Cadmium in PDB 7d30: Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)

The structure of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd), PDB code: 7d30 was solved by T.Li, H.Yao, H.Cai, W.Qin, D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.70 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.384, 73.384, 478.363, 90, 90, 120
R / Rfree (%)	19.5 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium atom in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) (pdb code 7d30). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 17 binding sites of Cadmium where determined in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd), PDB code: 7d30:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1314 b:69.2 occ:0.50 OXT B:ACT2104 2.2 84.8 1.0 OXT A:ACT1302 2.2 88.0 1.0 O A:ACT1302 2.2 87.3 1.0 OD2 A:ASP1062 2.2 81.5 1.0 OXT B:GLN539 2.2 99.0 1.0 O B:GLN539 2.2 93.8 1.0 OD1 A:ASP1062 2.3 72.6 1.0 C A:ACT1302 2.4 95.6 1.0 C B:GLN539 2.6 95.9 1.0 CG A:ASP1062 2.6 69.5 1.0 C B:ACT2104 2.9 94.5 1.0 O B:ACT2104 3.2 95.4 1.0 NZ A:LYS1065 3.9 68.3 1.0 CH3 A:ACT1302 4.0 85.2 1.0 CA B:GLN539 4.1 104.6 1.0 CB A:ASP1062 4.1 61.4 1.0 CH3 B:ACT2104 4.4 92.9 1.0 N B:GLN539 4.8 100.4 1.0 CB B:GLN539 4.8 103.0 1.0

Cadmium binding site 2 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1315 b:129.7 occ:0.48 O A:HOH1487 2.2 67.6 1.0 O A:HOH1505 2.2 85.8 1.0 OE2 A:GLU89 2.3 64.2 1.0 CD A:GLU89 3.2 71.7 1.0 OE1 A:GLU89 3.5 89.1 1.0 CD A:PRO88 3.8 56.1 1.0 CG A:PRO88 4.2 50.5 1.0 CG A:GLU89 4.6 66.3 1.0 CB A:PRO88 4.7 54.9 1.0 N A:PRO88 4.7 57.6 1.0 CB A:LYS87 4.7 55.6 1.0 N A:GLU89 5.0 39.7 1.0

Cadmium binding site 3 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1316 b:107.3 occ:0.56 SD A:MET1054 3.3 70.3 1.0 CG A:MET1054 4.6 62.7 1.0 CE A:MET1054 4.7 73.8 1.0 NE1 A:TRP1030 4.8 62.7 1.0 CB A:MET1054 4.9 52.9 1.0

Cadmium binding site 4 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1317 b:150.8 occ:0.60 O A:HOH1468 2.2 34.5 1.0 O A:HOH1471 2.3 54.5 1.0 CD A:CD1323 3.3 123.5 0.3 CD A:CD1324 3.7 39.8 0.7 CE A:LYS99 3.8 69.0 1.0 O A:VAL98 3.9 42.8 1.0 OD2 A:ASP109 4.1 53.3 1.0 ND2 A:ASN97 4.3 41.2 1.0 CA A:LYS99 4.4 36.6 1.0 NZ A:LYS99 4.4 75.6 1.0 CG A:ASP109 4.4 64.7 1.0 OD1 A:ASP100 4.5 35.1 1.0 CD A:LYS99 4.6 60.2 1.0 OD1 A:ASP109 4.6 71.7 1.0 O A:HOH1478 4.7 57.0 1.0 N A:ASP100 4.7 38.6 1.0 OD1 A:ASN97 4.7 51.6 1.0 N A:ASP101 4.8 39.5 1.0 C A:VAL98 4.8 37.3 1.0 C A:LYS99 4.9 37.9 1.0 CG A:LYS99 5.0 55.8 1.0

Cadmium binding site 5 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1318 b:129.1 occ:0.32 OXT A:ACT1303 2.2 95.0 1.0 OE1 A:GLU1089 2.2 96.7 1.0 O A:ACT1303 2.2 114.6 1.0 OE2 A:GLU1089 2.2 74.6 1.0 CD A:GLU1089 2.4 81.4 1.0 C A:ACT1303 2.4 94.6 1.0 CG A:GLU1089 3.7 81.3 1.0 CH3 A:ACT1303 4.0 84.9 1.0 O A:HOH1496 4.1 78.7 1.0 CD A:PRO1088 4.8 61.8 1.0 CG A:LYS1087 4.9 74.9 1.0 CB A:LYS1087 4.9 65.5 1.0 CB A:GLU1089 4.9 62.3 1.0 CD A:LYS1087 4.9 75.0 1.0

