Zinc in PDB 7xx1: Crystal Structure of Sars-Cov-2 N-Ntd

The structure of Crystal Structure of Sars-Cov-2 N-Ntd, PDB code: 7xx1 was solved by X.D.Luan, X.M.Li, Y.F.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.66 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.466, 76.783, 109.702, 90, 91.79, 90
R / Rfree (%)	21 / 25.8

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 N-Ntd (pdb code 7xx1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 N-Ntd, PDB code: 7xx1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 N-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:37.9 occ:1.00 OD2 A:ASP82 1.9 30.5 1.0 NE2 B:HIS59 2.0 48.0 1.0 NE2 A:HIS145 2.1 43.0 1.0 O A:HOH362 2.2 18.2 1.0 CE1 B:HIS59 2.8 49.2 1.0 CG A:ASP82 2.8 35.7 1.0 CD2 A:HIS145 2.9 45.0 1.0 CD2 B:HIS59 3.1 45.0 1.0 OD1 A:ASP82 3.2 40.9 1.0 CE1 A:HIS145 3.2 41.7 1.0 ND1 B:HIS59 4.0 47.5 1.0 CG1 A:ILE146 4.0 40.7 1.0 CD1 A:ILE146 4.0 41.5 1.0 N A:SER79 4.1 40.6 1.0 CG A:HIS145 4.1 42.2 1.0 CG B:HIS59 4.1 43.4 1.0 CB A:ASP82 4.2 36.8 1.0 CG2 B:THR57 4.2 49.2 1.0 ND1 A:HIS145 4.3 41.6 1.0 CA A:SER78 4.4 41.0 1.0 OG A:SER79 4.5 55.8 1.0 CB A:SER78 4.6 39.0 1.0 CB A:SER79 4.7 49.8 1.0 C A:SER78 4.7 37.7 1.0 CB B:THR57 4.8 43.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 N-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:35.0 occ:1.00 NE2 B:HIS145 1.9 37.2 1.0 OD2 B:ASP82 2.0 28.7 1.0 ND1 C:HIS59 2.1 30.0 1.0 O B:HOH358 2.3 21.8 1.0 CG B:ASP82 2.7 32.1 1.0 OD1 B:ASP82 2.7 30.6 1.0 CE1 B:HIS145 2.9 38.0 1.0 CD2 B:HIS145 2.9 40.7 1.0 CE1 C:HIS59 3.0 34.4 1.0 CG C:HIS59 3.1 35.0 1.0 CB C:HIS59 3.5 33.3 1.0 OG B:SER79 3.8 40.7 1.0 ND1 B:HIS145 4.0 36.6 1.0 CG B:HIS145 4.0 38.7 1.0 NE2 C:HIS59 4.1 31.8 1.0 O C:HOH324 4.1 40.7 1.0 CB B:ASP82 4.2 32.4 1.0 CD2 C:HIS59 4.2 36.0 1.0 N B:SER79 4.2 33.7 1.0 CB B:SER79 4.3 37.1 1.0 CA C:HIS59 4.4 37.1 1.0 CD1 B:ILE146 4.6 42.0 1.0 CG1 B:ILE146 4.6 43.2 1.0 O B:HOH333 4.8 33.8 1.0 O C:HIS59 4.8 38.7 1.0 CA B:SER79 4.9 34.7 1.0 CA B:SER78 5.0 35.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 N-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Sars-Cov-2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:44.1 occ:1.00 OD2 C:ASP82 2.0 49.7 1.0 NE2 C:HIS145 2.0 45.1 1.0 NE2 D:HIS59 2.0 51.3 1.0 O C:HOH364 2.3 24.5 1.0 CD2 C:HIS145 2.8 50.9 1.0 CG C:ASP82 2.9 50.4 1.0 CE1 D:HIS59 2.9 53.1 1.0 CD2 D:HIS59 3.1 50.0 1.0 CE1 C:HIS145 3.2 51.3 1.0 OD1 C:ASP82 3.2 46.9 1.0 CD1 C:ILE146 4.0 48.5 1.0 CG1 C:ILE146 4.0 41.8 1.0 CG C:HIS145 4.0 46.3 1.0 ND1 D:HIS59 4.0 53.4 1.0 ND1 C:HIS145 4.2 41.0 1.0 CG D:HIS59 4.2 57.4 1.0 N C:SER79 4.2 49.6 1.0 CB C:ASP82 4.2 45.9 1.0 CG2 D:THR57 4.3 55.6 1.0 CA C:SER78 4.4 44.3 1.0 OG C:SER79 4.6 46.7 1.0 CB C:SER78 4.6 43.9 1.0 CB C:SER79 4.8 47.5 1.0 C C:SER78 4.8 43.1 1.0 CB D:THR57 4.9 51.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 N-Ntd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Sars-Cov-2 N-Ntd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:36.1 occ:1.00 OD2 D:ASP82 2.0 30.6 1.0 NE2 D:HIS145 2.0 35.7 1.0 ND1 A:HIS59 2.0 34.0 1.0 O D:HOH334 2.4 22.7 1.0 CG D:ASP82 2.7 30.6 1.0 OD1 D:ASP82 2.7 33.7 1.0 CE1 A:HIS59 2.9 34.5 1.0 CD2 D:HIS145 2.9 37.7 1.0 CE1 D:HIS145 3.0 35.8 1.0 CG A:HIS59 3.1 36.8 1.0 CB A:HIS59 3.4 33.3 1.0 OG D:SER79 3.8 41.6 1.0 ND1 D:HIS145 4.0 35.4 1.0 NE2 A:HIS59 4.0 33.6 1.0 CG D:HIS145 4.0 37.9 1.0 CD2 A:HIS59 4.1 36.0 1.0 CB D:ASP82 4.1 31.2 1.0 N D:SER79 4.2 36.6 1.0 CB D:SER79 4.3 38.0 1.0 O A:HOH311 4.3 46.9 1.0 CA A:HIS59 4.3 36.0 1.0 O D:HOH317 4.6 35.4 1.0 CD1 D:ILE146 4.6 37.0 1.0 CG1 D:ILE146 4.6 34.4 1.0 O A:HIS59 4.8 37.4 1.0 CA D:SER79 4.9 38.0 1.0 CA D:SER78 5.0 39.4 1.0

X.Luan, X.Li, Y.Li, G.Su, W.Yin, Y.Jiang, N.Xu, F.Wang, W.Cheng, Y.Jin, L.Zhang, H.E.Xu, Y.Xue, S.Zhang. Antiviral Drug Design Based on Structural Insights Into the N-Terminal Domain and C-Terminal Domain of the Sars-Cov-2 Nucleocapsid Protein. Sci Bull (Beijing) V. 67 2327 2022.
ISSN: ISSN 2095-9273
PubMed: 36317101
DOI: 10.1016/J.SCIB.2022.10.021