Gold in PDB 7vit: Crystal Structure of Au(400EQ)-Apo-R168H/L169C-Rhlfr

The structure of Crystal Structure of Au(400EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vit 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)	12.96 / 1.90
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.889, 180.889, 180.889, 90, 90, 90
R / Rfree (%)	18.3 / 21.7

The structure of Crystal Structure of Au(400EQ)-Apo-R168H/L169C-Rhlfr also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Cadmium	(Cd)	3 atoms

The binding sites of Gold atom in the Crystal Structure of Au(400EQ)-Apo-R168H/L169C-Rhlfr (pdb code 7vit). 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(400EQ)-Apo-R168H/L169C-Rhlfr, PDB code: 7vit:
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(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au203 b:18.6 occ:1.00 ND1 A:HIS49 2.0 19.5 1.0 SG A:CYS48 2.3 12.1 1.0 CE1 A:HIS49 2.8 21.8 1.0 N A:HIS49 3.1 13.0 1.0 CG A:HIS49 3.2 18.8 1.0 C A:CYS48 3.2 12.2 1.0 CB A:CYS48 3.2 11.3 1.0 CA A:HIS49 3.4 12.8 1.0 O A:GLU45 3.4 15.7 1.0 AU A:AU204 3.5 17.1 1.0 OE1 A:GLU45 3.6 31.0 1.0 CB A:HIS49 3.7 15.1 1.0 O A:CYS48 3.8 12.1 1.0 CA A:CYS48 3.8 12.5 1.0 CD A:GLU45 3.9 25.3 1.0 NE2 A:HIS49 4.0 21.3 1.0 CG A:GLU45 4.2 22.6 1.0 CD2 A:HIS49 4.2 19.3 1.0 O A:HOH503 4.3 33.0 1.0 OE2 A:GLU45 4.5 20.8 1.0 CD A:ARG52 4.5 19.5 1.0 C A:GLU45 4.5 16.9 1.0 NE A:ARG52 4.6 24.2 1.0 NH2 A:ARG52 4.7 34.8 1.0 N A:CYS48 4.7 11.7 1.0 CZ A:ARG52 4.8 31.8 1.0 CB A:ARG52 4.8 13.5 1.0 C A:HIS49 4.8 13.4 1.0 O A:HOH450 4.8 24.4 1.0 O A:HOH470 4.9 41.9 1.0

Gold binding site 2 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au204 b:17.1 occ:1.00 SG A:CYS48 2.2 12.1 1.0 CL A:CL214 2.2 14.1 1.0 O A:CYS48 3.2 12.1 1.0 C A:GLY34 3.3 11.0 1.0 CB A:CYS48 3.4 11.3 1.0 AU A:AU203 3.5 18.6 1.0 O A:GLY34 3.5 10.3 1.0 CA A:GLY34 3.5 11.2 1.0 C A:CYS48 3.5 12.2 1.0 CA A:CYS48 3.7 12.5 1.0 N A:PHE35 3.8 9.9 1.0 CB A:ARG52 3.9 13.5 1.0 O A:HOH503 4.1 33.0 1.0 CD A:ARG52 4.4 19.5 1.0 N A:HIS49 4.5 13.0 1.0 CA A:PHE35 4.5 11.0 1.0 CG A:ARG52 4.5 16.2 1.0 CD2 A:PHE35 4.7 11.9 1.0 N A:ARG52 4.7 11.7 1.0 CA A:ARG52 4.7 12.6 1.0 CE2 A:PHE35 4.7 13.4 1.0 CG A:PHE35 4.8 11.5 1.0 N A:GLY34 4.8 11.2 1.0 CZ A:PHE35 4.8 14.5 1.0 CD1 A:PHE35 4.9 12.2 1.0 CE1 A:PHE35 5.0 13.2 1.0

Gold binding site 3 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au205 b:18.0 occ:0.80 SG A:CYS126 2.1 19.1 1.0 CL A:CL215 2.3 14.6 0.8 CB A:CYS126 3.4 15.4 1.0 O A:ASP122 3.5 12.5 1.0 AU A:AU206 3.6 17.4 0.8 C A:ASP122 3.7 12.4 1.0 N A:SER118 3.7 14.6 1.0 CA A:SER118 3.8 16.0 1.0 O A:GLY117 3.8 13.7 1.0 CA A:PRO123 3.8 11.1 1.0 C A:GLY117 3.9 14.8 1.0 N A:PRO123 3.9 12.7 1.0 N A:ASP122 4.1 13.9 1.0 CB A:SER118 4.3 16.5 1.0 CA A:CYS126 4.5 14.9 1.0 CA A:ASP122 4.6 13.0 1.0 N A:CYS126 4.6 13.3 1.0 CB A:PRO123 4.6 12.2 1.0 CA A:GLY117 4.8 13.9 1.0 C A:PRO123 4.8 10.7 1.0 OG A:SER118 4.8 17.0 1.0 CD A:PRO123 4.9 11.5 1.0 C A:ALA121 4.9 14.2 1.0 C A:SER118 5.0 16.5 1.0

