Atomistry » Cadmium » PDB 6fv4-6ozy » 6gxj
Atomistry »
  Cadmium »
    PDB 6fv4-6ozy »
      6gxj »

Cadmium in PDB 6gxj: X-Ray Structure of Diru-1-Encapsulated Apoferritin

Protein crystallography data

The structure of X-Ray Structure of Diru-1-Encapsulated Apoferritin, PDB code: 6gxj was solved by A.Pica, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.26 / 1.43
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.404, 180.404, 180.404, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.1

Other elements in 6gxj:

The structure of X-Ray Structure of Diru-1-Encapsulated Apoferritin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 1 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:31.6
occ:0.15
 O A:HOH318 2.0 16.2 0.5
OE1 A:GLU130 2.3 30.1 1.0
CD A:GLU130 3.2 36.5 1.0
O A:HOH315 3.3 57.1 1.0
OE2 A:GLU130 3.4 25.8 1.0
O A:HOH318 3.4 29.9 0.5
CD A:CD202 4.4 25.2 0.1
CG A:GLU130 4.6 25.6 1.0

Cadmium binding site 2 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 2 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:25.2
occ:0.10
 O A:HOH315 2.2 57.1 1.0
O A:HOH362 2.2 15.0 0.2
OD1 A:ASP127 3.7 29.4 1.0
OE1 A:GLU130 4.2 30.1 1.0
OG A:SER131 4.2 39.2 1.0
CD A:CD201 4.4 31.6 0.1
CG A:ASP127 4.8 31.3 1.0
CB A:GLU130 4.9 23.5 1.0

Cadmium binding site 3 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 3 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:23.3
occ:0.26
 O A:HOH363 2.2 56.7 1.0
OE1 A:GLU11 2.4 21.1 1.0
OE2 A:GLU11 2.7 33.8 1.0
CL A:CL211 2.7 31.4 0.5
CD A:GLU11 2.9 32.9 1.0
OG1 A:THR10 3.9 24.2 1.0
CG A:GLU11 4.4 21.4 1.0
CB A:SER9 4.4 16.2 1.0
OE1 A:GLN120 4.5 31.5 1.0
N A:THR10 4.6 15.8 1.0
NE2 A:GLN120 4.6 34.4 1.0
N A:GLU11 4.9 15.7 1.0
CD A:GLN120 4.9 34.9 1.0

Cadmium binding site 4 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 4 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:32.7
occ:0.16
 O A:HOH302 2.2 22.7 0.6
OE2 A:GLU60 2.3 47.4 1.0
OE2 A:GLU56 2.6 62.0 1.0
OE1 A:GLU60 2.7 41.8 1.0
CD A:GLU60 2.8 50.6 1.0
CD A:GLU56 3.4 57.0 1.0
CG A:GLU56 3.8 27.1 1.0
O A:HOH455 4.3 33.1 0.4
OE1 A:GLU56 4.3 45.2 1.0
CG A:GLU60 4.3 27.8 1.0
OE1 A:GLU53 4.4 38.9 0.4
O A:HOH348 4.5 17.2 0.2
CB A:GLU56 5.0 17.5 1.0

Cadmium binding site 5 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 5 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:17.1
occ:0.49
 OD1 A:ASP80 2.3 15.5 1.0
OD2 A:ASP80 2.4 17.1 1.0
CL A:CL210 2.5 19.9 0.8
CG A:ASP80 2.7 16.6 1.0
CB A:ASP80 4.2 14.7 1.0
O A:HOH312 4.7 31.2 1.0

Cadmium binding site 6 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 6 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:24.5
occ:0.27
 O A:HOH377 2.1 49.1 1.0
O A:HOH441 2.2 41.0 1.0
NE2 A:HIS132 2.5 33.0 1.0
O A:HOH350 3.1 38.1 1.0
CE1 A:HIS132 3.4 32.8 1.0
CD2 A:HIS132 3.6 32.5 1.0
ND1 A:HIS132 4.6 33.1 1.0
O A:HOH305 4.6 31.6 1.0
CG A:HIS132 4.7 29.9 1.0
OD2 A:ASP127 4.7 39.2 1.0
CD1 A:PHE128 4.9 19.1 1.0
CB A:SER131 5.0 28.4 1.0