Cadmium binding site 6 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1319 b:103.0 occ:0.39 OXT A:ACT1306 2.2 99.9 1.0 O A:ACT1306 2.2 96.6 1.0 O A:ACT1307 2.2 92.0 1.0 OXT A:ACT1307 2.2 64.8 1.0 C A:ACT1307 2.4 84.6 1.0 C A:ACT1306 2.4 91.2 1.0 O A:ASN74 3.7 46.8 1.0 CH3 A:ACT1307 3.8 48.6 1.0 CH3 A:ACT1306 4.0 64.1 1.0 O A:HOH1404 4.0 76.2 1.0 OE2 A:GLU30 4.2 58.7 1.0 C A:ASN74 4.3 46.4 1.0 OE1 A:GLU30 4.3 47.2 1.0 CB A:ASN74 4.6 51.2 1.0 CD A:GLU30 4.7 56.6 1.0 CA A:ASN74 4.9 46.9 1.0 N A:ALA75 4.9 45.6 1.0 OD1 A:ASN77 4.9 41.5 1.0

Cadmium binding site 7 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1320 b:143.3 occ:0.61 OD2 A:ASP62 2.2 104.6 1.0 CG A:ASP62 3.2 83.1 1.0 OD1 A:ASP62 3.4 83.8 1.0 CG2 B:THR478 3.6 83.7 1.0 CB A:ASP62 4.5 63.9 1.0 CB B:GLU484 4.8 76.3 1.0 CB B:THR478 5.0 84.0 1.0

Cadmium binding site 8 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1321 b:135.2 occ:0.50 OE2 A:GLU46 2.9 64.0 1.0 O A:HOH1497 2.9 80.6 1.0 OE1 A:GLU46 3.2 56.0 1.0 CD A:GLU46 3.4 63.1 1.0 OG A:SER63 3.8 54.2 1.0 CB A:SER63 4.0 50.1 1.0 NH2 A:ARG38 4.2 41.8 1.0 O A:HOH1467 4.2 53.5 1.0 O A:HOH1405 4.4 52.5 1.0 CG A:GLU46 4.8 57.0 1.0

Cadmium binding site 9 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1322 b:107.0 occ:0.49 O A:HOH1443 2.3 53.2 1.0 O A:PHE68 3.0 43.1 1.0 N A:GLY66 3.5 56.4 1.0 CA A:GLY66 4.1 53.1 1.0 CE2 A:TYR60 4.1 42.1 1.0 CZ A:TYR60 4.1 34.9 1.0 C A:PHE68 4.2 40.5 1.0 CD2 A:TYR60 4.3 42.3 1.0 OG1 A:THR69 4.3 42.5 1.0 CE1 A:TYR60 4.4 34.9 1.0 CG A:TYR60 4.5 38.0 1.0 C A:GLY66 4.5 51.3 1.0 CD1 A:TYR60 4.5 31.6 1.0 N A:ARG67 4.6 43.2 1.0 C A:LYS65 4.6 52.5 1.0 OH A:TYR60 4.6 38.4 1.0 N A:PHE68 4.7 43.1 1.0 CA A:LYS65 4.7 52.0 0.6 CA A:LYS65 4.7 52.0 0.5 O A:VAL64 4.9 42.6 1.0 CA A:THR69 4.9 37.8 1.0

Cadmium binding site 10 out of 17 in the Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Sybody MR17-SR31 Fusion in Complex with the Sars-Cov-2 S Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1323 b:123.5 occ:0.27 CD A:CD1324 2.2 39.8 0.7 O A:VAL98 2.3 42.8 1.0 OD1 A:ASP100 2.3 35.1 1.0 OD1 A:ASP109 2.3 71.7 1.0 CG A:ASP109 3.0 64.7 1.0 O A:HOH1406 3.2 49.7 1.0 CD A:CD1317 3.3 150.8 0.6 OD2 A:ASP109 3.4 53.3 1.0 C A:VAL98 3.5 37.3 1.0 CG A:ASP100 3.5 47.0 1.0 CG1 A:VAL98 3.7 36.3 1.0 N A:ASP100 3.8 38.6 1.0 CD A:CD1325 4.0 65.1 0.3 OD1 A:ASN97 4.1 51.6 1.0 CB A:ASP109 4.1 60.3 1.0 OD2 A:ASP100 4.2 37.6 1.0 O A:HOH1468 4.3 34.5 1.0 CA A:VAL98 4.3 39.0 1.0 N A:LYS99 4.4 32.4 1.0 N A:VAL98 4.4 40.0 1.0 CA A:LYS99 4.5 36.6 1.0 CB A:ASP100 4.5 33.1 1.0 CB A:VAL98 4.6 42.8 1.0 O A:HOH1471 4.6 54.5 1.0 C A:LYS99 4.7 37.9 1.0 CA A:ASP100 4.7 38.4 1.0 CG A:ASN97 4.7 49.4 1.0 ND2 A:ASN97 4.8 41.2 1.0

T.Li, H.Cai, H.Yao, B.Zhou, Y.Zhao, W.Qin, D.Lavillette, D.Li. Potent Synthetic Nanobodies Against Sars-Cov-2 and Molecular Basis For Neutratlization To Be Published.