Gold binding site 4 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au206 b:17.4 occ:0.80 ND1 A:HIS114 2.0 15.6 1.0 SG A:CYS126 2.3 19.1 1.0 CE1 A:HIS114 2.9 16.7 1.0 CG A:HIS114 3.0 15.1 1.0 CB A:CYS126 3.2 15.4 1.0 O A:HIS114 3.2 11.4 1.0 CB A:HIS114 3.3 13.3 1.0 CA A:HIS114 3.5 12.7 1.0 AU A:AU205 3.6 18.0 0.8 C A:HIS114 3.7 12.4 1.0 CA A:CYS126 3.8 14.9 1.0 NE2 A:HIS114 4.1 14.9 1.0 CD2 A:HIS114 4.1 15.0 1.0 N A:SER118 4.1 14.6 1.0 CB A:SER118 4.3 16.5 1.0 N A:CYS126 4.6 13.3 1.0 CA A:SER118 4.6 16.0 1.0 C A:GLY117 4.8 14.8 1.0 N A:ALA115 4.9 13.1 1.0 N A:HIS114 4.9 12.4 1.0

Gold binding site 5 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au207 b:20.6 occ:0.43 SD A:MET96 1.6 2.7 0.5 ND1 A:HIS147 2.3 14.5 1.0 SD A:MET96 2.5 22.9 0.5 CE A:MET96 2.7 3.5 0.5 CG A:MET96 2.9 19.6 0.5 CE A:MET96 3.0 20.5 0.5 CG A:HIS147 3.1 12.8 1.0 CG A:MET96 3.2 4.9 0.5 CB A:HIS147 3.2 11.4 1.0 CE1 A:HIS147 3.4 14.8 1.0 CE2 A:PHE50 3.4 14.3 1.0 CZ A:PHE50 3.6 14.4 1.0 CB A:MET96 4.0 5.9 0.5 CD2 A:PHE50 4.1 13.5 1.0 CD2 A:HIS147 4.3 13.4 1.0 CE1 A:PHE50 4.4 14.5 1.0 CB A:MET96 4.4 15.2 0.5 NE2 A:HIS147 4.4 15.5 1.0 CD1 A:ILE151 4.7 17.6 1.0 CG A:PHE50 4.7 12.3 1.0 CA A:HIS147 4.8 11.8 1.0 CD1 A:PHE50 4.8 14.0 1.0

Gold binding site 6 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au208 b:51.8 occ:0.70 ND1 A:HIS168 2.5 42.5 1.0 CG A:HIS168 3.2 37.6 1.0 CE1 A:HIS168 3.3 38.5 1.0 AU A:AU209 3.4 38.3 0.5 CB A:HIS168 3.5 37.2 1.0 CA A:HIS168 3.9 34.7 1.0 O A:HIS168 4.2 35.3 1.0 CD2 A:HIS168 4.2 35.1 1.0 NE2 A:HIS168 4.3 40.8 1.0 C A:HIS168 4.5 35.0 1.0

Gold binding site 7 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au209 b:38.3 occ:0.50 AU A:AU208 3.4 51.8 0.7 CB A:HIS168 3.8 37.2 1.0 ND1 A:HIS168 3.9 42.5 1.0 AU A:AU210 4.1 42.0 0.6 CG A:HIS168 4.4 37.6 1.0 O A:HIS168 4.5 35.3 1.0 CA A:HIS168 4.8 34.7 1.0 C A:HIS168 4.8 35.0 1.0

Gold binding site 8 out of 8 in the Crystal Structure of Au(400EQ)-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(400EQ)-Apo-R168H/L169C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Au210 b:42.0 occ:0.60 CB A:CYS169 2.8 40.3 1.0 CA A:CYS169 3.2 30.3 1.0 N A:CYS169 3.5 30.7 1.0 C A:HIS168 3.8 35.0 1.0 O A:HIS168 4.0 35.3 1.0 AU A:AU209 4.1 38.3 0.5 CB A:HIS168 4.4 37.2 1.0 CA A:HIS168 4.7 34.7 1.0 C A:CYS169 4.7 31.1 1.0 O A:LEU165 4.7 23.5 1.0 CD2 A:LEU165 5.0 27.6 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