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

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

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

Cadmium

(Cd)

9 atoms

The binding sites of Gold 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 Gold atom.
In total 7 binding sites of Gold where determined in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7;

Gold binding site 1 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au201 b:20.0 occ:0.40 ND1 A:HIS114 2.2 22.9 1.0 O A:HOH304 2.2 24.0 0.6 SG A:CYS126 2.2 26.6 1.0 O A:HOH512 2.6 21.4 1.0 O A:HIS114 2.8 22.3 1.0 CE1 A:HIS114 2.9 14.7 1.0 CB A:CYS126 3.1 22.7 1.0 CG A:HIS114 3.1 28.0 1.0 C A:HIS114 3.5 22.0 1.0 CB A:HIS114 3.5 22.9 1.0 CA A:HIS114 3.5 22.2 1.0 AU A:AU204 3.7 20.6 0.5 CA A:CYS126 3.8 20.4 1.0 NE2 A:HIS114 3.9 16.2 1.0 N A:SER118 4.0 23.5 1.0 CD2 A:HIS114 4.1 24.6 1.0 CB A:SER118 4.2 27.1 1.0 CA A:SER118 4.5 24.0 1.0 N A:ALA115 4.7 21.3 1.0 N A:CYS126 4.7 20.2 1.0 C A:GLY117 4.7 22.3 1.0 CA A:GLY117 4.9 22.4 1.0 N A:HIS114 5.0 18.6 1.0 C A:CYS126 5.0 21.2 1.0

Gold binding site 2 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au202 b:34.9 occ:0.30 SG A:CYS48 1.9 16.4 1.0 CD A:ARG52 2.0 26.6 0.7 CG A:ARG52 2.5 21.1 0.3 NE A:ARG52 2.6 25.9 0.3 CG A:ARG52 2.7 24.1 0.7 CD A:ARG52 2.7 23.0 0.3 AU A:AU206 3.1 38.7 0.5 O A:CYS48 3.2 12.3 1.0 O A:GLY34 3.3 12.7 1.0 CB A:CYS48 3.3 13.8 1.0 C A:GLY34 3.3 12.7 1.0 NE A:ARG52 3.4 31.0 0.7 C A:CYS48 3.5 13.6 1.0 CA A:GLY34 3.6 12.6 1.0 NH1 A:ARG52 3.6 39.6 0.7 CA A:CYS48 3.7 13.3 1.0 CB A:ARG52 3.7 18.7 0.3 CB A:ARG52 3.8 19.9 0.7 CZ A:ARG52 3.8 30.1 0.3 CZ A:ARG52 4.0 40.0 0.7 N A:PHE35 4.0 11.3 1.0 NH1 A:ARG52 4.4 31.2 0.3 O A:HOH484 4.4 23.4 0.6 N A:HIS49 4.4 13.2 1.0 CA A:PHE35 4.5 12.2 1.0 CD2 A:PHE35 4.8 14.1 1.0 CB A:ASP38 4.8 13.5 1.0 NH2 A:ARG52 4.8 30.5 0.3 CA A:ARG52 4.8 16.8 0.3 CG A:PHE35 4.8 12.9 1.0 N A:ARG52 4.8 15.1 0.3 N A:ARG52 4.8 14.8 0.7 CE2 A:PHE35 4.8 14.5 1.0 CA A:ARG52 4.9 17.2 0.7 CD1 A:PHE35 4.9 13.2 1.0 CZ A:PHE35 4.9 15.2 1.0 CE1 A:PHE35 5.0 13.3 1.0 CA A:HIS49 5.0 15.9 1.0

Gold binding site 3 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au203 b:29.5 occ:0.35 ND1 A:HIS49 2.1 33.1 1.0 CE1 A:HIS49 2.9 33.5 1.0 O A:HOH462 3.1 38.5 0.7 CG A:HIS49 3.2 28.9 1.0 CA A:HIS49 3.7 15.9 1.0 CB A:HIS49 3.7 20.1 1.0 AU A:AU206 3.9 38.7 0.5 CB A:ARG52 4.1 19.9 0.7 CB A:ARG52 4.1 18.7 0.3 NE2 A:HIS49 4.1 33.8 1.0 OE2 A:GLU53 4.2 19.5 0.3 O A:HIS49 4.3 13.5 1.0 CD2 A:HIS49 4.3 34.1 1.0 NE A:ARG52 4.4 25.9 0.3 NH1 A:ARG52 4.4 31.2 0.3 CD A:ARG52 4.5 26.6 0.7 C A:HIS49 4.5 13.9 1.0 NE A:ARG52 4.6 31.0 0.7 NH1 A:ARG52 4.6 39.6 0.7 CZ A:ARG52 4.6 40.0 0.7 CZ A:ARG52 4.7 30.1 0.3 CG A:GLU53 4.7 17.0 0.3 N A:HIS49 4.7 13.2 1.0 CD A:GLU53 4.8 17.6 0.3 CG A:ARG52 4.9 21.1 0.3 CG A:ARG52 4.9 24.1 0.7 O A:CYS48 5.0 12.3 1.0

