Zinc in PDB 7fau: Structure Determination of the NB1B11-Rbd Complex

The structure of Structure Determination of the NB1B11-Rbd Complex, PDB code: 7fau was solved by Z.Z.Shi, X.X.Li, L.Wang, Z.C.Sun, H.W.Zhang, X.C.Chen, Q.Q.Cui, H.R.Qiao, Z.Y.Lan, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.53 / 2.08
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	62.512, 88.835, 190.112, 90, 90, 90
R / Rfree (%)	19.8 / 22.8

The binding sites of Zinc atom in the Structure Determination of the NB1B11-Rbd Complex (pdb code 7fau). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure Determination of the NB1B11-Rbd Complex, PDB code: 7fau:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure Determination of the NB1B11-Rbd Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Determination of the NB1B11-Rbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:46.3 occ:1.00 O B:HOH369 2.2 49.1 1.0 ND1 B:HIS94 2.3 40.9 1.0 O B:HOH370 2.4 33.4 1.0 CG B:HIS94 3.2 36.8 1.0 CB B:HIS94 3.3 27.5 1.0 CE1 B:HIS94 3.4 41.3 1.0 NE B:ARG45 4.1 47.7 1.0 CD2 B:HIS94 4.3 40.2 1.0 CZ3 B:TRP117 4.4 30.9 1.0 OE1 B:GLN39 4.4 52.9 1.0 NE2 B:HIS94 4.4 42.5 1.0 CE3 B:TRP117 4.7 31.4 1.0 NH1 B:ARG45 4.7 60.8 1.0 CA B:HIS94 4.8 23.9 1.0 CD B:ARG45 4.9 45.6 1.0 CZ B:ARG45 4.9 70.6 1.0 CB B:GLN39 4.9 43.7 1.0

Zinc binding site 2 out of 5 in the Structure Determination of the NB1B11-Rbd Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Determination of the NB1B11-Rbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:38.9 occ:1.00 O B:HOH319 2.1 26.9 1.0 O B:HOH336 2.2 30.8 1.0 OD2 B:ASP79 2.2 33.6 1.0 O B:HOH342 2.2 34.0 1.0 OD2 B:ASP72 2.2 28.9 1.0 CG B:ASP79 3.0 32.7 1.0 CG B:ASP72 3.1 27.6 1.0 OD1 B:ASP79 3.2 24.4 1.0 CB B:ASP72 3.3 26.2 1.0 O B:HOH303 4.2 32.3 1.0 OD1 B:ASP72 4.3 28.9 1.0 CB B:ASP79 4.4 24.7 1.0 NH2 B:ARG19 4.4 24.2 1.0 NE B:ARG19 4.5 27.7 1.0 CA B:ASP72 4.7 26.3 1.0 CD B:LYS75 4.8 42.2 1.0 OG B:SER21 4.8 49.8 1.0 CE B:LYS75 4.9 44.9 1.0 CZ B:ARG19 5.0 32.8 1.0 NZ B:LYS75 5.0 43.7 1.0

Zinc binding site 3 out of 5 in the Structure Determination of the NB1B11-Rbd Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure Determination of the NB1B11-Rbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:78.5 occ:1.00 CE1 B:HIS110 2.3 56.2 1.0 O B:HOH350 3.0 61.6 1.0 ND1 B:HIS110 3.1 50.0 1.0 NE2 B:HIS110 3.2 53.1 1.0 OD1 B:ASP106 3.4 63.9 1.0 CB B:ASP106 3.5 55.6 1.0 CG B:ASP106 3.6 61.0 1.0 O B:HOH309 3.6 52.6 1.0 O B:HOH301 4.2 43.2 1.0 CG B:HIS110 4.2 51.3 1.0 CD2 B:HIS110 4.2 48.9 1.0 OD2 B:ASP106 4.4 69.7 1.0 O B:HOH305 4.4 57.9 1.0 CA B:ASP106 4.9 47.9 1.0 O B:ASP106 4.9 44.2 1.0

Zinc binding site 4 out of 5 in the Structure Determination of the NB1B11-Rbd Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure Determination of the NB1B11-Rbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:52.2 occ:1.00 ND1 D:HIS94 2.4 52.5 1.0 CG D:HIS94 2.8 47.1 1.0 CE1 D:HIS94 3.1 50.6 1.0 CB D:HIS94 3.2 35.4 1.0 NE D:ARG45 3.6 66.3 1.0 NH2 D:ARG45 3.8 72.5 1.0 CD2 D:HIS94 3.8 61.7 1.0 NE2 D:HIS94 3.9 45.2 1.0 CZ D:ARG45 4.0 68.4 1.0 CD D:ARG45 4.3 66.6 1.0 CZ3 D:TRP117 4.3 31.7 1.0 OE1 D:GLN39 4.6 51.2 1.0 CG D:ARG45 4.6 61.0 1.0 CE3 D:TRP117 4.6 31.5 1.0 CA D:HIS94 4.7 29.1 1.0 OH C:TYR449 4.9 61.9 1.0 CB D:GLN39 5.0 49.0 1.0

Zinc binding site 5 out of 5 in the Structure Determination of the NB1B11-Rbd Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure Determination of the NB1B11-Rbd Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:41.4 occ:1.00 O D:HOH322 2.0 31.1 1.0 O D:HOH331 2.1 32.9 1.0 O D:HOH364 2.1 34.3 1.0 OD1 D:ASP79 2.2 39.8 1.0 OD2 D:ASP72 2.3 29.0 1.0 CG D:ASP79 3.0 36.8 1.0 CG D:ASP72 3.1 28.1 1.0 OD2 D:ASP79 3.2 26.7 1.0 CB D:ASP72 3.3 27.5 1.0 O D:HOH313 4.1 31.8 1.0 O D:HOH339 4.2 43.6 1.0 OD1 D:ASP72 4.3 27.3 1.0 NH2 D:ARG19 4.4 28.0 1.0 CB D:ASP79 4.4 33.9 1.0 NE D:ARG19 4.5 28.4 1.0 CD D:LYS75 4.6 33.8 1.0 CA D:ASP72 4.7 24.4 1.0 OG D:SER21 4.7 46.3 1.0 NZ D:LYS75 4.8 46.4 1.0 CZ D:ARG19 4.9 27.8 1.0

Z.Shi, X.Li, L.Wang, Z.Sun, H.Zhang, X.Chen, Q.Cui, H.Qiao, Z.Lan, X.Zhang, X.Li, L.Li, J.Xu, R.Gong, C.Fan, Y.Geng. Structural Basis of Nanobodies Neutralizing Sars-Cov-2 Variants. Structure V. 30 707 2022.
ISSN: ISSN 0969-2126
PubMed: 35276082
DOI: 10.1016/J.STR.2022.02.011