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Gold 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:

Cadmium (Cd) 9 atoms

Gold Binding Sites:

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 5ix6

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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 5ix6

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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 5ix6

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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 5ix6

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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 5ix6

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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 5ix6

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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 5ix6

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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

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 01:54:19 2020

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