Zinc in PDB 6wkp: Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form

The structure of Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form, PDB code: 6wkp was solved by C.Chang, K.Michalska, R.Jedrzejczak, N.Maltseva, M.Endres, A.Godzik, Y.Kim, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.61 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.388, 71.848, 106.961, 90.00, 92.98, 90.00
R / Rfree (%)	19.7 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form (pdb code 6wkp). 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 Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form, PDB code: 6wkp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form


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 Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:49.6 occ:1.00 OD2 A:ASP82 2.0 66.0 1.0 NE2 A:HIS145 2.0 56.7 1.0 O A:HOH306 2.2 25.5 1.0 CD2 A:HIS145 2.7 51.4 1.0 CG A:ASP82 2.9 57.8 1.0 NE2 D:HIS59 3.0 67.1 1.0 CE1 A:HIS145 3.1 55.1 1.0 OD1 A:ASP82 3.2 58.9 1.0 OG A:SER79 3.3 70.7 1.0 CE1 D:HIS59 3.7 65.5 1.0 CG A:HIS145 3.9 59.5 1.0 CD2 D:HIS59 4.0 71.5 1.0 ND1 A:HIS145 4.1 56.0 1.0 CB A:ASP82 4.2 46.3 1.0 CB A:SER79 4.2 63.8 1.0 N A:SER79 4.3 54.5 1.0 CG2 D:THR57 4.4 36.3 1.0 CG1 A:ILE146 4.5 63.8 1.0 CB D:THR57 4.5 32.9 1.0 CD1 A:ILE146 4.5 63.9 1.0 OG1 D:THR57 4.8 29.2 1.0 CA A:SER79 4.9 52.3 1.0 ND1 D:HIS59 4.9 71.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form


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 Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:58.7 occ:1.00 OD2 B:ASP82 2.1 41.7 1.0 NE2 A:HIS59 2.2 87.4 1.0 NE2 B:HIS145 2.2 50.8 1.0 O A:HOH301 2.4 6.2 1.0 CE1 A:HIS59 2.6 85.2 1.0 CD2 A:HIS59 2.7 84.4 1.0 CG B:ASP82 2.9 40.1 1.0 OD1 B:ASP82 3.0 49.1 1.0 CE1 B:HIS145 3.0 43.3 1.0 CD2 B:HIS145 3.2 40.9 1.0 OG B:SER79 3.2 34.4 1.0 ND1 A:HIS59 3.3 86.7 1.0 CG A:HIS59 3.4 84.7 1.0 O B:HOH309 3.6 12.6 1.0 N B:SER79 4.1 22.1 1.0 ND1 B:HIS145 4.1 40.9 1.0 CB B:SER79 4.2 25.1 1.0 CG B:HIS145 4.2 40.4 1.0 CB B:ASP82 4.4 38.0 1.0 CD1 B:ILE146 4.6 19.7 1.0 CB A:HIS59 4.6 76.3 1.0 CG1 B:ILE146 4.7 25.3 1.0 CA B:SER79 4.8 20.2 1.0 CA B:SER78 4.9 30.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form


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 Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:26.5 occ:1.00 OD2 C:ASP82 2.0 27.8 1.0 NE2 B:HIS59 2.1 29.7 1.0 O B:HOH310 2.3 14.4 1.0 NE2 C:HIS145 2.5 40.8 1.0 CD2 C:HIS145 2.8 34.0 1.0 CE1 B:HIS59 2.9 21.9 1.0 CG C:ASP82 2.9 22.9 1.0 OD1 C:ASP82 3.2 29.2 1.0 CD2 B:HIS59 3.3 29.4 1.0 OG C:SER79 3.5 88.5 1.0 CE1 C:HIS145 3.7 46.8 1.0 ND1 B:HIS59 4.1 22.1 1.0 N C:SER79 4.1 60.2 1.0 CG C:HIS145 4.1 34.0 1.0 CB C:ASP82 4.2 28.3 1.0 CB C:SER79 4.3 71.4 1.0 CG B:HIS59 4.3 26.1 1.0 CD1 C:ILE146 4.4 33.7 1.0 CG2 B:THR57 4.4 12.0 1.0 CG1 C:ILE146 4.5 33.8 1.0 CB B:THR57 4.5 18.2 1.0 ND1 C:HIS145 4.5 47.9 1.0 CA C:SER78 4.7 35.2 1.0 OG1 B:THR57 4.8 25.7 1.0 CA C:SER79 4.8 60.3 1.0 O B:HOH301 4.9 30.3 1.0 C C:SER78 4.9 46.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form


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 Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:30.2 occ:1.00 NE2 C:HIS59 2.1 40.7 1.0 OD2 D:ASP82 2.1 47.8 1.0 O C:HOH305 2.2 0.6 1.0 NE2 D:HIS145 2.3 45.6 1.0 CD2 D:HIS145 2.9 48.6 1.0 CE1 C:HIS59 3.0 38.0 1.0 CD2 C:HIS59 3.1 32.1 1.0 CG D:ASP82 3.1 45.3 1.0 CE1 D:HIS145 3.5 55.2 1.0 OD1 D:ASP82 3.6 51.7 1.0 N D:SER79 3.9 23.9 1.0 CD1 D:ILE146 4.0 48.5 1.0 ND1 C:HIS59 4.1 32.8 1.0 OG D:SER79 4.2 30.3 1.0 CG D:HIS145 4.2 36.9 1.0 CG1 D:ILE146 4.2 45.5 1.0 CG C:HIS59 4.2 33.4 1.0 CB D:ASP82 4.3 37.4 1.0 CB D:SER78 4.3 35.8 1.0 CA D:SER78 4.3 32.6 1.0 ND1 D:HIS145 4.4 49.4 1.0 CG2 C:THR57 4.5 31.5 1.0 CB D:SER79 4.6 24.9 1.0 C D:SER78 4.7 33.5 1.0 CB C:THR57 4.8 31.3 1.0 CA D:SER79 4.9 28.5 1.0

C.Chang, K.Michalska, R.Jedrzejczak, N.Maltseva, M.Endres, A.Godzik, Y.Kim, A.Joachimiak. Crystal Structure of Rna-Binding Domain of Nucleocapsid Phosphoprotein From Sars Cov-2, Monoclinic Crystal Form To Be Published.