Gold in PDB 7w2d: The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA

The structure of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA, PDB code: 7w2d was solved by F.Meng, Z.Sun, X.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 3.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.299, 147.888, 171.395, 90, 91.67, 90
R / Rfree (%)	23.9 / 26.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Gold atom in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA (pdb code 7w2d). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 24 binding sites of Gold where determined in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA, PDB code: 7w2d:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ A:Au401 b:122.7 occ:1.00 SG A:CYS91 2.4 91.7 1.0 AU A:AU402 3.1 119.4 1.0 CB A:CYS91 3.3 104.0 1.0 CD1 A:ILE59 3.8 88.1 1.0 CD1 A:LEU103 3.8 88.2 1.0 CZ2 A:TRP78 3.9 88.3 1.0 CE2 A:TRP78 4.2 92.5 1.0 NE1 A:TRP78 4.3 95.8 1.0 CH2 A:TRP78 4.6 87.2 1.0 CD2 A:LEU93 4.7 86.8 1.0 CD1 A:LEU76 4.8 98.0 1.0 CA A:CYS91 4.8 84.4 1.0 CG A:LEU103 5.0 79.3 1.0

Gold binding site 2 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ A:Au402 b:119.4 occ:1.00 SG A:CYS91 2.6 91.7 1.0 AU A:AU401 3.1 122.7 1.0 N A:GLN77 3.5 89.4 1.0 CB A:CYS91 3.5 104.0 1.0 NE1 A:TRP78 3.7 95.8 1.0 C A:GLN77 3.7 90.5 1.0 CA A:GLN77 3.7 93.9 1.0 CD1 A:TRP78 3.7 89.2 1.0 CB A:LEU76 3.7 92.9 1.0 N A:TRP78 3.8 84.8 1.0 C A:LEU76 3.8 92.8 1.0 CE2 A:TRP78 4.1 92.5 1.0 O A:GLN77 4.1 86.9 1.0 CG A:TRP78 4.1 85.8 1.0 CA A:LEU76 4.3 91.5 1.0 CD2 A:TRP78 4.3 87.4 1.0 O A:LEU76 4.3 95.4 1.0 CA A:CYS91 4.4 84.4 1.0 CA A:TRP78 4.6 79.2 1.0 CZ2 A:TRP78 4.7 88.3 1.0 CG A:LEU76 4.8 93.7 1.0 CD1 A:LEU76 4.9 98.0 1.0 CB A:TRP78 4.9 81.4 1.0

Gold binding site 3 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ C:Au401 b:102.1 occ:1.00 SG C:CYS91 2.6 78.3 1.0 AU C:AU402 3.0 102.3 1.0 CB C:CYS91 3.4 89.4 1.0 CZ2 C:TRP78 3.7 87.5 1.0 CD1 C:LEU103 3.8 78.3 1.0 CD1 C:ILE59 3.9 96.4 1.0 CE2 C:TRP78 4.0 95.4 1.0 NE1 C:TRP78 4.2 100.9 1.0 NH2 I:ARG41 4.2 111.5 1.0 CH2 C:TRP78 4.4 83.6 1.0 NE I:ARG41 4.6 108.9 1.0 CZ I:ARG41 4.7 110.2 1.0 CD1 C:LEU76 4.8 90.0 1.0 CD2 C:LEU93 4.8 79.7 1.0 CA C:CYS91 4.9 85.2 1.0 CG C:LEU103 4.9 74.5 1.0

