Chlorine in PDB 7tn0: Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab

The structure of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 7tn0 was solved by M.Mccallum, N.Czudnochowski, J.C.Nix, T.I.Croll, Ssgcid, J.R.Dillen, G.Snell, D.Veesler, Seattle Structural Genomics Center For Infectiousdisease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.28, 183.65, 194.55, 90, 95.98, 90
R / Rfree (%)	23 / 26.8

The structure of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab (pdb code 7tn0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 21 binding sites of Chlorine where determined in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab, PDB code: 7tn0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:84.4 occ:1.00 CA A:PHE116 3.6 39.1 1.0 CD A:LYS207 3.7 41.5 1.0 O A:VAL115 3.7 44.2 1.0 N A:ILE117 3.7 59.5 1.0 CE A:LYS207 4.0 45.0 1.0 NZ A:LYS207 4.1 69.9 1.0 CD1 A:PHE116 4.1 39.3 1.0 CB A:PHE116 4.2 39.4 1.0 C A:PHE116 4.2 41.9 1.0 CG A:LYS207 4.2 35.2 1.0 CG2 A:ILE117 4.4 49.5 1.0 N A:PHE116 4.5 33.1 1.0 C A:VAL115 4.5 33.1 1.0 CG A:PHE116 4.5 39.1 1.0 CB A:LYS207 4.6 41.2 1.0 O A:ILE117 4.7 51.9 1.0 CB B:SER141 4.8 77.5 1.0 CA A:ILE117 4.9 50.0 1.0

Chlorine binding site 2 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:60.3 occ:1.00 O A:HOH413 3.0 42.2 1.0 OE1 A:GLN38 3.5 48.3 1.0 CD A:ARG46 3.8 64.8 1.0 NH1 A:ARG46 4.1 67.0 1.0 CD A:GLN38 4.3 46.4 1.0 NE2 A:GLN38 4.4 41.2 1.0 NZ A:LYS40 4.4 80.0 1.0 CD2 A:LEU48 4.6 43.3 1.0 CG A:ARG46 4.7 48.6 1.0 NE A:ARG46 4.8 59.6 1.0 CD1 A:ILE59 4.8 42.5 1.0 CD A:PRO60 4.9 46.5 1.0 CZ A:ARG46 4.9 70.4 1.0 CZ A:PHE63 4.9 54.8 1.0 CE2 A:PHE63 4.9 55.6 1.0 O A:HOH407 5.0 45.6 1.0

Chlorine binding site 3 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:71.0 occ:1.00 NH2 A:ARG46 2.9 69.4 1.0 O A:LEU47 2.9 34.4 1.0 NE A:ARG46 3.0 59.6 1.0 CZ A:ARG46 3.3 70.4 1.0 N A:LEU47 3.4 44.8 1.0 O B:ASP115 3.6 71.0 1.0 C A:LEU47 3.8 32.2 1.0 CA A:LEU47 4.0 31.6 1.0 CB A:ARG46 4.0 42.4 1.0 CB A:LEU47 4.0 52.8 1.0 CD A:ARG46 4.1 64.8 1.0 C A:ARG46 4.2 53.9 1.0 CG A:ARG46 4.3 48.6 1.0 CD1 A:ILE59 4.4 42.5 1.0 O A:THR57 4.4 63.7 1.0 CB A:ALA56 4.4 34.3 1.0 CA A:ARG46 4.4 41.4 1.0 C B:ASP115 4.6 61.4 1.0 NH1 A:ARG46 4.6 67.0 1.0 CA B:ASP115 4.9 50.6 1.0 CG1 A:ILE59 4.9 53.7 1.0

Chlorine binding site 4 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:76.4 occ:1.00 N A:PHE98 3.5 39.3 1.0 O B:LEU45 3.6 59.8 1.0 CA B:GLU46 3.6 40.8 1.0 N B:TRP47 3.6 43.5 1.0 CA A:THR97 4.0 31.8 1.0 C B:GLU46 4.1 40.1 1.0 CB A:PHE98 4.2 34.5 1.0 CD2 A:PHE98 4.2 47.0 1.0 C A:THR97 4.2 38.0 1.0 C B:LEU45 4.3 42.6 1.0 CA A:PHE98 4.4 31.3 1.0 CB B:GLU46 4.4 42.7 1.0 CG B:GLU46 4.4 54.3 1.0 N B:GLU46 4.4 35.6 1.0 O A:LEU96 4.6 57.3 1.0 CB A:THR97 4.6 39.1 1.0 O A:PHE98 4.6 49.5 1.0 CG A:PHE98 4.7 44.5 1.0 CA B:TRP47 4.7 53.9 1.0 CB B:TRP47 4.7 39.4 1.0 CG2 A:THR97 4.9 56.8 1.0 C A:PHE98 5.0 35.0 1.0 O A:HOH414 5.0 43.6 1.0

