Atomistry » Cadmium » PDB 5gu2-5qrf » 5ix6
Atomistry »
  Cadmium »
    PDB 5gu2-5qrf »
      5ix6 »

Cadmium in PDB 5ix6: X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6 was solved by G.Ferraro, N.Pontillo, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.30 / 1.85
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.645, 180.645, 180.645, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 5ix6:

The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold (Au) 7 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin (pdb code 5ix6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 1 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:40.5
occ:0.40
 O A:HOH325 2.2 11.0 0.4
O A:HOH311 2.2 53.6 1.0
OE1 A:GLU11 2.6 19.5 1.0
O A:HOH446 2.7 20.4 1.0
OE2 A:GLU11 2.8 27.9 1.0
O A:HOH547 2.8 41.3 1.0
CD A:GLU11 3.0 24.7 1.0
OG1 A:THR10 3.8 22.7 1.0
CB A:SER9 4.4 14.1 1.0
OE1 A:GLN120 4.5 35.6 1.0
CG A:GLU11 4.5 21.1 1.0
O A:HOH439 4.7 45.8 1.0
N A:THR10 4.7 13.8 1.0
NE2 A:GLN120 4.8 34.1 1.0
N A:GLU11 5.0 15.3 1.0
CD A:GLN120 5.0 32.3 1.0

Cadmium binding site 2 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 2 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:58.7
occ:0.45
 OE1 A:GLU53 2.4 18.3 0.3
OE1 A:GLU56 2.5 52.8 1.0
OE2 A:GLU53 2.7 19.5 0.3
CD A:GLU53 2.9 17.6 0.3
CD A:GLU56 3.3 38.8 1.0
OE2 A:GLU56 3.4 51.5 1.0
O A:HOH329 3.9 40.6 1.0
CG A:GLU53 4.4 17.0 0.3
CG A:GLU56 4.7 30.0 1.0
CG A:GLU53 4.7 27.3 0.7

Cadmium binding site 3 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 3 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:15.6
occ:0.50
 OD2 A:ASP80 2.2 13.8 1.0
O A:HOH495 2.4 5.4 1.0
OD1 A:ASP80 2.4 13.3 1.0
CG A:ASP80 2.7 14.1 1.0
CB A:ASP80 4.2 13.4 1.0
O A:HOH402 4.3 14.4 1.0
O A:HOH380 4.6 27.8 1.0

Cadmium binding site 4 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 4 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:43.6
occ:0.50
 O A:HOH415 2.1 13.9 0.5
NE2 A:HIS132 2.3 54.7 1.0
CE1 A:HIS132 2.8 52.1 1.0
CD2 A:HIS132 3.5 49.3 1.0
O A:HOH417 3.8 14.0 0.5
ND1 A:HIS132 4.0 54.4 1.0
CG A:HIS132 4.4 44.8 1.0
O A:HOH478 4.9 45.0 1.0

Cadmium binding site 5 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 5 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:28.2
occ:0.30
 OE1 A:GLU130 2.5 34.1 1.0
OE2 A:GLU130 2.5 36.1 1.0
CD A:GLU130 2.8 31.6 1.0
O A:HOH301 4.0 28.4 1.0
O A:HOH490 4.2 33.0 1.0
CG A:GLU130 4.4 29.6 1.0
O A:HOH307 4.4 40.4 1.0
CD A:CD214 5.0 37.4 0.2

Cadmium binding site 6 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 6 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd213

b:65.1
occ:0.35
 O A:HOH465 2.0 11.2 0.3
O A:HOH388 2.9 40.2 1.0
OE1 A:GLU45 2.9 28.7 1.0
O A:HOH349 3.2 32.4 1.0
O A:HOH345 3.3 29.5 1.0
CD A:GLU45 3.9 32.1 1.0
OE2 A:GLU45 4.2 43.1 1.0
CD2 A:HIS173 4.4 77.5 1.0
NH1 A:ARG168 4.5 14.9 1.0
NH2 A:ARG168 4.8 14.9 1.0
O A:HOH330 4.9 51.6 1.0

Cadmium binding site 7 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 7 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd214

b:37.4
occ:0.20
 O A:HOH301 2.3 28.4 1.0
O A:HOH427 2.4 37.8 1.0
OD1 A:ASP127 3.8 28.5 1.0
OE1 A:GLU130 4.0 34.1 1.0
OG A:SER131 4.5 44.4 1.0
O A:HOH350 4.7 27.2 0.4
CB A:GLU130 4.9 28.0 1.0
CD A:CD212 5.0 28.2 0.3

Cadmium binding site 8 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 8 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd215

b:41.9
occ:0.40
 OE2 A:GLU60 2.4 37.5 1.0
O A:HOH472 2.5 19.7 0.4
OE2 A:GLU56 2.7 51.5 1.0
OE2 A:GLU57 2.7 42.2 1.0
OE1 A:GLU60 2.8 34.0 1.0
CD A:GLU60 2.9 28.2 1.0
O A:HOH329 3.4 40.6 1.0
CD A:GLU56 3.5 38.8 1.0
CD A:GLU57 3.9 35.0 1.0
CG A:GLU56 3.9 30.0 1.0
O A:HOH456 4.2 70.1 1.0
O A:HOH303 4.2 39.3 1.0
OE1 A:GLU57 4.4 46.2 1.0
CG A:GLU60 4.4 23.2 1.0
OE1 A:GLU56 4.6 52.8 1.0

Cadmium binding site 9 out of 9 in 5ix6

Go back to Cadmium Binding Sites List in 5ix6
Cadmium binding site 9 out of 9 in the X-Ray Structure of AUOXO3-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 AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd216

b:42.0
occ:0.15
 OE2 A:GLU53 1.9 47.3 0.7
CD A:GLU53 3.1 35.5 0.7
O A:HOH316 3.3 52.6 1.0
O A:HOH462 3.4 38.5 0.7
OE1 A:GLU53 3.7 37.1 0.7
CB A:LYS172 4.1 57.7 1.0
CG A:GLU53 4.3 27.3 0.7
CG A:GLU53 4.5 17.0 0.3
OE1 A:GLU53 4.8 18.3 0.3
CD A:GLU53 4.9 17.6 0.3

Reference:

G.Ferraro, D.M.Monti, A.Amoresano, N.Pontillo, G.Petruk, F.Pane, M.A.Cinellu, A.Merlino. Gold-Based Drug Encapsulation Within A Ferritin Nanocage: X-Ray Structure and Biological Evaluation As A Potential Anticancer Agent of the AUOXO3-Loaded Protein. Chem.Commun.(Camb.) V. 52 9518 2016.
ISSN: ESSN 1364-548X
PubMed: 27326513
DOI: 10.1039/C6CC02516A
Page generated: Sat Dec 12 08:26:52 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy