Chlorine in PDB 8gz6: Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain

The structure of Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain, PDB code: 8gz6 was solved by K.Yamaguchi, I.Anzai, R.Maeda, M.Moriguchi, T.Watanabe, A.Imura, A.Takaori-Kondo, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.18 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.758, 32.113, 84.566, 90, 93.96, 90
R / Rfree (%)	14.9 / 18

The binding sites of Chlorine atom in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain (pdb code 8gz6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain, PDB code: 8gz6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:19.6 occ:1.00 O A:HOH708 3.1 37.2 1.0 N A:ASN33 3.2 15.6 1.0 N A:GLY100 3.4 15.7 1.0 CA A:GLY99 3.6 14.4 1.0 ND2 A:ASN33 3.7 15.7 1.0 CG A:ASN33 3.7 14.4 1.0 CB A:ASN33 3.8 14.3 1.0 CA A:TYR32 3.8 16.8 1.0 CD1 A:TYR32 3.9 23.9 1.0 C A:GLY99 3.9 15.0 1.0 O A:GLY100 4.0 15.9 1.0 C A:TYR32 4.0 16.0 1.0 CA A:ASN33 4.0 14.2 1.0 N A:GLY99 4.1 14.8 1.0 CB A:TYR32 4.2 18.7 1.0 OD1 A:ASN33 4.2 16.3 1.0 O A:ASN33 4.4 14.7 1.0 CA A:GLY100 4.5 15.7 1.0 CG A:TYR32 4.5 21.1 1.0 C A:GLY100 4.6 15.1 1.0 C A:ASN33 4.7 13.1 1.0 O A:VAL31 4.9 25.4 1.0 CE1 A:TYR32 4.9 26.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:19.2 occ:1.00 O A:HOH692 3.0 44.5 1.0 NH1 A:ARG105 3.2 17.7 1.0 N A:ARG45 3.2 17.4 1.0 CG A:ARG45 3.7 19.7 1.0 CB A:ARG45 3.7 18.4 1.0 CD A:ARG105 3.8 17.0 1.0 CA A:GLU44 3.9 21.9 1.0 C A:GLU44 4.1 20.2 1.0 CB A:GLU44 4.1 25.5 1.0 CA A:ARG45 4.1 17.8 1.0 CD A:ARG45 4.1 21.3 1.0 NE2 A:GLN39 4.2 20.8 1.0 CZ A:ARG105 4.3 16.4 1.0 CG A:GLU44 4.4 32.1 1.0 NE A:ARG45 4.5 21.6 1.0 NE A:ARG105 4.5 16.8 1.0 O A:ARG45 4.7 20.7 1.0 C A:ARG45 4.9 17.6 1.0 CD A:GLN39 5.0 19.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:20.2 occ:1.00 N B:ASN33 3.2 16.2 1.0 N B:GLY100 3.4 16.4 1.0 CA B:GLY99 3.6 16.4 1.0 ND2 B:ASN33 3.7 16.7 1.0 CG B:ASN33 3.7 15.0 1.0 CB B:ASN33 3.8 15.2 1.0 CA B:TYR32 3.8 18.4 1.0 C B:GLY99 3.9 17.5 1.0 O B:GLY100 4.0 17.3 1.0 C B:TYR32 4.0 18.0 1.0 CD1 B:TYR32 4.0 24.2 1.0 N B:GLY99 4.1 15.4 1.0 CA B:ASN33 4.1 14.8 1.0 OD1 B:ASN33 4.3 17.6 1.0 CB B:TYR32 4.3 19.6 1.0 O B:ASN33 4.4 16.4 1.0 CA B:GLY100 4.5 17.8 1.0 C B:GLY100 4.6 16.6 1.0 O B:VAL31 4.7 23.9 1.0 CG B:TYR32 4.7 22.1 1.0 C B:ASN33 4.7 15.1 1.0 CE1 B:TYR32 5.0 25.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Neutralizing Vhh P17 in Complex with Sars-Cov-2 Alpha Variant Spike Receptor-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:19.9 occ:1.00 N B:ARG45 3.2 17.9 0.6 N B:ARG45 3.2 18.8 0.4 O B:HOH718 3.2 38.9 1.0 NH1 B:ARG105 3.2 18.2 1.0 NH1 B:ARG45 3.5 18.8 0.4 CB B:ARG45 3.7 18.2 0.4 CB B:ARG45 3.7 16.7 0.6 CG B:ARG45 3.7 17.4 0.6 CD B:ARG45 3.8 20.2 0.4 CG B:ARG45 3.8 19.7 0.4 CD B:ARG105 3.8 17.0 1.0 CA B:GLU44 3.9 20.9 1.0 C B:GLU44 4.0 20.2 1.0 CA B:ARG45 4.0 17.0 0.6 CA B:ARG45 4.1 18.1 0.4 CD B:ARG45 4.1 18.5 0.6 CB B:GLU44 4.1 23.1 1.0 NE2 B:GLN39 4.1 20.5 1.0 CZ B:ARG105 4.3 17.6 1.0 NE B:ARG45 4.5 18.4 0.6 CZ B:ARG45 4.5 19.1 0.4 NE B:ARG105 4.5 17.0 1.0 O B:HOH651 4.6 61.1 1.0 NE B:ARG45 4.6 19.1 0.4 O B:ARG45 4.7 22.4 0.6 O B:ARG45 4.8 20.5 0.4 CG B:GLU44 4.8 30.6 1.0 C B:ARG45 4.9 18.8 0.6 CD B:GLN39 5.0 18.7 1.0 C B:ARG45 5.0 18.5 0.4

K.Yamaguchi, I.Anzai, R.Maeda, M.Moriguchi, T.Watanabe, A.Imura, A.Takaori-Kondo, T.Inoue. Structural Insights Into the Rational Design of A Nanobody That Binds with High Affinity to the Sars-Cov-2 Spike Variant. J.Biochem. 2022.
ISSN: ISSN 0021-924X
PubMed: 36413757
DOI: 10.1093/JB/MVAC096