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Cadmium in PDB 5erk: X-Ray Structure of Horse Spleen Apoferritin (Control)

Protein crystallography data

The structure of X-Ray Structure of Horse Spleen Apoferritin (Control), PDB code: 5erk was solved by N.Pontillo, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.28 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.619, 180.619, 180.619, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 18.1

Other elements in 5erk:

The structure of X-Ray Structure of Horse Spleen Apoferritin (Control) also contains other interesting chemical elements:

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 Horse Spleen Apoferritin (Control) (pdb code 5erk). 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 Horse Spleen Apoferritin (Control), PDB code: 5erk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 5erk

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Cadmium binding site 1 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:42.4
occ:0.40
O A:HOH377 2.3 18.1 0.4
OE1 A:GLU11 2.5 23.4 1.0
CL A:CL216 2.6 19.9 0.4
OE2 A:GLU11 2.7 31.3 1.0
O A:HOH396 2.8 59.8 1.0
CD A:GLU11 3.0 26.3 1.0
OG1 A:THR10 3.9 21.5 1.0
CB A:SER9 4.4 14.2 1.0
CG A:GLU11 4.5 23.8 1.0
N A:THR10 4.5 15.4 1.0
OE1 A:GLN120 4.6 40.0 1.0
NE2 A:GLN120 4.8 36.4 1.0
N A:GLU11 4.9 17.1 1.0
CA A:SER9 5.0 15.0 1.0

Cadmium binding site 2 out of 13 in 5erk

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Cadmium binding site 2 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:51.9
occ:0.30
O A:HOH340 2.3 20.6 0.3
OE1 A:GLU53 2.5 26.9 0.4
OE1 A:GLU56 2.5 58.8 1.0
OE2 A:GLU53 2.6 24.1 0.4
CD A:GLU53 2.9 22.3 0.4
OE2 A:GLU53 2.9 39.2 0.6
CD A:GLU56 3.5 50.9 1.0
OE2 A:GLU56 3.7 68.5 1.0
CD A:GLU53 4.1 29.5 0.6
CG A:GLU53 4.4 19.3 0.4
OE1 A:GLU53 4.7 30.8 0.6
CG A:GLU56 4.8 33.0 1.0

Cadmium binding site 3 out of 13 in 5erk

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Cadmium binding site 3 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:69.1
occ:0.30
OE1 A:GLU60 2.5 40.5 1.0
O A:HOH447 2.8 20.3 0.3
OE2 A:GLU56 3.2 68.5 1.0
CD A:GLU60 3.3 39.1 1.0
OE2 A:GLU60 3.4 45.2 1.0
OE1 A:GLU53 4.2 30.8 0.6
O A:HOH494 4.2 71.2 1.0
O A:HOH426 4.3 54.5 1.0
CD A:GLU56 4.3 50.9 1.0
CG A:GLU57 4.7 27.9 1.0
CG A:GLU60 4.7 28.4 1.0
CG A:GLU56 4.9 33.0 1.0

Cadmium binding site 4 out of 13 in 5erk

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Cadmium binding site 4 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:15.7
occ:0.50
OD2 A:ASP80 2.1 11.8 1.0
OD1 A:ASP80 2.4 14.4 1.0
CG A:ASP80 2.6 14.6 1.0
CL A:CL215 2.6 25.0 1.0
O A:HOH343 4.1 18.6 1.0
CB A:ASP80 4.1 14.4 1.0
O A:HOH331 4.4 34.5 1.0

Cadmium binding site 5 out of 13 in 5erk

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Cadmium binding site 5 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:61.0
occ:0.20
OE2 A:GLU88 2.3 46.6 1.0
O A:HOH313 2.5 54.7 1.0
O A:HOH441 2.7 51.0 1.0
CD A:GLU88 3.2 41.9 1.0
OE1 A:GLU88 3.4 42.3 1.0
O A:HOH358 3.5 49.5 1.0
NH2 A:ARG39 3.5 29.4 1.0
NH1 A:ARG39 4.1 23.7 1.0
CZ A:ARG39 4.3 26.2 1.0
CG A:GLU88 4.6 31.8 1.0
O A:HOH436 5.0 45.3 1.0

