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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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