Gold binding site 4 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ C:Au402 b:102.3 occ:1.00 SG C:CYS91 2.5 78.3 1.0 AU C:AU401 3.0 102.1 1.0 CB C:CYS91 3.4 89.4 1.0 NE1 C:TRP78 3.6 100.9 1.0 N C:GLN77 3.6 99.4 1.0 CB C:LEU76 3.7 94.2 1.0 CD1 C:TRP78 3.7 92.5 1.0 C C:GLN77 3.8 85.9 1.0 CA C:GLN77 3.9 92.0 1.0 C C:LEU76 3.9 102.7 1.0 CE2 C:TRP78 4.0 95.4 1.0 N C:TRP78 4.0 87.8 1.0 NH2 I:ARG41 4.1 111.5 1.0 CG C:TRP78 4.1 85.3 1.0 O C:GLN77 4.3 84.1 1.0 CD2 C:TRP78 4.3 87.4 1.0 CA C:LEU76 4.3 99.0 1.0 CA C:CYS91 4.4 85.2 1.0 O C:LEU76 4.4 107.0 1.0 CZ2 C:TRP78 4.6 87.5 1.0 CA C:TRP78 4.6 83.1 1.0 CG C:LEU76 4.7 92.8 1.0 CD1 C:LEU76 4.7 90.0 1.0 CB C:TRP78 5.0 82.3 1.0

Gold binding site 5 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ E:Au401 b:132.7 occ:1.00 SG E:CYS91 2.5 83.5 1.0 AU E:AU402 3.1 134.5 1.0 CB E:CYS91 3.3 103.7 1.0 CD1 E:LEU103 3.8 97.6 1.0 CD1 E:ILE59 4.0 110.3 1.0 CZ2 E:TRP78 4.0 85.5 1.0 CE2 E:TRP78 4.3 89.3 1.0 NE1 E:TRP78 4.4 98.8 1.0 CH2 E:TRP78 4.6 82.5 1.0 CD2 E:LEU93 4.7 93.4 1.0 CA E:CYS91 4.8 94.9 1.0 CG E:LEU103 4.9 90.7 1.0 CD1 E:LEU76 5.0 99.5 1.0

Gold binding site 6 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ E:Au402 b:134.5 occ:1.00 SG E:CYS91 2.5 83.5 1.0 AU E:AU401 3.1 132.7 1.0 CB E:CYS91 3.4 103.7 1.0 N E:GLN77 3.5 111.0 1.0 C E:GLN77 3.6 103.2 1.0 CA E:GLN77 3.8 110.1 1.0 N E:TRP78 3.8 105.4 1.0 NE1 E:TRP78 3.8 98.8 1.0 CD1 E:TRP78 3.8 93.0 1.0 CB E:LEU76 3.9 107.5 1.0 C E:LEU76 3.9 106.8 1.0 O E:GLN77 4.0 98.5 1.0 CE2 E:TRP78 4.1 89.3 1.0 CG E:TRP78 4.1 88.2 1.0 CD2 E:TRP78 4.3 86.7 1.0 CA E:CYS91 4.3 94.9 1.0 CA E:LEU76 4.4 100.2 1.0 CA E:TRP78 4.5 92.4 1.0 O E:LEU76 4.5 111.8 1.0 CZ2 E:TRP78 4.8 85.5 1.0 CB E:TRP78 4.9 92.9 1.0 CG E:LEU76 4.9 98.5 1.0

Gold binding site 7 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ B:Au401 b:115.8 occ:1.00 SG B:CYS91 2.5 78.7 1.0 AU B:AU402 3.0 111.3 1.0 CB B:CYS91 3.4 90.8 1.0 CZ2 B:TRP78 3.8 70.5 1.0 CD1 B:LEU103 3.8 79.5 1.0 CD1 B:ILE59 3.9 78.1 1.0 NE1 B:TRP78 3.9 83.1 1.0 CE2 B:TRP78 4.0 78.2 1.0 CH2 B:TRP78 4.6 69.7 1.0 CD2 B:LEU93 4.8 72.5 1.0 CA B:CYS91 4.8 76.3 1.0 CD1 B:LEU76 4.8 82.8 1.0 CD1 B:TRP78 4.9 81.8 1.0 CD2 B:TRP78 4.9 77.8 1.0 CG B:LEU103 5.0 71.4 1.0