Cadmium binding site 6 out of 13 in 5erk

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Cadmium binding site 6 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:69.3
occ:0.40
O A:HOH349 2.2 28.9 0.4
O A:HOH448 2.5 49.9 0.8
OD2 A:ASP127 2.9 48.5 1.0
OD1 A:ASP127 3.1 38.0 1.0
O A:HOH456 3.1 33.7 1.0
CG A:ASP127 3.3 41.1 1.0
OG A:SER131 3.3 43.5 1.0
CD A:CD207 4.0 39.9 0.4
O A:HOH384 4.2 50.8 1.0
CB A:SER131 4.2 35.1 1.0
O A:ASP127 4.7 22.3 1.0
CB A:ASP127 4.8 31.4 1.0
C A:ASP127 5.0 24.1 1.0

Cadmium binding site 7 out of 13 in 5erk

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Cadmium binding site 7 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:39.9
occ:0.40
O A:HOH425 2.1 25.5 0.4
O A:HOH448 2.2 49.9 0.8
O A:HOH456 2.2 33.7 1.0
NE2 A:HIS132 2.7 40.3 1.0
CE1 A:HIS132 3.6 44.9 1.0
CD2 A:HIS132 3.6 38.2 1.0
CD A:CD206 4.0 69.3 0.4
O A:HOH384 4.7 50.8 1.0
ND1 A:HIS132 4.7 41.8 1.0
CG A:HIS132 4.8 34.3 1.0
CD1 A:PHE128 4.9 20.9 1.0
CB A:SER131 4.9 35.1 1.0

Cadmium binding site 8 out of 13 in 5erk

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Cadmium binding site 8 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:46.6
occ:0.20
CL A:CL214 2.3 28.3 0.4
OE1 A:GLU130 2.5 45.2 1.0
CD A:GLU130 3.2 32.8 1.0
OE2 A:GLU130 3.3 41.2 1.0
O A:HOH461 4.2 36.7 0.3
CD A:CD209 4.6 59.1 0.2
CG A:GLU130 4.7 30.7 1.0

Cadmium binding site 9 out of 13 in 5erk

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Cadmium binding site 9 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:59.1
occ:0.20
CE1 A:HIS114 2.9 23.7 0.8
NE2 A:HIS114 3.0 18.7 0.2
NE2 A:HIS114 3.3 22.4 0.8
O A:HOH480 3.3 51.4 1.0
OE2 A:GLU130 3.3 41.2 1.0
CE1 A:HIS114 3.4 18.5 0.2
CB A:CYS126 3.5 24.0 1.0
CL A:CL214 3.6 28.3 0.4
SG A:CYS126 3.7 29.6 1.0
ND1 A:HIS114 4.1 21.9 0.8
CD2 A:HIS114 4.2 18.3 0.2
O A:HOH454 4.4 58.3 1.0
CD A:GLU130 4.5 32.8 1.0
CD2 A:HIS114 4.6 21.6 0.8
CD A:CD208 4.6 46.6 0.2
ND1 A:HIS114 4.6 18.3 0.2
CA A:CYS126 4.9 21.4 1.0
CG A:HIS114 4.9 19.4 0.8

Cadmium binding site 10 out of 13 in 5erk

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Cadmium binding site 10 out of 13 in the X-Ray Structure of Horse Spleen Apoferritin (Control)


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 Horse Spleen Apoferritin (Control) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:51.5
occ:0.20
OE1 A:GLU63 2.6 39.9 1.0
OE2 A:GLU63 3.2 40.3 1.0
CD A:GLU63 3.2 35.3 1.0
NH1 A:ARG59 3.6 30.1 0.5
CZ A:ARG59 4.2 29.2 0.5
NH2 A:ARG59 4.7 33.1 0.5
CG A:GLU63 4.7 25.6 1.0
NE A:ARG59 4.8 26.8 0.5

Reference:

N.Pontillo, F.Pane, L.Messori, A.Amoresano, A.Merlino. Cisplatin Encapsulation Within A Ferritin Nanocage: A High-Resolution Crystallographic Study. Chem.Commun.(Camb.) V. 52 4136 2016.
ISSN: ESSN 1364-548X
PubMed: 26888424
DOI: 10.1039/C5CC10365G
Page generated: Sat Dec 12 08:26:35 2020

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