Cadmium binding site 7 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 7 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:29.9
occ:0.21
 O A:HOH348 2.2 17.2 0.2
OE1 A:GLU53 2.4 51.7 0.6
OE1 A:GLU56 2.5 45.2 1.0
OE2 A:GLU53 2.6 46.5 0.6
OE2 A:GLU53 2.6 48.1 0.4
CD A:GLU53 2.8 48.0 0.6
CD A:GLU56 3.4 57.0 1.0
CD A:GLU53 3.7 49.0 0.4
OE2 A:GLU56 3.8 62.0 1.0
OE1 A:GLU53 4.1 38.9 0.4
CG A:GLU53 4.3 21.6 0.6
CG A:GLU56 4.7 27.1 1.0
CG A:GLU53 4.9 24.1 0.4
CB A:GLU56 5.0 17.5 1.0

Cadmium binding site 8 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 8 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:23.5
occ:0.20
 SG A:CYS48 2.1 18.5 1.0
O A:HOH471 2.2 44.1 1.0
CB A:CYS48 3.0 14.9 1.0
C A:CYS48 3.4 16.6 1.0
N A:HIS49 3.4 16.1 0.5
N A:HIS49 3.5 15.5 0.5
CD A:ARG52 3.6 28.5 1.0
ND1 A:HIS49 3.6 27.0 0.5
CE1 A:HIS49 3.7 26.9 0.5
CG A:HIS49 3.8 24.2 0.5
O A:CYS48 3.8 15.9 1.0
CA A:CYS48 3.8 14.3 1.0
CA A:HIS49 3.9 16.8 0.5
NH1 A:ARG52 3.9 38.7 1.0
CA A:HIS49 3.9 15.9 0.5
NE2 A:HIS49 3.9 27.4 0.5
CD2 A:HIS49 4.0 27.7 0.5
O A:GLU45 4.3 17.2 0.5
O A:GLU45 4.3 15.4 0.5
CG A:ARG52 4.3 23.2 1.0
CB A:HIS49 4.4 19.0 0.5
CB A:HIS49 4.6 17.9 0.5
NE A:ARG52 4.6 29.7 1.0
CZ A:ARG52 4.7 50.9 1.0
CB A:ARG52 4.8 16.7 1.0
N A:CYS48 4.9 13.9 1.0
O A:HOH415 4.9 35.3 1.0

Cadmium binding site 9 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 9 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:41.1
occ:0.16
 SG A:CYS126 2.2 24.5 1.0
O A:HOH452 2.2 40.2 1.0
CB A:CYS126 3.2 19.7 1.0
CA A:SER118 3.5 19.4 1.0
CB A:SER118 3.5 23.2 1.0
N A:SER118 3.8 18.9 1.0
CE1 A:HIS114 3.8 20.7 1.0
OG A:SER118 3.9 30.7 1.0
O A:HOH318 3.9 29.9 0.5
O A:HOH465 4.3 51.3 1.0
NE2 A:HIS114 4.3 21.1 1.0
C A:GLY117 4.4 20.2 1.0
ND1 A:HIS114 4.5 21.5 1.0
O A:HIS114 4.5 18.6 1.0
CA A:CYS126 4.6 17.2 1.0
O A:GLY117 4.7 19.2 1.0
O A:HOH449 4.8 50.0 1.0
O A:ASP122 4.9 16.9 1.0
C A:SER118 4.9 22.8 1.0

Cadmium binding site 10 out of 10 in 6gxj

Go back to Cadmium Binding Sites List in 6gxj
Cadmium binding site 10 out of 10 in the X-Ray Structure of Diru-1-Encapsulated 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 Diru-1-Encapsulated Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:23.6
occ:0.11
 O A:HOH383 2.2 50.3 1.0
O A:HOH427 2.2 28.5 0.5
O A:HOH413 2.2 48.5 1.0
O A:HOH412 2.8 39.0 0.6
OE1 A:GLU45 2.9 18.7 0.5
O A:HOH304 3.0 32.7 1.0
O A:HOH412 3.2 22.3 0.4
CD A:GLU45 3.9 39.1 0.5
OE2 A:GLU45 4.4 31.3 0.5
NH2 A:ARG168 4.5 17.6 1.0
O A:HIS173 4.7 56.8 1.0
NH1 A:ARG168 4.9 16.7 1.0
CG A:GLU45 4.9 31.2 0.5

Reference:

G.Petruk, D.M.Monti, G.Ferraro, A.Pica, L.D'elia, F.Pane, A.Amoresano, J.Furrer, K.Kowalski, A.Merlino. Encapsulation of the Dinuclear Trithiolato-Bridged Arene Ruthenium Complex Diruthenium-1 in An Apoferritin Nanocage: Structure and Cytotoxicity. Chemmedchem V. 14 594 2019.
ISSN: ESSN 1860-7187
PubMed: 30674089
DOI: 10.1002/CMDC.201800805
Page generated: Fri Jul 19 19:21:15 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy