Gold in PDB 7vir: Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr

The structure of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vir was solved by C.Lu, X.Peng, B.Maity, N.Ito, S.Abe, T.Ueno, D.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.91 / 1.90
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.213, 180.213, 180.213, 90, 90, 90
R / Rfree (%)	17 / 20.9

The structure of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr also contains other interesting chemical elements:

Cadmium

(Cd)

4 atoms

The binding sites of Gold atom in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr (pdb code 7vir). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 8 binding sites of Gold where determined in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vir:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Gold binding site 1 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au205 b:22.9 occ:0.90 SG A:CYS48 2.3 13.5 1.0 CD2 A:HIS49 2.8 35.1 1.0 CG A:HIS49 2.9 29.0 1.0 OE2 A:GLU45 3.0 37.7 1.0 NE2 A:HIS49 3.1 36.4 1.0 AU A:AU211 3.1 23.0 0.3 N A:HIS49 3.1 13.2 1.0 ND1 A:HIS49 3.1 38.0 1.0 CB A:CYS48 3.2 10.7 1.0 C A:CYS48 3.2 11.9 1.0 CE1 A:HIS49 3.2 34.7 1.0 CA A:HIS49 3.3 13.8 1.0 CD A:GLU45 3.6 35.0 1.0 CB A:HIS49 3.6 18.1 1.0 O A:CYS48 3.7 9.9 1.0 O A:GLU45 3.8 13.0 1.0 CA A:CYS48 3.8 12.8 1.0 O A:HOH396 3.9 20.8 1.0 OE1 A:GLU45 4.0 32.0 1.0 CD A:ARG52 4.0 27.9 1.0 NH1 A:ARG52 4.4 40.0 1.0 CG A:GLU45 4.5 25.1 1.0 CG A:ARG52 4.7 22.1 1.0 N A:CYS48 4.7 10.7 1.0 C A:HIS49 4.8 13.2 1.0 C A:GLU45 4.8 12.7 1.0 CB A:ARG52 5.0 15.5 1.0

Gold binding site 2 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au207 b:25.9 occ:0.60 SG A:CYS126 1.9 11.0 0.5 ND1 A:HIS114 2.0 22.5 1.0 CE1 A:HIS114 2.9 24.8 1.0 CB A:CYS126 3.0 15.3 0.5 SG A:CYS126 3.0 32.8 0.5 O A:HOH426 3.1 18.3 1.0 CB A:CYS126 3.1 23.0 0.5 CG A:HIS114 3.2 25.2 1.0 AU A:AU213 3.4 29.0 0.7 CB A:HIS114 3.7 20.1 1.0 CA A:CYS126 3.8 16.5 0.5 CA A:CYS126 3.8 19.8 0.5 NE2 A:HIS114 4.1 23.7 1.0 CD2 A:HIS114 4.3 28.7 1.0 O A:HOH424 4.3 25.7 1.0 CA A:HIS114 4.3 16.5 1.0 O A:HIS114 4.3 18.4 1.0 OE2 A:GLU130 4.5 28.6 1.0 O A:CYS126 4.5 22.2 1.0 C A:CYS126 4.5 18.6 1.0 C A:HIS114 4.6 17.4 1.0 CG A:GLU130 4.8 22.9 1.0 CD A:GLU130 4.9 24.0 1.0 AU A:AU212 4.9 30.6 0.4 N A:CYS126 5.0 15.4 1.0

Gold binding site 3 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au208 b:46.3 occ:0.60 SG A:CYS169 2.6 51.9 1.0 AU A:AU209 3.0 36.3 0.3 N A:CYS169 3.3 35.4 1.0 C A:HIS168 3.3 33.3 1.0 CB A:HIS168 3.3 34.5 1.0 AU A:AU210 3.4 38.0 0.3 CB A:CYS169 3.6 43.7 1.0 CA A:CYS169 3.6 34.6 1.0 O A:HIS168 3.6 30.9 1.0 ND1 A:HIS168 3.9 45.9 1.0 CA A:HIS168 3.9 34.9 1.0 CG A:HIS168 4.1 41.1 1.0 CD2 A:LEU165 4.5 28.0 1.0 O A:LEU165 4.6 19.2 1.0 N A:HIS168 4.9 29.6 1.0

