Atomistry » Cadmium » PDB 5an6-5gu1 » 5erj
Atomistry »
  Cadmium »
    PDB 5an6-5gu1 »
      5erj »

Cadmium in PDB 5erj: X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin, PDB code: 5erj 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) 104.44 / 1.45
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.899, 180.899, 180.899, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.3

Other elements in 5erj:

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

Platinum (Pt) 1 atom
Chlorine (Cl) 4 atoms

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

Cadmium binding site 1 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 1 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:22.9
occ:0.40
O A:HOH386 2.2 41.0 1.0
OE1 A:GLU11 2.3 20.9 1.0
O A:HOH484 2.3 29.0 0.4
OE2 A:GLU11 2.6 30.8 1.0
CL A:CL203 2.6 19.2 0.4
CD A:GLU11 2.8 27.2 1.0
OG1 A:THR10 3.8 21.8 1.0
CG A:GLU11 4.3 20.8 1.0
CB A:SER9 4.5 14.7 1.0
N A:THR10 4.6 14.2 1.0
OE1 A:GLN120 4.6 31.2 1.0
NE2 A:GLN120 4.7 33.4 1.0
N A:GLU11 4.8 14.1 1.0
CD A:GLN120 5.0 28.8 1.0

Cadmium binding site 2 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 2 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:43.7
occ:0.40
OE1 A:GLU53 2.3 19.1 0.3
OE2 A:GLU53 2.4 36.0 0.7
O A:HOH331 2.5 60.1 1.0
OE1 A:GLU56 2.5 44.3 1.0
OE1 A:GLU53 2.9 48.4 0.7
CD A:GLU53 3.0 29.7 0.7
CD A:GLU56 3.3 40.5 1.0
OE2 A:GLU56 3.5 54.4 1.0
CD A:GLU53 3.5 19.8 0.3
OE2 A:GLU53 4.0 21.2 0.3
CG A:GLU53 4.5 22.4 0.7
CG A:GLU53 4.7 15.0 0.3
CG A:GLU56 4.7 24.7 1.0
CB A:GLU53 5.0 13.4 0.3

Cadmium binding site 3 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 3 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:44.0
occ:0.30
CD A:CD207 0.0 44.0 0.3
CD A:CD207 1.8 35.8 0.2
OE2 A:GLU60 2.2 36.5 1.0
OE2 A:GLU56 2.4 54.4 1.0
OE1 A:GLU60 2.7 34.1 1.0
CD A:GLU60 2.8 29.9 1.0
O A:HOH448 3.1 54.1 1.0
CD A:GLU56 3.4 40.5 1.0
CG A:GLU56 3.9 24.7 1.0
OE2 A:GLU53 4.1 21.2 0.3
CG A:GLU60 4.3 21.7 1.0
OE1 A:GLU56 4.4 44.3 1.0

Cadmium binding site 4 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 4 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:35.8
occ:0.20
CD A:CD207 0.0 35.8 0.2
CD A:CD207 1.8 44.0 0.3
O A:HOH448 2.2 54.1 1.0
OE1 A:GLU60 2.4 34.1 1.0
CD A:GLU60 3.2 29.9 1.0
OE2 A:GLU60 3.3 36.5 1.0
O A:HOH477 4.0 50.3 1.0
OE2 A:GLU56 4.1 54.4 1.0
OE2 A:GLU53 4.3 21.2 0.3
CG A:GLU57 4.4 17.2 0.6
CG A:GLU60 4.7 21.7 1.0
CD A:GLU56 4.9 40.5 1.0

Cadmium binding site 5 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 5 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:10.4
occ:0.40
CD A:CD208 0.0 10.4 0.4
CD A:CD208 0.7 19.5 0.1
OD1 A:ASP80 2.3 10.7 1.0
CL A:CL201 2.4 18.4 1.0
OD2 A:ASP80 2.5 12.8 1.0
CG A:ASP80 2.8 11.7 1.0
O A:HOH342 4.2 16.7 1.0
CB A:ASP80 4.2 10.8 1.0
O A:HOH330 4.6 25.8 1.0
O A:HOH426 4.6 27.4 0.2

Cadmium binding site 6 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 6 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:19.5
occ:0.10
CD A:CD208 0.0 19.5 0.1
CD A:CD208 0.7 10.4 0.4
OD2 A:ASP80 1.8 12.8 1.0
OD1 A:ASP80 2.1 10.7 1.0
CG A:ASP80 2.3 11.7 1.0
CL A:CL201 2.8 18.4 1.0
CB A:ASP80 3.7 10.8 1.0
O A:HOH426 3.9 27.4 0.2
O A:HOH330 3.9 25.8 1.0
O A:HOH342 4.1 16.7 1.0
CA A:ASP80 4.7 10.1 1.0
N A:ASP80 5.0 10.5 1.0

Cadmium binding site 7 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 7 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:44.4
occ:0.30
O A:HOH305 1.9 36.8 1.0
O A:HOH432 2.2 44.5 1.0
OE2 A:GLU88 2.3 36.6 1.0
O A:HOH419 2.6 52.4 1.0
CD A:GLU88 3.0 34.0 1.0
OE1 A:GLU88 3.1 40.1 1.0
CG A:GLU88 4.3 20.9 1.0
O A:HOH495 4.4 57.5 1.0
NH2 A:ARG39 4.4 23.9 1.0
NH1 A:ARG39 4.6 20.4 1.0

Cadmium binding site 8 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 8 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:45.2
occ:0.40
O A:HOH463 2.5 32.8 1.0
O A:HOH465 2.5 39.4 0.9
OG A:SER131 2.7 41.8 1.0
OD1 A:ASP127 3.0 31.4 1.0
CG A:ASP127 3.3 35.3 1.0
CD A:CD211 3.4 42.0 0.5
OD2 A:ASP127 3.4 45.8 1.0
CB A:SER131 3.5 35.2 1.0
O A:HOH417 4.0 48.0 1.0
O A:ASP127 4.3 22.1 1.0
NE2 A:HIS132 4.6 38.2 1.0
CB A:ASP127 4.6 27.7 1.0
C A:ASP127 4.6 23.0 1.0
O A:HOH328 4.8 35.8 0.5

Cadmium binding site 9 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 9 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:42.0
occ:0.50
O A:HOH328 1.7 35.8 0.5
O A:HOH463 2.4 32.8 1.0
NE2 A:HIS132 2.5 38.2 1.0
O A:HOH465 2.5 39.4 0.9
CE1 A:HIS132 3.3 42.4 1.0
CD A:CD210 3.4 45.2 0.4
CD2 A:HIS132 3.6 34.6 1.0
ND1 A:HIS132 4.5 41.7 1.0
CB A:SER131 4.6 35.2 1.0
CG A:HIS132 4.7 34.6 1.0
O A:HOH417 4.9 48.0 1.0
OG A:SER131 4.9 41.8 1.0
CD1 A:PHE128 5.0 19.1 1.0

Cadmium binding site 10 out of 15 in 5erj

Go back to Cadmium Binding Sites List in 5erj
Cadmium binding site 10 out of 15 in the X-Ray Structure of Cisplatin-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 Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:42.0
occ:0.20
CL A:CL202 1.9 12.6 0.2
OE1 A:GLU130 2.4 39.5 1.0
O A:HOH337 2.5 31.7 0.8
CD A:GLU130 3.3 38.4 1.0
OE2 A:GLU130 3.6 38.2 1.0
CG A:GLU130 4.7 27.7 1.0

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 08:26:34 2020

Last articles

Zn in 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy