Gold in PDB 5y0y: Rvfv Gn-Au

The structure of Rvfv Gn-Au, PDB code: 5y0y was solved by Y.Wu, F.Gao, J.X.Qi, Y.Chai, G.F.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.97 / 3.40
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.180, 97.180, 184.128, 90.00, 90.00, 120.00
R / Rfree (%)	27.5 / 31.7

The binding sites of Gold atom in the Rvfv Gn-Au (pdb code 5y0y). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 6 binding sites of Gold where determined in the Rvfv Gn-Au, PDB code: 5y0y:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6;

Gold binding site 1 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au401 b:0.1 occ:1.00 CG A:HIS82 2.1 0.0 1.0 ND1 A:HIS82 2.3 0.4 1.0 CB A:HIS82 2.3 89.4 1.0 CD2 A:HIS82 2.9 85.7 1.0 CE1 A:HIS82 3.1 74.9 1.0 NE2 A:HIS82 3.4 69.2 1.0 CA A:HIS82 3.8 82.9 1.0 C A:HIS82 4.2 78.5 1.0 O A:HIS82 4.5 81.1 1.0 N A:HIS82 4.7 81.9 1.0 N A:GLY83 4.8 70.9 1.0

Gold binding site 2 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au402 b:0.4 occ:1.00 ND1 A:HIS56 2.0 39.2 1.0 CE1 A:HIS56 2.4 34.9 1.0 CG A:HIS56 3.3 35.0 1.0 N A:HIS56 3.5 41.7 1.0 O A:GLY286 3.6 69.0 1.0 N A:HIS55 3.7 36.9 1.0 NE2 A:HIS56 3.7 27.3 1.0 CA A:TYR53 3.8 40.5 1.0 C A:HIS55 3.8 51.1 1.0 C A:TYR53 3.8 39.1 1.0 CB A:TYR53 3.8 36.3 1.0 CA A:SER287 3.9 57.9 1.0 C A:GLY286 3.9 63.7 1.0 N A:ALA54 4.0 39.7 1.0 CA A:HIS55 4.1 47.7 1.0 N A:SER287 4.1 59.8 1.0 CB A:HIS56 4.1 32.3 1.0 CD2 A:HIS56 4.2 30.0 1.0 O A:TYR53 4.2 41.5 1.0 CB A:HIS55 4.3 50.7 1.0 CA A:HIS56 4.3 33.6 1.0 CD2 A:TYR53 4.3 44.5 1.0 O A:HIS55 4.3 51.0 1.0 CB A:SER287 4.5 59.6 1.0 CG A:TYR53 4.6 36.0 1.0 C A:ALA54 4.6 27.7 1.0 CA A:GLY286 4.9 67.7 1.0 CA A:ALA54 4.9 34.0 1.0

Gold binding site 3 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au403 b:0.4 occ:1.00 CG A:PRO28 1.7 0.4 1.0 CB A:PRO28 2.5 96.7 1.0 NE2 A:HIS13 3.0 87.7 1.0 CD A:PRO28 3.1 92.8 1.0 CD2 A:HIS13 3.7 80.5 1.0 CA A:PRO28 3.7 77.0 1.0 CE1 A:HIS13 3.7 82.8 1.0 N A:PRO28 3.8 81.8 1.0 O A:LYS11 4.2 63.2 1.0 CB A:LYS11 4.6 50.6 1.0 ND1 A:HIS13 4.6 83.0 1.0 CG A:HIS13 4.6 77.7 1.0 C A:LYS11 4.6 57.7 1.0 C A:LYS27 4.9 84.3 1.0 CA A:LYS11 4.9 54.3 1.0

Gold binding site 4 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au404 b:0.7 occ:1.00 CE A:MET19 2.3 91.1 1.0 SD A:MET19 2.5 55.7 1.0 NE2 A:GLN102 3.1 0.1 1.0 CD A:LYS117 3.2 94.0 1.0 CE A:LYS117 3.4 90.8 1.0 CG A:LYS117 3.5 80.8 1.0 CD A:GLN102 3.8 91.7 1.0 CG A:GLN102 4.0 81.4 1.0 CB A:LYS117 4.1 69.2 1.0 NZ A:LYS117 4.2 72.5 1.0 CG A:MET19 4.2 87.8 1.0 CB A:SER103 4.4 60.6 1.0 O A:GLN102 4.4 61.4 1.0 O A:CYS118 4.4 71.4 1.0 CA A:LYS117 4.7 59.5 1.0 OE1 A:GLN102 4.7 82.0 1.0 N A:CYS118 4.9 63.4 1.0 C A:GLN102 4.9 59.5 1.0

Gold binding site 5 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au405 b:0.8 occ:0.50 CD2 A:HIS187 3.3 17.8 1.0 N A:HIS187 4.0 42.9 1.0 NE2 A:HIS187 4.1 14.2 1.0 CG A:HIS187 4.2 42.5 1.0 CA A:ALA186 4.4 30.7 1.0 CB A:HIS187 4.6 42.1 1.0 CB A:ALA186 4.7 35.4 1.0 C A:ALA186 4.8 34.2 1.0 CA A:HIS187 4.8 36.3 1.0 O A:HIS187 4.9 47.6 1.0

Gold binding site 6 out of 6 in the Rvfv Gn-Au


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Rvfv Gn-Au within 5.0Å range: probe atom residue distance (Å) B Occ A:Au406 b:97.9 occ:1.00 ND1 A:HIS13 2.2 83.0 1.0 CE1 A:HIS13 2.6 82.8 1.0 CG A:HIS13 2.6 77.7 1.0 NE2 A:HIS13 3.1 87.7 1.0 CD2 A:HIS13 3.2 80.5 1.0 CG A:HIS64 3.3 44.8 1.0 ND1 A:HIS64 3.3 41.0 1.0 CB A:HIS13 3.4 80.0 1.0 CE1 A:TYR15 3.5 58.0 1.0 CD2 A:HIS64 3.5 41.2 1.0 CE1 A:HIS64 3.5 38.4 1.0 NE2 A:HIS64 3.6 48.6 1.0 OH A:TYR15 3.9 56.4 1.0 CB A:HIS64 3.9 39.1 1.0 CZ A:TYR15 4.2 57.4 1.0 NZ A:LYS11 4.2 49.5 1.0 CD A:LYS11 4.3 58.5 1.0 O A:HIS64 4.5 32.9 1.0 CD1 A:TYR15 4.5 55.0 1.0 CE A:LYS11 4.7 51.4 1.0 CE A:LYS27 4.8 67.5 1.0 CA A:HIS13 4.8 59.6 1.0

Y.Wu, Y.H.Zhu, F.Gao, Y.J.Jiao, B.O.Oladejo, Y.Chai, Y.H.Bi, S.Lu, M.Q.Dong, C.Zhang, G.M.Huang, G.Wong, N.Li, Y.F.Zhang, Y.Li, W.H.Feng, Y.Shi, M.F.Liang, R.G.Zhang, J.X.Qi, G.F.Gao. Structures of Phlebovirus Glycoprotein Gn and Identification of A Neutralizing Antibody Epitope Proc. Natl. Acad. Sci. V. 114 E7564 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28827346
DOI: 10.1073/PNAS.1705176114