Gold binding site 4 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au209 b:36.3 occ:0.30 AU A:AU210 1.8 38.0 0.3 SG A:CYS169 2.0 51.9 1.0 AU A:AU208 3.0 46.3 0.6 CB A:CYS169 3.4 43.7 1.0 CA A:CYS169 4.2 34.6 1.0 N A:CYS169 4.9 35.4 1.0 CD2 A:LEU165 5.0 28.0 1.0

Gold binding site 5 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au210 b:38.0 occ:0.30 AU A:AU209 1.8 36.3 0.3 SG A:CYS169 2.6 51.9 1.0 CB A:CYS169 2.9 43.7 1.0 CA A:CYS169 3.2 34.6 1.0 AU A:AU208 3.4 46.3 0.6 N A:CYS169 4.2 35.4 1.0 O A:CYS169 4.2 37.1 1.0 C A:CYS169 4.2 37.6 1.0 O A:HIS168 4.4 30.9 1.0 C A:HIS168 4.6 33.3 1.0

Gold binding site 6 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au211 b:23.0 occ:0.30 OE1 A:GLU45 2.3 32.0 1.0 OE2 A:GLU45 2.3 37.7 1.0 O A:HOH396 2.5 20.8 1.0 CD A:GLU45 2.6 35.0 1.0 OD1 A:ASP38 2.7 13.2 1.0 SG A:CYS48 2.7 13.5 1.0 AU A:AU205 3.1 22.9 0.9 CG A:ASP38 3.3 12.0 1.0 CB A:ASP38 3.6 11.1 1.0 CB A:CYS48 3.8 10.7 1.0 CG A:GLU45 4.1 25.1 1.0 OD2 A:ASP38 4.3 11.3 1.0 CA A:ASP38 4.3 10.5 1.0 NE2 A:HIS49 4.9 36.4 1.0 NH1 A:ARG52 4.9 40.0 1.0 CD2 A:HIS49 5.0 35.1 1.0

Gold binding site 7 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au212 b:30.6 occ:0.40 SG A:CYS126 2.6 32.8 0.5 O A:HOH426 2.9 18.3 1.0 CB A:CYS126 3.4 23.0 0.5 O A:ASP122 3.5 15.5 1.0 CB A:CYS126 3.6 15.3 0.5 CA A:PRO123 3.7 14.4 1.0 C A:ASP122 3.8 15.9 1.0 N A:PRO123 3.9 14.2 1.0 CA A:SER118 4.0 24.8 1.0 O A:GLY117 4.2 19.4 1.0 N A:SER118 4.2 23.3 1.0 AU A:AU213 4.3 29.0 0.7 C A:GLY117 4.3 20.0 1.0 N A:ASP122 4.3 14.5 1.0 CB A:SER118 4.5 26.3 1.0 CB A:PRO123 4.5 14.2 1.0 SG A:CYS126 4.6 11.0 0.5 CA A:CYS126 4.7 19.8 0.5 CA A:ASP122 4.7 14.7 1.0 CA A:CYS126 4.7 16.5 0.5 C A:PRO123 4.7 13.3 1.0 N A:CYS126 4.8 15.4 1.0 AU A:AU207 4.9 25.9 0.6 CD A:PRO123 4.9 13.9 1.0 O A:PRO123 4.9 12.3 1.0 C A:ALA121 5.0 16.7 1.0

Gold binding site 8 out of 8 in the Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of Crystal Structure of Au(100EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au213 b:29.0 occ:0.70 O A:HOH426 2.3 18.3 1.0 O A:HOH431 2.3 10.0 0.3 SG A:CYS126 2.4 11.0 0.5 O A:HOH424 3.1 25.7 1.0 OE2 A:GLU130 3.2 28.6 1.0 CB A:CYS126 3.3 15.3 0.5 AU A:AU207 3.4 25.9 0.6 CB A:CYS126 3.5 23.0 0.5 CD A:CD201 3.6 22.7 0.2 CD A:GLU130 3.9 24.0 1.0 SG A:CYS126 4.2 32.8 0.5 AU A:AU212 4.3 30.6 0.4 OE1 A:GLU130 4.4 25.4 1.0 CA A:CYS126 4.7 19.8 0.5 CA A:CYS126 4.7 16.5 0.5 CG A:GLU130 4.9 22.9 1.0 C A:CYS126 4.9 18.6 1.0

C.Lu, B.Maity, X.Peng, N.Ito, S.Abe, X.Sheng, T.Ueno, D.Lu. Design of A Gold Clustering Site in An Engineered Apo-Ferritin Cage Commun Chem V. 5 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00651-1