Chlorine in PDB 7msq: Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)

The structure of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd), PDB code: 7msq was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.29
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	109.764, 115.494, 240.758, 90, 90, 90
R / Rfree (%)	19.4 / 24.5

The binding sites of Chlorine atom in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) (pdb code 7msq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd), PDB code: 7msq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:84.9 occ:1.00 NH1 A:ARG457 3.5 53.0 1.0 CZ A:ARG457 3.5 52.5 1.0 CB A:LYS458 3.8 77.8 1.0 NH2 A:ARG457 3.8 53.1 1.0 CG A:ARG457 3.9 58.0 1.0 OG A:SER459 3.9 61.6 1.0 N A:LYS458 3.9 70.3 1.0 NE A:ARG457 4.0 54.4 1.0 N A:SER459 4.0 67.0 1.0 CE A:LYS458 4.3 81.6 1.0 CA A:LYS458 4.3 74.8 1.0 O A:SER459 4.4 57.3 1.0 CD A:ARG457 4.5 55.5 1.0 C A:LYS458 4.6 71.8 1.0 CG A:LYS458 4.6 80.7 1.0 CB A:SER459 4.8 63.0 1.0 CA A:SER459 4.8 63.4 1.0 C A:ARG457 5.0 64.9 1.0

Chlorine binding site 2 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:77.5 occ:1.00 CB B:PRO463 3.8 39.3 1.0 O B:HOH706 3.9 51.0 1.0 CB B:PRO426 4.2 38.1 1.0 CG B:PRO426 4.4 36.0 1.0 CD2 B:PHE464 4.5 37.9 1.0 CG B:PRO463 4.5 40.0 1.0 O B:PRO463 4.6 37.1 1.0 CE2 B:PHE464 4.9 37.7 1.0

Chlorine binding site 3 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:63.5 occ:1.00 O D:TYR59 3.3 53.5 1.0 CB E:TYR94 3.7 40.4 1.0 CH2 D:TRP47 3.9 41.1 1.0 CZ3 D:TRP47 3.9 42.0 1.0 N E:PRO95 4.0 42.3 1.0 CA E:PRO95 4.0 41.1 1.0 CD D:PRO61 4.1 59.3 1.0 CB E:PRO95 4.1 41.6 1.0 C D:TYR59 4.2 48.6 1.0 C E:TYR94 4.3 43.1 1.0 CD E:PRO95 4.3 43.0 1.0 CG E:TYR94 4.4 38.4 1.0 CG D:PRO61 4.5 58.4 1.0 N D:TYR59 4.5 46.6 1.0 CA E:TYR94 4.5 42.1 1.0 CD1 E:TYR94 4.6 37.6 1.0 CB D:ASN58 4.6 43.5 1.0 CG E:PRO95 4.8 43.5 1.0 N D:ASN60 4.9 50.1 1.0 CA D:ASN60 4.9 50.5 1.0 C D:ASN58 5.0 46.8 1.0

Chlorine binding site 4 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl302 b:89.4 occ:1.00 O D:GLY120 3.8 46.4 1.0 O D:GLN119 4.4 39.0 1.0 C D:GLY120 4.5 45.4 1.0 O E:GLY41 4.7 46.9 1.0 CG1 D:VAL92 4.9 35.6 1.0

Chlorine binding site 5 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl301 b:59.9 occ:1.00 ND2 E:ASN137 3.3 42.2 1.0 OG E:SER114 3.5 39.3 1.0 CB E:SER114 3.6 40.1 1.0 CB E:ASN137 4.0 40.5 1.0 CG2 D:THR197 4.1 47.4 1.0 CG2 D:THR149 4.1 63.5 1.0 CG E:ASN137 4.2 40.2 1.0 CE1 E:PHE116 4.2 37.9 1.0 CZ E:PHE116 4.2 38.7 1.0 CB D:THR197 4.6 46.2 1.0 ND2 E:ASN138 4.6 41.8 1.0 OG1 D:THR197 4.7 46.8 1.0 CB D:THR149 4.8 62.6 1.0 O E:ASN137 4.9 39.2 1.0 O E:HOH409 5.0 22.1 1.0

Chlorine binding site 6 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl302 b:64.1 occ:1.00 O D:HOH424 3.1 48.6 1.0 N E:ALA50 3.3 42.5 1.0 CD1 E:LEU91 3.3 44.6 1.0 CA E:ALA50 3.8 45.6 1.0 CB E:LEU91 3.9 38.8 1.0 N E:LEU33 4.0 41.2 1.0 CA E:TYR32 4.1 43.6 1.0 CG E:LEU91 4.2 43.1 1.0 C E:TYR32 4.3 42.4 1.0 CB E:ALA50 4.4 44.1 1.0 O E:LEU33 4.4 40.0 1.0 C E:TYR49 4.4 40.7 1.0 CB E:TYR49 4.4 41.2 1.0 O E:SER31 4.5 42.5 1.0 CD1 E:TYR32 4.5 46.0 1.0 C E:LEU33 4.6 41.3 1.0 CA E:TYR49 4.7 39.5 1.0 CB E:TYR32 4.7 45.5 1.0 CA E:LEU33 4.9 42.8 1.0

Chlorine binding site 7 out of 7 in the Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Complex Between the Fab Arm of Ab-3467 and the Sars-Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:63.3 occ:1.00 O H:TYR59 3.5 52.5 1.0 CB L:TYR94 3.7 43.5 1.0 CA L:PRO95 4.0 45.5 1.0 N L:PRO95 4.0 47.8 1.0 CD H:PRO61 4.1 60.7 1.0 CB L:PRO95 4.1 48.1 1.0 CZ3 H:TRP47 4.2 41.3 1.0 CH2 H:TRP47 4.3 40.4 1.0 C L:TYR94 4.3 46.7 1.0 C H:TYR59 4.4 50.3 1.0 CD L:PRO95 4.4 48.0 1.0 CG L:TYR94 4.5 40.9 1.0 CA L:TYR94 4.5 45.1 1.0 O H:HOH424 4.6 46.2 1.0 CD1 L:TYR94 4.6 40.6 1.0 CB H:ASN58 4.7 48.1 1.0 N H:TYR59 4.8 46.9 1.0 CG L:PRO95 4.8 46.8 1.0 O L:TYR94 4.9 48.9 1.0 CG H:PRO61 4.9 65.2 1.0 N H:PRO61 4.9 57.8 1.0

D.L.Burnett, K.J.L.Jackson, D.B.Langley, A.Aggrawal, A.O.Stella, M.D.Johansen, H.Balachandran, H.Lenthall, R.Rouet, G.Walker, B.M.Saunders, M.Singh, H.Li, J.Y.Henry, J.Jackson, A.G.Stewart, F.Witthauer, M.A.Spence, N.G.Hansbro, C.Jackson, P.Schofield, C.Milthorpe, M.Martinello, S.R.Schulz, E.Roth, A.Kelleher, S.Emery, W.J.Britton, W.D.Rawlinson, R.Karl, S.Schafer, T.H.Winkler, R.Brink, R.A.Bull, P.M.Hansbro, H.M.Jack, S.Turville, D.Christ, C.C.Goodnow. Immunizations with Diverse Sarbecovirus Receptor-Binding Domains Elicit Sars-Cov-2 Neutralizing Antibodies Against A Conserved Site of Vulnerability. Immunity V. 54 2908 2021.
ISSN: ISSN 1074-7613
PubMed: 34788600
DOI: 10.1016/J.IMMUNI.2021.10.019