Arsenic in PDB 7jvb: Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20

The structure of Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20, PDB code: 7jvb was solved by Y.Xiang, Z.Xiao, H.Liu, Z.Sang, D.Schneidman-Duhovny, C.Zhang, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.96 / 3.29
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.716, 70.716, 435.037, 90.00, 90.00, 90.00
R / Rfree (%)	28.1 / 32.2

The binding sites of Arsenic atom in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20 (pdb code 7jvb). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20, PDB code: 7jvb:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20 within 5.0Å range: probe atom residue distance (Å) B Occ A:As601 b:0.1 occ:0.94 AS A:CAC601 0.0 0.1 0.9 O1 A:CAC601 1.7 79.9 0.9 O2 A:CAC601 1.7 0.0 0.9 C1 A:CAC601 2.0 77.7 0.9 C2 A:CAC601 2.0 0.2 0.9 CG2 A:THR376 3.5 79.8 1.0 NZ A:LYS378 3.8 0.9 1.0 CG1 A:VAL407 4.1 75.8 1.0 CE A:LYS378 4.2 0.4 1.0 CB A:THR376 4.2 79.1 1.0 O A:VAL407 4.4 88.1 1.0 C A:VAL407 4.6 0.1 1.0 CA A:ARG408 4.6 91.9 1.0 N A:ARG408 4.7 0.3 1.0 OG1 A:THR376 4.7 97.3 1.0 CB A:VAL407 4.7 95.2 1.0 CG A:ARG408 4.8 78.0 1.0

Arsenic binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20 within 5.0Å range: probe atom residue distance (Å) B Occ C:As201 b:0.3 occ:1.00 AS C:CAC201 0.0 0.3 1.0 O1 C:CAC201 1.7 0.8 1.0 O2 C:CAC201 1.7 0.8 1.0 C1 C:CAC201 1.9 70.2 1.0 C2 C:CAC201 1.9 71.3 1.0 CA C:GLY50 3.9 80.6 1.0 NH1 C:ARG31 4.1 0.0 1.0 N C:ALA51 4.1 0.1 1.0 CA A:GLN493 4.1 71.3 1.0 CB C:ARG31 4.3 74.0 1.0 N A:GLN493 4.4 70.3 1.0 N A:SER494 4.4 84.6 1.0 C A:GLN493 4.4 79.2 1.0 C C:GLY50 4.6 94.6 1.0 CG C:ARG31 4.6 73.5 1.0 C A:LEU492 4.6 73.9 1.0 O A:LEU492 4.6 75.9 1.0 CE2 A:PHE490 4.6 87.2 1.0 CD2 A:PHE490 4.6 83.7 1.0 OE1 A:GLN493 4.7 0.8 1.0 CD C:ARG31 4.7 72.5 1.0 CA C:ARG31 4.8 89.9 1.0 CB A:SER494 4.9 0.1 1.0 CD2 A:LEU452 4.9 0.0 1.0 CD A:GLN493 5.0 0.8 1.0

Arsenic binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20 within 5.0Å range: probe atom residue distance (Å) B Occ B:As601 b:0.1 occ:1.00 AS B:CAC601 0.0 0.1 1.0 O1 B:CAC601 1.7 74.2 1.0 O2 B:CAC601 1.7 0.3 1.0 C1 B:CAC601 2.0 74.2 1.0 C2 B:CAC601 2.0 0.8 1.0 O B:VAL407 3.9 93.2 1.0 OG1 B:THR376 4.0 74.4 1.0 NZ B:LYS378 4.0 0.4 1.0 CG1 B:VAL407 4.1 70.8 1.0 C B:VAL407 4.3 96.3 1.0 CB B:THR376 4.4 97.9 1.0 CE B:LYS378 4.4 0.8 1.0 CA B:ARG408 4.4 87.8 1.0 N B:ARG408 4.5 0.2 1.0 CB B:VAL407 4.6 0.4 1.0 CG2 B:THR376 4.8 0.8 1.0

Arsenic binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of the Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) with Nanobody NB20 within 5.0Å range: probe atom residue distance (Å) B Occ D:As201 b:80.0 occ:0.87 AS D:CAC201 0.0 80.0 0.9 O1 D:CAC201 1.7 97.2 0.9 O2 D:CAC201 1.7 0.4 0.9 C2 D:CAC201 1.9 65.4 0.9 C1 D:CAC201 2.0 65.4 0.9 NH1 D:ARG31 3.7 87.8 1.0 CA D:GLY50 4.1 73.8 1.0 CA B:GLN493 4.2 64.9 1.0 CB D:ARG31 4.3 83.0 1.0 N B:GLN493 4.4 65.6 1.0 N D:ALA51 4.4 75.8 1.0 C B:GLN493 4.4 89.0 1.0 CG D:ARG31 4.5 65.3 1.0 CE2 B:PHE490 4.5 81.5 1.0 O B:LEU492 4.5 66.1 1.0 N B:SER494 4.5 82.5 1.0 CD D:ARG31 4.6 66.0 1.0 C B:LEU492 4.6 66.4 1.0 CD2 B:PHE490 4.6 88.8 1.0 OE1 B:GLN493 4.8 90.0 1.0 CA D:ARG31 4.8 75.7 1.0 C D:GLY50 4.8 79.8 1.0 CB B:SER494 4.9 0.5 1.0 CZ D:ARG31 4.9 76.3 1.0 CB B:LEU492 5.0 67.0 1.0 O B:GLN493 5.0 94.3 1.0

Y.Xiang, S.Nambulli, Z.Xiao, H.Liu, Z.Sang, W.P.Duprex, D.Schneidman-Duhovny, C.Zhang, Y.Shi. Versatile and Multivalent Nanobodies Efficiently Neutralize Sars-Cov-2. Science 2020.
ISSN: ESSN 1095-9203
PubMed: 33154108
DOI: 10.1126/SCIENCE.ABE4747