Calcium in PDB 1c8n: Tobacco Necrosis Virus

The structure of Tobacco Necrosis Virus, PDB code: 1c8n was solved by Y.Oda, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.25
Space group	P 42 3 2
Cell size a, b, c (Å), α, β, γ (°)	336.400, 336.400, 336.400, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 27.3

The binding sites of Calcium atom in the Tobacco Necrosis Virus (pdb code 1c8n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tobacco Necrosis Virus, PDB code: 1c8n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tobacco Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tobacco Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:13.7 occ:1.00 O A:THR219 2.6 10.9 1.0 OD1 A:ASN275 2.6 14.7 1.0 OD1 C:ASP163 2.8 15.4 1.0 O A:HOH841 2.9 11.9 1.0 OD2 C:ASP160 3.1 22.1 1.0 O A:ASN275 3.5 21.3 1.0 CB C:ASP160 3.6 14.4 1.0 CG C:ASP160 3.6 14.2 1.0 CG A:ASN275 3.7 14.9 1.0 O C:HOH880 3.8 22.3 1.0 C A:THR219 3.8 10.7 1.0 CG C:ASP163 3.9 16.7 1.0 OG A:SER218 4.1 25.1 1.0 CA A:ASN275 4.2 17.5 1.0 C A:ASN275 4.2 17.6 1.0 OD2 C:ASP163 4.4 19.6 1.0 N A:THR219 4.6 9.5 1.0 CB A:ASN275 4.6 15.7 1.0 ND2 A:ASN275 4.6 15.8 1.0 CA A:THR219 4.7 10.1 1.0 OD1 C:ASP160 4.7 12.4 1.0 N A:ILE220 4.8 11.3 1.0 CA A:ILE220 4.9 11.3 1.0 CB A:THR219 4.9 10.1 1.0

Calcium binding site 2 out of 5 in the Tobacco Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tobacco Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:16.5 occ:1.00 O A:SER173 2.6 14.0 1.0 O A:THR175 2.9 15.4 1.0 O A:GLN174 3.4 9.4 1.0 C A:GLN174 3.4 11.1 1.0 C A:SER173 3.6 10.2 1.0 C A:THR175 3.7 11.7 1.0 N A:THR175 3.8 9.0 1.0 CA A:GLN174 3.9 10.8 1.0 CB A:ALA178 3.9 7.7 1.0 N A:GLN174 4.2 9.2 1.0 CA A:THR175 4.3 9.9 1.0 N A:ALA178 4.4 10.0 1.0 N A:TYR176 4.5 11.1 1.0 CA A:ALA178 4.7 9.3 1.0 CA A:TYR176 4.8 11.4 1.0 CA A:SER173 4.8 10.3 1.0 N A:LYS177 4.9 10.7 1.0 O A:ALA178 4.9 12.2 1.0

Calcium binding site 3 out of 5 in the Tobacco Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tobacco Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.7 occ:1.00 O C:THR219 2.5 9.4 1.0 OD1 C:ASN275 2.7 17.0 1.0 OD2 B:ASP160 2.9 20.4 1.0 OD1 B:ASP163 2.9 19.9 1.0 O C:ASN275 3.6 23.8 1.0 CG B:ASP160 3.7 13.7 1.0 OG C:SER218 3.7 23.5 1.0 CG C:ASN275 3.8 17.9 1.0 C C:THR219 3.8 13.5 1.0 CB B:ASP160 3.8 13.7 1.0 CG B:ASP163 4.0 19.9 1.0 CA C:ASN275 4.4 18.5 1.0 C C:ASN275 4.4 20.6 1.0 OD2 B:ASP163 4.4 20.6 1.0 N C:THR219 4.5 13.2 1.0 ND2 C:ASN275 4.5 16.9 1.0 CA C:THR219 4.6 12.3 1.0 CB C:ASN275 4.7 20.0 1.0 N C:ILE220 4.7 12.7 1.0 OD1 B:ASP160 4.8 12.7 1.0 CB C:THR219 4.9 14.5 1.0 CA C:ILE220 4.9 12.0 1.0 CB C:SER218 4.9 14.3 1.0

Calcium binding site 4 out of 5 in the Tobacco Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tobacco Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:19.0 occ:1.00 O B:THR219 2.5 9.7 1.0 OD1 B:ASN275 2.6 22.1 1.0 OD1 A:ASP163 2.8 12.4 1.0 OD2 A:ASP160 2.8 17.0 1.0 O B:ASN275 3.3 26.4 1.0 O A:HOH422 3.4 16.6 1.0 CG A:ASP160 3.7 12.1 1.0 CG B:ASN275 3.7 20.6 1.0 C B:THR219 3.7 10.8 1.0 CB A:ASP160 3.7 10.1 1.0 OG B:SER218 3.9 20.2 1.0 C B:ASN275 4.0 25.0 1.0 CG A:ASP163 4.0 15.0 1.0 O B:HOH671 4.2 11.7 1.0 CA B:ASN275 4.2 22.2 1.0 ND2 B:ASN275 4.6 19.9 1.0 CA B:ILE220 4.6 10.0 1.0 N B:ILE220 4.6 11.3 1.0 CB B:ASN275 4.6 20.2 1.0 OD2 A:ASP163 4.6 16.4 1.0 O A:HOH420 4.7 7.7 1.0 N B:THR219 4.7 12.0 1.0 CA B:THR219 4.7 10.3 1.0 OD1 A:ASP160 4.8 12.5 1.0 CB B:THR219 4.9 10.4 1.0

Calcium binding site 5 out of 5 in the Tobacco Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tobacco Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:19.2 occ:1.00 O C:SER173 2.7 15.2 1.0 O C:THR175 2.8 13.9 1.0 O C:GLN174 3.3 11.9 1.0 C C:GLN174 3.6 11.0 1.0 C C:THR175 3.8 11.9 1.0 C C:SER173 3.8 12.9 1.0 CB C:ALA178 4.0 7.1 1.0 N C:THR175 4.1 12.7 1.0 CA C:GLN174 4.1 10.5 1.0 N C:GLN174 4.4 12.3 1.0 N C:ALA178 4.5 10.5 1.0 CA C:THR175 4.5 10.4 1.0 N C:TYR176 4.6 11.5 1.0 CA C:ALA178 4.8 7.7 1.0 O C:ALA178 4.8 9.9 1.0 N C:LYS177 4.9 8.6 1.0 CA C:TYR176 4.9 9.8 1.0 CA C:SER173 4.9 13.5 1.0

Y.Oda, K.Saeki, Y.Takahashi, T.Maeda, H.Naitow, T.Tsukihara, K.Fukuyama. Crystal Structure of Tobacco Necrosis Virus at 2.25 A Resolution. J.Mol.Biol. V. 300 153 2000.
ISSN: ISSN 0022-2836
PubMed: 10864506
DOI: 10.1006/JMBI.2000.3831