Atomistry » Cadmium » PDB 5wgr-6fpc » 6env
Atomistry »
  Cadmium »
    PDB 5wgr-6fpc »
      6env »

Cadmium in PDB 6env: X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin, PDB code: 6env 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) 104.48 / 1.82
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.967, 180.967, 180.967, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.5

Other elements in 6env:

The structure of X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold (Au) 2 atoms
Chlorine (Cl) 1 atom

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 AU2PHEN-Encapsulated Horse Spleen Apoferritin (pdb code 6env). 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 AU2PHEN-Encapsulated Horse Spleen Apoferritin, PDB code: 6env:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 1 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:44.0
occ:0.35
O A:HOH378 2.1 17.6 0.4
OE1 A:GLU11 2.5 18.3 1.0
OE2 A:GLU11 2.8 23.2 1.0
O A:HOH592 2.8 64.3 1.0
O A:HOH432 2.9 22.5 1.0
O A:HOH475 3.0 55.1 1.0
CD A:GLU11 3.0 21.4 1.0
OG1 A:THR10 3.9 19.6 1.0
O A:HOH456 4.0 59.7 1.0
CB A:SER9 4.5 12.7 1.0
CG A:GLU11 4.6 17.7 1.0
OE1 A:GLN120 4.6 27.3 1.0
N A:THR10 4.7 13.4 1.0
NE2 A:GLN120 4.7 26.7 1.0

Cadmium binding site 2 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 2 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:54.0
occ:0.40
O A:HOH315 2.1 11.2 0.3
OE2 A:GLU53 2.6 48.5 1.0
OE1 A:GLU56 2.7 37.1 1.0
OE1 A:GLU53 2.9 52.6 1.0
CD A:GLU53 3.1 39.1 1.0
CD A:GLU56 3.4 34.3 1.0
OE2 A:GLU56 3.4 44.1 1.0
O A:HOH322 3.7 40.4 1.0
CG A:GLU53 4.7 27.7 1.0
CG A:GLU56 4.7 22.8 1.0
CD A:CD203 5.0 27.9 0.3

Cadmium binding site 3 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 3 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:31.1
occ:0.30
CD A:CD203 0.0 31.1 0.3
CD A:CD203 1.9 27.9 0.3
O A:HOH304 1.9 30.0 1.0
OE2 A:GLU57 2.2 46.5 1.0
OE1 A:GLU60 2.4 31.4 1.0
O A:HOH494 2.5 17.6 0.3
CD A:GLU57 3.0 36.0 1.0
CD A:GLU60 3.0 25.4 1.0
OE2 A:GLU60 3.1 33.5 1.0
OE1 A:GLU57 3.1 41.6 1.0
OE2 A:GLU56 3.8 44.1 1.0
O A:HOH322 4.0 40.4 1.0
O A:HOH490 4.0 60.3 1.0
O A:HOH560 4.4 67.7 1.0
CG A:GLU57 4.5 28.1 1.0
CG A:GLU60 4.5 20.4 1.0
CD A:GLU56 4.6 34.3 1.0
CG A:GLU56 4.7 22.8 1.0
O A:HOH479 4.7 52.9 1.0

Cadmium binding site 4 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 4 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:27.9
occ:0.30
CD A:CD203 0.0 27.9 0.3
CD A:CD203 1.9 31.1 0.3
OE2 A:GLU56 2.1 44.1 1.0
OE2 A:GLU60 2.2 33.5 1.0
O A:HOH494 2.7 17.6 0.3
CD A:GLU60 2.9 25.4 1.0
OE1 A:GLU60 3.0 31.4 1.0
CD A:GLU56 3.1 34.3 1.0
OE2 A:GLU57 3.1 46.5 1.0
CG A:GLU56 3.5 22.8 1.0
O A:HOH304 3.7 30.0 1.0
O A:HOH322 3.8 40.4 1.0
OE1 A:GLU56 4.2 37.1 1.0
CD A:GLU57 4.3 36.0 1.0
CG A:GLU60 4.3 20.4 1.0
O A:HOH315 4.4 11.2 0.3
O A:HOH490 4.5 60.3 1.0
OE1 A:GLU57 4.7 41.6 1.0
CB A:GLU56 4.9 17.8 1.0
CD A:CD202 5.0 54.0 0.4

Cadmium binding site 5 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 5 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:13.0
occ:0.50
OD2 A:ASP80 2.2 13.2 1.0
OD1 A:ASP80 2.4 12.5 1.0
CL A:CL211 2.5 19.9 1.0
CG A:ASP80 2.7 13.4 1.0
CB A:ASP80 4.1 12.6 1.0
O A:HOH369 4.3 14.3 1.0
O A:HOH387 4.7 20.9 1.0

