Zinc in PDB 6lxt: Structure of Post Fusion Core of 2019-Ncov S2 Subunit

The structure of Structure of Post Fusion Core of 2019-Ncov S2 Subunit, PDB code: 6lxt was solved by Y.Zhu, F.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.32 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.240, 57.580, 115.720, 90.00, 91.58, 90.00
R / Rfree (%)	25.9 / 29

The binding sites of Zinc atom in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit (pdb code 6lxt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit, PDB code: 6lxt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:0.3 occ:1.00 OD1 A:ASP950 2.7 89.7 1.0 OE1 A:GLN1180 3.4 89.5 1.0 OE1 A:GLN949 3.5 64.2 1.0 CG A:ASP950 3.9 92.0 1.0 CD A:GLN949 3.9 64.4 1.0 O A:GLY946 3.9 55.9 1.0 CG A:GLN949 3.9 63.6 1.0 CB A:GLN949 4.2 55.9 1.0 OD2 A:ASP950 4.5 0.8 1.0 N A:ASP950 4.5 64.2 1.0 CD A:GLN1180 4.7 92.0 1.0 CA A:GLY946 4.7 55.5 1.0 C A:GLY946 4.7 58.4 1.0 NE2 A:GLN949 4.8 62.5 1.0 CA A:ASP950 4.9 70.9 1.0 CB A:ASP950 5.0 83.1 1.0

Zinc binding site 2 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1304 b:0.2 occ:1.00 OD2 A:ASP1165 1.8 0.7 1.0 OD1 E:ASP1163 2.5 1.0 1.0 OD1 E:ASP1165 2.6 0.1 1.0 OD2 E:ASP1165 2.7 0.4 1.0 CG A:ASP1165 3.0 0.7 1.0 CG E:ASP1165 3.0 0.4 1.0 CG E:ASP1163 3.4 0.6 1.0 OD1 A:ASP1165 3.8 0.7 1.0 OD2 E:ASP1163 3.8 0.9 1.0 CB A:ASP1165 4.0 0.7 1.0 N A:ASP1165 4.3 0.1 1.0 CB E:ASP1163 4.4 0.9 1.0 CB E:ASP1165 4.5 0.4 1.0 CA A:ASP1165 4.8 0.1 1.0 C A:VAL1164 4.9 0.4 1.0 CA A:VAL1164 5.0 0.1 1.0

Zinc binding site 3 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:0.9 occ:1.00 OD1 B:ASP936 1.9 91.2 1.0 CG B:ASP936 2.9 73.2 1.0 OD2 B:ASP936 3.3 73.5 1.0 O B:GLY932 4.1 57.2 1.0 CB B:ASP936 4.2 51.1 1.0 CA B:ASP936 4.6 47.2 1.0 N B:ASP936 4.6 46.5 1.0

Zinc binding site 4 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:0.1 occ:1.00 OD2 B:ASP985 3.5 0.9 1.0 CG B:ASP985 4.2 0.8 1.0 CA B:SER982 4.5 86.8 1.0 CD B:PRO1162 4.5 0.7 1.0 CB B:ASP985 4.6 0.5 1.0 N B:PRO1162 4.6 0.4 1.0 O B:PRO1162 4.7 0.0 1.0 CB B:SER982 4.7 88.7 1.0 N B:SER982 5.0 0.8 1.0

Zinc binding site 5 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1301 b:0.6 occ:1.00 OD1 F:ASP950 2.3 94.7 1.0 CG F:ASP950 3.3 90.8 1.0 OD2 F:ASP950 3.5 96.6 1.0 NE2 F:GLN1180 3.9 93.9 1.0 OE1 F:GLN949 4.6 68.5 1.0 CB F:ASP950 4.6 78.9 1.0 O F:GLY946 4.9 58.2 1.0 CA F:ASP950 5.0 73.5 1.0

Zinc binding site 6 out of 6 in the Structure of Post Fusion Core of 2019-Ncov S2 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Post Fusion Core of 2019-Ncov S2 Subunit within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1302 b:0.9 occ:1.00 OE1 F:GLU918 2.7 0.7 1.0 OE2 F:GLU918 3.3 0.1 1.0 CD F:GLU918 3.4 0.8 1.0 NZ F:LYS921 4.5 91.8 1.0 CD F:LYS921 4.7 92.8 1.0 CG F:GLU918 4.9 0.5 1.0

Y.Zhu, F.Sun. Crystal Structure of HR2 Domain of 2019-Ncov S2 Subunit To Be Published.