Gold binding site 4 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au204 b:20.6 occ:0.45 SG A:CYS126 2.2 26.6 1.0 O A:HOH512 2.6 21.4 1.0 CB A:CYS126 3.1 22.7 1.0 O A:ASP122 3.4 20.9 1.0 AU A:AU201 3.7 20.0 0.4 C A:ASP122 3.7 21.6 1.0 CA A:SER118 3.8 24.0 1.0 N A:SER118 3.8 23.5 1.0 O A:GLY117 3.8 20.5 1.0 C A:GLY117 3.8 22.3 1.0 CA A:PRO123 3.8 22.3 1.0 N A:PRO123 4.0 22.9 1.0 N A:ASP122 4.1 18.6 1.0 CB A:SER118 4.4 27.1 1.0 CA A:CYS126 4.5 20.4 1.0 N A:CYS126 4.6 20.2 1.0 CA A:ASP122 4.6 19.3 1.0 CB A:PRO123 4.7 24.3 1.0 CA A:GLY117 4.7 22.4 1.0 C A:PRO123 4.8 21.5 1.0 C A:SER118 4.9 23.7 1.0 CD A:PRO123 5.0 22.9 1.0 C A:ALA121 5.0 20.2 1.0 OG A:SER118 5.0 29.6 1.0

Gold binding site 5 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au205 b:38.9 occ:0.25 NE2 A:HIS147 2.6 14.0 1.0 CE1 A:HIS147 3.3 13.9 1.0 CE1 A:PHE50 3.4 15.6 1.0 CD1 A:PHE50 3.5 14.5 1.0 CD A:LYS143 3.5 20.9 0.5 CD2 A:HIS147 3.7 13.6 1.0 CD2 A:LEU171 3.9 17.5 1.0 CD A:LYS143 3.9 19.4 0.5 CE A:LYS143 4.1 22.5 0.5 CG A:LYS143 4.1 18.2 0.5 CG A:LYS143 4.2 19.3 0.5 ND1 A:HIS147 4.5 14.2 1.0 CZ A:PHE50 4.6 14.1 1.0 NZ A:LYS143 4.6 23.9 0.5 CE A:LYS143 4.6 21.3 0.5 CG A:PHE50 4.7 13.2 1.0 CG A:HIS147 4.7 12.9 1.0 O A:HOH550 5.0 26.4 0.5

Gold binding site 6 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au206 b:38.7 occ:0.45 SG A:CYS48 2.3 16.4 1.0 O A:HOH484 2.5 23.4 0.6 CB A:CYS48 3.0 13.8 1.0 AU A:AU202 3.1 34.9 0.3 N A:HIS49 3.2 13.2 1.0 ND1 A:HIS49 3.2 33.1 1.0 CE1 A:HIS49 3.3 33.5 1.0 CG A:HIS49 3.3 28.9 1.0 C A:CYS48 3.4 13.6 1.0 NE2 A:HIS49 3.4 33.8 1.0 CD2 A:HIS49 3.4 34.1 1.0 CA A:HIS49 3.7 15.9 1.0 O A:GLU45 3.8 14.5 1.0 CA A:CYS48 3.8 13.3 1.0 O A:CYS48 3.9 12.3 1.0 AU A:AU203 3.9 29.5 0.3 CD A:ARG52 4.1 26.6 0.7 CB A:HIS49 4.1 20.1 1.0 NH1 A:ARG52 4.1 39.6 0.7 NE A:ARG52 4.2 25.9 0.3 NH1 A:ARG52 4.6 31.2 0.3 CG A:GLU45 4.7 26.4 1.0 CG A:ARG52 4.8 21.1 0.3 N A:CYS48 4.8 10.8 1.0 C A:GLU45 4.9 14.8 1.0 CZ A:ARG52 4.9 30.1 0.3 CG A:ARG52 4.9 24.1 0.7 NE A:ARG52 4.9 31.0 0.7 CZ A:ARG52 4.9 40.0 0.7 O A:HOH438 5.0 31.6 1.0

Gold binding site 7 out of 7 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au 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:Au207 b:50.5 occ:0.20 ND1 A:HIS132 2.5 54.4 1.0 CG A:HIS132 3.3 44.8 1.0 CB A:HIS132 3.4 39.1 1.0 CE1 A:HIS132 3.5 52.1 1.0 CA A:HIS132 3.5 33.4 1.0 CZ A:ARG64 3.6 27.9 0.5 NH1 A:ARG64 3.7 28.1 0.5 NE A:ARG64 3.9 26.5 0.5 NH2 A:ARG64 4.0 30.7 0.5 O A:SER131 4.0 34.8 1.0 O A:HIS132 4.1 29.1 1.0 OE2 A:GLU136 4.3 40.5 0.7 C A:HIS132 4.3 28.4 1.0 CD A:ARG64 4.4 21.7 0.5 NE A:ARG64 4.4 23.0 0.5 CD A:ARG64 4.4 23.6 0.5 CZ A:ARG64 4.5 24.7 0.5 NH1 A:ARG64 4.5 26.3 0.5 CD2 A:HIS132 4.5 49.3 1.0 N A:HIS132 4.6 30.0 1.0 NE2 A:HIS132 4.6 54.7 1.0 C A:SER131 4.7 35.0 1.0 O A:HOH477 4.7 43.0 1.0 CD A:GLU136 4.9 35.0 0.7

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