Cadmium binding site 6 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 6 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:54.2
occ:0.20
O A:HOH358 2.3 49.2 1.0
OE2 A:GLU88 2.5 36.7 1.0
OE1 A:GLU88 2.9 33.6 1.0
CD A:GLU88 3.0 31.9 1.0
O A:HOH471 3.3 53.0 1.0
CG A:GLU88 4.5 22.5 1.0
O A:HOH454 4.6 44.1 1.0
NH2 A:ARG39 4.6 23.9 1.0
O A:HOH590 4.8 46.7 1.0
NH1 A:ARG39 4.8 23.6 1.0

Cadmium binding site 7 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 7 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:62.6
occ:0.20
OD2 A:ASP127 2.4 15.7 0.5
CD A:CD207 2.4 29.0 0.2
OD2 A:ASP127 2.9 21.9 0.5
CG A:ASP127 3.2 14.8 0.5
OG A:SER131 3.2 32.1 1.0
OD1 A:ASP127 3.3 16.8 0.5
CB A:SER131 3.7 27.2 1.0
O A:HOH335 3.9 9.7 0.4
CG A:ASP127 4.0 19.7 0.5
O A:HOH325 4.2 20.4 1.0
O A:ASP127 4.2 15.9 0.5
CD A:CD207 4.2 38.1 0.4
O A:HOH329 4.4 32.9 1.0
O A:ASP127 4.5 15.2 0.5
O A:HOH535 4.6 27.1 0.4
CB A:ASP127 4.6 15.0 0.5
NE2 A:HIS132 4.7 38.9 1.0
C A:ASP127 4.7 15.8 0.5
C A:ASP127 4.8 14.8 0.5
OD1 A:ASP127 4.8 18.3 0.5
CB A:ASP127 4.8 17.7 0.5

Cadmium binding site 8 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 8 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:38.1
occ:0.40
CD A:CD207 0.0 38.1 0.4
O A:HOH458 1.9 18.6 0.4
CD A:CD207 2.0 29.0 0.2
NE2 A:HIS132 2.3 38.9 1.0
O A:HOH535 2.8 27.1 0.4
CE1 A:HIS132 3.1 39.3 1.0
CD2 A:HIS132 3.4 37.7 1.0
CD A:CD206 4.2 62.6 0.2
ND1 A:HIS132 4.3 37.5 1.0
CG A:HIS132 4.5 30.9 1.0
NH1 A:ARG64 4.9 48.5 1.0

Cadmium binding site 9 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 9 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:29.0
occ:0.20
CD A:CD207 0.0 29.0 0.2
CD A:CD207 2.0 38.1 0.4
CD A:CD206 2.4 62.6 0.2
NE2 A:HIS132 3.1 38.9 1.0
O A:HOH535 3.6 27.1 0.4
O A:HOH458 3.7 18.6 0.4
CD2 A:HIS132 3.7 37.7 1.0
OD2 A:ASP127 3.8 15.7 0.5
CE1 A:HIS132 4.1 39.3 1.0
O A:HOH325 4.2 20.4 1.0
CB A:SER131 4.4 27.2 1.0
OG A:SER131 4.7 32.1 1.0
CG A:ASP127 4.9 14.8 0.5
CG A:HIS132 5.0 30.9 1.0

Cadmium binding site 10 out of 12 in 6env

Go back to Cadmium Binding Sites List in 6env
Cadmium binding site 10 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:33.3
occ:0.20
OE1 A:GLU130 2.4 32.9 1.0
CD A:GLU130 3.3 26.6 1.0
O A:HOH515 3.4 44.2 1.0
OE2 A:GLU130 3.5 22.0 1.0
OD1 A:ASP127 4.0 18.3 0.5
CG A:GLU130 4.7 21.7 1.0
CG A:ASP127 4.9 19.7 0.5
CD A:CD210 4.9 30.0 0.3
CB A:ASP127 4.9 17.7 0.5

Reference:

D.M.Monti, G.Ferraro, G.Petruk, L.Maiore, F.Pane, A.Amoresano, M.A.Cinellu, A.Merlino. Ferritin Nanocages Loaded with Gold Ions Induce Oxidative Stress and Apoptosis in Mcf-7 Human Breast Cancer Cells. Dalton Trans V. 46 15354 2017.
ISSN: ESSN 1477-9234
PubMed: 29072740
DOI: 10.1039/C7DT02370G
Page generated: Sat Dec 12 08:28:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy