Cadmium in PDB 9f5j: Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I

The structure of Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I, PDB code: 9f5j was solved by K.Dhamotharan, A.Schlundt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.12 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.78, 49.715, 114.248, 90, 90, 90
R / Rfree (%)	20.2 / 24.2

The binding sites of Cadmium atom in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I (pdb code 9f5j). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I, PDB code: 9f5j:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:36.3 occ:1.00 OD1 A:ASP103 2.3 37.8 1.0 OG A:SER105 2.3 37.1 1.0 OE1 A:GLU174 2.3 39.2 1.0 ND1 A:HIS59 2.3 35.0 1.0 O A:HOH378 2.5 41.0 1.0 OE2 A:GLU174 2.6 41.3 1.0 OD2 A:ASP103 2.6 34.9 1.0 CG A:ASP103 2.8 38.0 1.0 CD A:GLU174 2.8 40.7 1.0 HB2 A:SER105 3.2 34.9 1.0 CE1 A:HIS59 3.2 35.1 1.0 HE1 A:HIS59 3.3 35.2 1.0 HB3 A:HIS59 3.3 38.7 1.0 CB A:SER105 3.3 35.5 1.0 CG A:HIS59 3.4 33.9 1.0 HA A:HIS59 3.6 40.6 1.0 H A:SER105 3.6 37.5 1.0 CB A:HIS59 3.7 37.0 1.0 H A:GLU174 3.9 41.5 1.0 HB3 A:SER105 4.0 35.7 1.0 HA A:ALA173 4.2 40.2 1.0 O A:HOH377 4.2 46.3 1.0 CA A:HIS59 4.2 41.5 1.0 N A:SER105 4.2 38.1 1.0 CB A:ASP103 4.3 38.6 1.0 CA A:SER105 4.3 37.1 1.0 O A:HOH367 4.3 34.5 1.0 CG A:GLU174 4.3 42.9 1.0 NE2 A:HIS59 4.4 35.5 1.0 HB3 A:ALA173 4.5 42.2 1.0 CD2 A:HIS59 4.5 36.4 1.0 HB3 A:ASP103 4.6 36.6 1.0 HB2 A:HIS59 4.6 37.8 1.0 HA A:SER105 4.7 38.2 1.0 HG23 A:THR57 4.7 36.5 1.0 HB2 A:ASP103 4.7 37.6 1.0 HG3 A:GLU174 4.7 42.8 1.0 H A:LEU104 4.7 37.9 1.0 HG2 A:GLU174 4.7 44.3 1.0 HG21 A:THR57 4.8 36.4 1.0 N A:GLU174 4.8 42.3 1.0 HB1 A:ALA173 4.9 40.2 1.0 HB2 A:GLU174 4.9 44.8 1.0 CB A:ALA173 5.0 42.1 1.0 CA A:ALA173 5.0 40.0 1.0

Cadmium binding site 2 out of 4 in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:51.2 occ:1.00 OG A:SER79 2.2 43.2 1.0 NE2 A:HIS145 2.3 44.2 1.0 OD2 A:ASP82 2.3 51.5 1.0 OD1 A:ASP82 2.7 49.1 1.0 CG A:ASP82 2.8 48.5 1.0 CE1 A:HIS145 3.1 52.2 1.0 HE1 A:HIS145 3.2 48.4 1.0 H A:SER79 3.2 43.1 1.0 CD2 A:HIS145 3.5 47.0 1.0 CB A:SER79 3.6 41.8 1.0 HD12 A:ILE146 3.7 55.2 1.0 HD2 A:HIS145 3.7 46.8 1.0 HB3 A:SER79 3.9 43.7 1.0 N A:SER79 4.0 43.0 1.0 HA A:SER78 4.2 44.6 1.0 HB2 A:SER79 4.3 43.9 1.0 OD1 A:ASP81 4.3 53.0 1.0 CB A:ASP82 4.3 44.7 1.0 ND1 A:HIS145 4.3 46.0 1.0 CA A:SER79 4.4 43.4 1.0 OD2 A:ASP81 4.4 53.0 1.0 CG A:HIS145 4.5 47.0 1.0 O A:HOH307 4.5 44.9 1.0 CD1 A:ILE146 4.6 58.1 1.0 HB2 A:ASP82 4.6 44.5 1.0 CG A:ASP81 4.7 54.4 1.0 HB3 A:ASP82 4.7 44.0 1.0 HD13 A:ILE146 4.7 55.4 1.0 H A:ASP82 4.8 43.8 1.0 HG12 A:ILE146 4.9 50.0 1.0 HB2 A:SER78 4.9 42.1 1.0 C A:SER78 4.9 44.9 1.0 CA A:SER78 5.0 43.8 1.0

Cadmium binding site 3 out of 4 in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:159.6 occ:1.00 NE2 B:HIS59 2.2 101.9 1.0 CE1 B:HIS59 2.8 95.8 1.0 HE1 B:HIS59 2.8 94.2 1.0 HA B:GLU174 3.0 104.0 1.0 CD2 B:HIS59 3.3 91.0 1.0 OE1 B:GLU174 3.4 117.8 1.0 HD2 B:HIS59 3.7 94.3 1.0 CD B:GLU174 3.7 118.7 1.0 OE2 B:GLU174 3.8 122.2 1.0 ND1 B:HIS59 3.9 91.8 1.0 CA B:GLU174 4.0 106.9 1.0 CG B:HIS59 4.2 86.6 1.0 HG21 B:THR57 4.3 61.4 1.0 HB3 B:GLU174 4.4 114.5 1.0 C B:GLU174 4.6 102.3 1.0 CB B:GLU174 4.6 114.0 1.0 H B:GLU174 4.6 99.6 1.0 CG B:GLU174 4.7 115.6 1.0 HG23 B:THR57 4.8 60.9 1.0 N B:GLU174 4.8 102.6 1.0 HB B:THR57 4.9 57.4 1.0 CG2 B:THR57 5.0 60.5 1.0 O B:HOH313 5.0 59.6 1.0

Cadmium binding site 4 out of 4 in the Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Sars-Cov-2 Nucleocapsid N-Terminal Domain (Ntd) Mutant Q58I within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:146.4 occ:1.00 HB2 B:HIS145 2.5 63.0 1.0 ND1 B:HIS145 2.8 66.7 1.0 H B:HIS145 3.0 55.6 1.0 CG B:HIS145 3.2 72.6 1.0 CB B:HIS145 3.2 62.0 1.0 O B:HOH335 3.3 105.5 1.0 OD1 B:ASP144 3.4 77.7 1.0 CE1 B:HIS145 3.8 72.8 1.0 N B:HIS145 3.8 54.8 1.0 HB3 B:HIS145 3.9 63.5 1.0 HA B:LYS143 4.1 47.2 1.0 CA B:HIS145 4.2 59.3 1.0 HE1 B:HIS145 4.2 73.7 1.0 H B:ASP144 4.2 51.7 1.0 CD2 B:HIS145 4.3 74.9 1.0 O B:PRO142 4.3 51.9 1.0 NE2 B:HIS145 4.5 75.4 1.0 N B:ASP144 4.5 49.7 1.0 CG B:ASP144 4.6 69.6 1.0 HA B:HIS145 4.7 59.9 1.0 C B:ASP144 4.9 54.6 1.0 C B:LYS143 4.9 48.0 1.0 HD2 B:HIS145 4.9 74.6 1.0 CA B:LYS143 4.9 46.2 1.0

K.Dhamotharan, A.Schlundt, S.Guenther. Structure of N-Terminal Domain Mutant Q58I of Nucleocapsid Protein of Sars-Cov-2 To Be Published.