Gold binding site 8 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 8 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ B:Au402 b:111.3 occ:1.00 SG B:CYS91 2.6 78.7 1.0 AU B:AU401 3.0 115.8 1.0 CB B:CYS91 3.5 90.8 1.0 N B:GLN77 3.6 82.8 1.0 CD1 B:TRP78 3.6 81.8 1.0 NE1 B:TRP78 3.6 83.1 1.0 C B:GLN77 3.7 83.3 1.0 CB B:LEU76 3.7 85.7 1.0 CA B:GLN77 3.8 88.0 1.0 N B:TRP78 3.8 89.8 1.0 C B:LEU76 3.9 92.5 1.0 CG B:TRP78 4.1 80.5 1.0 CE2 B:TRP78 4.1 78.2 1.0 O B:GLN77 4.2 80.7 1.0 CA B:LEU76 4.3 89.8 1.0 CD2 B:TRP78 4.4 77.8 1.0 CA B:CYS91 4.4 76.3 1.0 O B:LEU76 4.4 95.4 1.0 CA B:TRP78 4.5 83.0 1.0 CG B:LEU76 4.7 84.4 1.0 CD1 B:LEU76 4.8 82.8 1.0 CB B:TRP78 4.8 81.6 1.0 CZ2 B:TRP78 4.9 70.5 1.0

Gold binding site 9 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 9 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ D:Au401 b:120.7 occ:1.00 SG D:CYS91 2.7 85.2 1.0 AU D:AU402 3.1 119.8 1.0 CB D:CYS91 3.5 95.9 1.0 CZ2 D:TRP78 3.8 89.3 1.0 CD1 D:LEU103 3.8 87.2 1.0 CD1 D:ILE59 3.9 105.4 1.0 CE2 D:TRP78 4.1 97.8 1.0 NE1 D:TRP78 4.2 103.8 1.0 CH2 D:TRP78 4.5 84.8 1.0 CD2 D:LEU93 4.8 89.0 1.0 CG D:LEU103 4.9 83.0 1.0 CB D:PHE55 5.0 89.5 1.0 CD2 D:TRP78 5.0 89.9 1.0 CD1 D:LEU76 5.0 92.3 1.0

Gold binding site 10 out of 24 in the The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 10 of The Closed Conformation of the Sigma-1 Receptor From Xenopus Laevis Complexed with S1RA within 5.0Å range: probe atom residue distance (Å) B Occ D:Au402 b:119.8 occ:1.00 SG D:CYS91 2.6 85.2 1.0 AU D:AU401 3.1 120.7 1.0 CB D:CYS91 3.5 95.9 1.0 NE1 D:TRP78 3.6 103.8 1.0 N D:GLN77 3.6 99.6 1.0 CD1 D:TRP78 3.6 95.8 1.0 C D:GLN77 3.7 86.3 1.0 N D:TRP78 3.8 93.5 1.0 CA D:GLN77 3.8 92.2 1.0 CB D:LEU76 3.9 97.3 1.0 CE2 D:TRP78 4.0 97.8 1.0 C D:LEU76 4.0 106.7 1.0 CG D:TRP78 4.0 88.5 1.0 O D:GLN77 4.1 84.6 1.0 CD2 D:TRP78 4.2 89.9 1.0 CA D:CYS91 4.4 92.3 1.0 CA D:LEU76 4.5 102.6 1.0 CA D:TRP78 4.5 87.9 1.0 O D:LEU76 4.6 110.7 1.0 CZ2 D:TRP78 4.7 89.3 1.0 CB D:TRP78 4.8 85.9 1.0 CG D:LEU76 4.9 95.3 1.0 CD1 D:LEU76 4.9 92.3 1.0

F.Meng, Y.Xiao, Y.Ji, Z.Sun, X.Zhou. An Open-Like Conformation of the Sigma-1 Receptor Reveals Its Ligand Entry Pathway. Nat Commun V. 13 1267 2022.
ISSN: ESSN 2041-1723
PubMed: 35273182
DOI: 10.1038/S41467-022-28946-W