3.1 27.4 1.0
OE2 A:GLU130 3.4 26.8 1.0
CG A:GLU130 4.5 22.7 1.0
CD A:CD214 4.6 46.0 0.2
CB A:GLU130 4.9 20.1 1.0

Cadmium binding site 8 out of 12 in 5mij

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Cadmium binding site 8 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:42.9
occ:0.20
O A:HOH531 2.2 42.6 1.0
NE2 A:HIS114 2.3 18.2 0.8
NE2 A:HIS114 2.6 12.9 0.2
CE1 A:HIS114 2.7 13.3 0.2
CE1 A:HIS114 3.0 15.3 0.8
SG A:CYS126 3.4 23.5 1.0
CD2 A:HIS114 3.4 15.2 0.8
OE2 A:GLU130 3.4 26.8 1.0
CB A:CYS126 3.6 16.9 1.0
CD2 A:HIS114 3.8 13.1 0.2
ND1 A:HIS114 3.9 12.8 0.2
ND1 A:HIS114 4.1 18.4 0.8
CG A:HIS114 4.4 15.7 0.8
CG A:HIS114 4.4 12.8 0.2
CB A:SER118 4.6 23.4 1.0
CL A:CL211 4.6 6.0 0.2
O A:HOH515 4.7 31.9 1.0
CD A:GLU130 4.7 27.4 1.0
CA A:CYS126 4.8 14.9 1.0
OG A:SER118 4.9 28.5 1.0

Cadmium binding site 9 out of 12 in 5mij

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Cadmium binding site 9 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:30.6
occ:0.45
O A:HOH533 2.1 22.4 0.3
SG A:CYS48 2.1 13.9 1.0
CB A:CYS48 3.1 11.8 1.0
C A:CYS48 3.4 10.2 1.0
CD A:ARG52 3.5 26.2 1.0
ND1 A:HIS49 3.5 22.4 0.5
N A:HIS49 3.5 9.8 1.0
O A:HOH335 3.7 47.0 1.0
CE1 A:HIS49 3.7 23.5 0.5
NH1 A:ARG52 3.8 33.2 1.0
CA A:CYS48 3.9 10.4 1.0
O A:CYS48 3.9 10.1 1.0
CG A:HIS49 3.9 18.1 0.5
CA A:HIS49 3.9 12.2 1.0
NE2 A:HIS49 4.2 19.9 0.5
O A:GLU45 4.3 10.8 1.0
CG A:ARG52 4.3 19.4 1.0
CD2 A:HIS49 4.3 22.8 0.5
CB A:HIS49 4.5 13.9 0.5
CB A:HIS49 4.6 13.3 0.5
NE A:ARG52 4.6 28.1 1.0
CZ A:ARG52 4.7 35.4 1.0
CB A:ARG52 4.8 13.7 1.0
O A:HOH461 4.9 18.7 0.5
N A:CYS48 5.0 9.8 1.0

Cadmium binding site 10 out of 12 in 5mij

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Cadmium binding site 10 out of 12 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:59.2
occ:0.30
O A:HOH481 2.2 52.5 1.0
OE1 A:GLU45 2.3 26.4 1.0
CD A:CD210 2.6 61.4 0.3
O A:HOH322 3.1 26.4 1.0
CD A:GLU45 3.2 30.6 1.0
OE2 A:GLU45 3.4 38.6 1.0
O A:HOH471 3.8 41.5 1.0
NH1 A:ARG168 4.5 13.0 1.0
CG A:GLU45 4.5 22.4 1.0
CB A:GLU45 4.8 16.2 1.0
NH2 A:ARG168 5.0 12.8 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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