Chlorine binding site 5 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1001 b:77.3 occ:1.00 O B:HOH1108 2.7 48.4 1.0 NE B:ARG102 3.3 58.1 1.0 NH2 B:ARG102 3.7 70.2 1.0 CZ B:ARG102 4.0 59.4 1.0 CD B:ARG102 4.3 47.1 1.0 CZ2 B:TRP47 4.4 52.6 1.0 ND2 B:ASN59 4.5 61.3 1.0 CB B:ARG102 4.5 45.3 1.0 OG1 B:THR101 4.6 47.5 1.0 CH2 B:TRP47 4.6 50.9 1.0 O A:SER95 4.7 48.9 1.0 CD1 A:LEU96 4.7 45.0 1.0 CB A:LEU96 4.8 41.7 1.0 C A:SER95 5.0 54.1 1.0

Chlorine binding site 6 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1002 b:80.0 occ:1.00 O B:THR72 3.1 66.5 1.0 OG1 B:THR74 3.6 75.7 1.0 N B:THR74 3.7 56.9 1.0 C B:THR72 3.9 54.6 1.0 CA B:ASP73 4.0 64.3 1.0 OG1 B:THR72 4.2 68.4 1.0 C B:ASP73 4.4 68.0 1.0 CB B:THR74 4.4 57.9 1.0 N B:ASP73 4.4 58.5 1.0 CA B:THR74 4.7 59.2 1.0

Chlorine binding site 7 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl301 b:83.8 occ:1.00 O C:HOH419 2.8 44.6 1.0 CG C:PRO41 3.5 42.7 1.0 O C:HOH420 3.7 36.6 1.0 CB C:LEU184 3.7 45.2 1.0 CB C:PRO41 3.7 33.2 1.0 N C:LEU184 4.3 42.9 1.0 CE2 C:TYR190 4.4 51.5 1.0 CD2 C:LEU184 4.5 65.3 1.0 CA C:LEU184 4.6 42.2 1.0 CG C:LEU184 4.7 39.9 1.0 CD2 C:TYR190 5.0 51.0 1.0 O C:ALA182 5.0 33.7 1.0 CD C:PRO41 5.0 42.1 1.0

Chlorine binding site 8 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl302 b:59.8 occ:1.00 N C:TRP47 3.2 36.4 1.0 O D:HOH408 3.5 45.5 1.0 N D:PHE98 3.6 46.7 1.0 CA C:GLU46 3.6 33.2 1.0 CA D:THR97 3.9 35.5 1.0 C C:GLU46 3.9 31.2 1.0 O C:LEU45 4.0 43.2 1.0 CB C:TRP47 4.1 50.0 1.0 CD2 D:PHE98 4.1 35.0 1.0 CA C:TRP47 4.2 37.0 1.0 C D:THR97 4.2 35.0 1.0 O D:LEU96 4.3 40.4 1.0 CB D:PHE98 4.3 31.6 1.0 CG C:GLU46 4.4 48.7 1.0 CB D:THR97 4.5 30.1 1.0 O C:TRP47 4.5 41.6 1.0 CB C:GLU46 4.5 48.3 1.0 N C:GLU46 4.5 27.3 1.0 CA D:PHE98 4.5 34.0 1.0 C C:LEU45 4.6 31.6 1.0 CG D:PHE98 4.7 35.9 1.0 CG2 D:THR97 4.7 40.9 1.0 C C:TRP47 4.8 39.0 1.0 N D:THR97 4.9 37.1 1.0 O D:PHE98 5.0 49.3 1.0 O D:HOH422 5.0 44.2 1.0

Chlorine binding site 9 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl303 b:83.0 occ:1.00 NH2 C:ARG84 3.5 64.9 1.0 NE C:ARG84 3.8 45.1 1.0 CZ C:ARG84 4.1 65.5 1.0 CG C:ARG85 4.1 42.0 1.0 NE C:ARG85 4.3 63.1 1.0 CD C:ARG85 4.4 43.2 1.0 CB C:ARG84 4.5 47.7 1.0 N C:ARG85 5.0 46.1 1.0 CZ C:ARG85 5.0 70.7 1.0 CD C:ARG84 5.0 46.1 1.0

Chlorine binding site 10 out of 21 in the Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Sars-Cov-2 Omicron Rbd in Complex with Human ACE2 and S304 Fab and S309 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl304 b:104.8 occ:1.00 N C:SER109 3.3 39.9 1.0 CB C:SER109 3.7 43.3 1.0 O S:HOH715 4.0 41.3 1.0 CA C:GLU108 4.0 34.5 1.0 NE S:ARG346 4.0 50.1 1.0 NH2 S:ARG346 4.0 53.7 1.0 CB C:GLU108 4.1 35.6 1.0 CA C:SER109 4.1 39.6 1.0 C C:GLU108 4.2 36.1 1.0 CG C:GLU108 4.5 40.2 1.0 CZ S:ARG346 4.5 75.8 1.0 OG1 S:THR345 5.0 52.3 1.0

M.Mccallum, N.Czudnochowski, L.E.Rosen, S.K.Zepeda, J.E.Bowen, A.C.Walls, K.Hauser, A.Joshi, C.Stewart, J.R.Dillen, A.E.Powell, T.I.Croll, J.Nix, H.W.Virgin, D.Corti, G.Snell, D.Veesler. Structural Basis of Sars-Cov-2 Omicron Immune Evasion and Receptor Engagement. Science V. 375 864 2022.
ISSN: ESSN 1095-9203
PubMed: 35076256
DOI: 10.1126/SCIENCE.ABN8652