Sodium in PDB 2ieq: Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein

The structure of Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein, PDB code: 2ieq was solved by J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.57 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.020, 51.688, 54.080, 90.00, 107.56, 90.00
R / Rfree (%)	19.6 / 24

The binding sites of Sodium atom in the Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein (pdb code 2ieq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein, PDB code: 2ieq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:22.8 occ:1.00 OE1 A:GLU77 2.6 16.1 1.0 O A:HOH1006 2.9 24.1 1.0 O A:ASN73 3.0 11.9 1.0 N A:SER76 3.0 12.8 1.0 OD1 A:ASN73 3.1 14.6 1.0 N A:SER75 3.3 10.8 1.0 CB A:SER76 3.4 14.7 1.0 OG A:SER76 3.5 17.6 1.0 C A:LEU74 3.5 12.7 1.0 CD A:GLU77 3.6 16.6 1.0 C A:ASN73 3.6 11.4 1.0 CA A:LEU74 3.7 11.3 1.0 CA A:SER76 3.7 13.8 1.0 NZ C:LYS33 3.8 23.9 1.0 OE2 A:GLU77 3.8 17.0 1.0 CG A:ASN73 3.9 14.7 1.0 O C:HOH1123 3.9 37.6 1.0 N A:LEU74 4.0 11.2 1.0 C A:SER75 4.0 12.2 1.0 N A:GLU77 4.0 12.7 1.0 CA A:SER75 4.1 11.8 1.0 O A:LEU74 4.2 12.3 1.0 O A:HOH1073 4.3 38.4 1.0 C A:SER76 4.4 13.8 1.0 O A:HOH1071 4.5 41.7 1.0 CB A:ASN73 4.5 13.3 1.0 CB A:SER75 4.6 11.3 1.0 CA A:ASN73 4.7 12.8 1.0 ND2 A:ASN73 4.7 16.6 1.0 CG A:GLU77 4.9 10.9 1.0

Sodium binding site 2 out of 3 in the Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:22.4 occ:1.00 OE1 B:GLU77 2.6 17.1 1.0 O B:ASN73 2.9 12.9 1.0 OD1 B:ASN73 3.0 16.5 1.0 N B:SER76 3.0 13.5 1.0 N B:SER75 3.3 12.6 1.0 CB B:SER76 3.5 15.8 1.0 C B:LEU74 3.5 13.8 1.0 CD B:GLU77 3.5 17.4 1.0 OG B:SER76 3.5 16.9 1.0 C B:ASN73 3.5 12.3 1.0 NZ A:LYS33 3.6 29.0 1.0 CA B:LEU74 3.7 12.9 1.0 OE2 B:GLU77 3.7 19.6 1.0 CG B:ASN73 3.7 15.0 1.0 O A:HOH1014 3.8 27.4 1.0 CA B:SER76 3.8 14.7 1.0 N B:LEU74 3.9 13.4 1.0 C B:SER75 4.0 13.4 1.0 N B:GLU77 4.0 12.9 1.0 CA B:SER75 4.1 13.2 1.0 O B:LEU74 4.2 13.0 1.0 CB B:ASN73 4.4 12.3 1.0 C B:SER76 4.5 14.1 1.0 CB B:SER75 4.5 14.1 1.0 ND2 B:ASN73 4.6 13.0 1.0 CA B:ASN73 4.6 13.2 1.0 CG B:GLU77 4.9 13.7 1.0 CE A:LYS33 4.9 24.0 1.0

Sodium binding site 3 out of 3 in the Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1003 b:28.8 occ:1.00 OE1 C:GLU77 2.7 15.3 1.0 O C:ASN73 2.7 13.5 1.0 O B:HOH1042 2.9 38.6 1.0 N C:SER76 3.1 14.1 1.0 N C:SER75 3.4 13.7 1.0 ND2 C:ASN73 3.5 18.3 1.0 CB C:SER76 3.5 16.2 1.0 C C:LEU74 3.5 14.2 1.0 C C:ASN73 3.6 14.0 1.0 O B:HOH1021 3.6 26.9 1.0 CD C:GLU77 3.6 19.1 1.0 OG C:SER76 3.6 19.5 1.0 NZ B:LYS33 3.7 23.3 1.0 CA C:LEU74 3.7 13.8 1.0 CG C:ASN73 3.7 15.8 1.0 CA C:SER76 3.8 14.2 1.0 OE2 C:GLU77 3.8 18.0 1.0 OD1 C:ASN73 3.8 16.7 1.0 O C:HOH1072 3.9 22.4 1.0 N C:LEU74 4.0 13.4 1.0 C C:SER75 4.1 13.2 1.0 N C:GLU77 4.1 12.3 1.0 O C:LEU74 4.1 13.8 1.0 CA C:SER75 4.2 13.9 1.0 C C:SER76 4.5 14.2 1.0 CB C:ASN73 4.5 15.6 1.0 CA C:ASN73 4.7 15.5 1.0 CB C:SER75 4.7 16.1 1.0 CE B:LYS33 4.9 20.6 1.0

Q.Zheng, Y.Deng, J.Liu, L.V.Hoek, B.Berkhout, M.Lu. Core Structure of S2 From the Human Coronavirus NL63 Spike Glycoprotein Biochemistry V. 45 15205 2006.
ISSN: ISSN 0006-2960
PubMed: 17176042
DOI: 10.1021/BI061686W