Calcium in PDB 1x33: T=3 Recombinant Capsid of Semv Cp

The structure of T=3 Recombinant Capsid of Semv Cp, PDB code: 1x33 was solved by V.Sangita, G.L.Lokesh, P.S.Satheshkumar, V.Saravanan, C.S.Vijay, H.S.Savithri, M.R.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 3.60
Space group	R 3
Cell size a, b, c (Å), α, β, γ (°)	291.315, 291.315, 291.315, 61.63, 61.63, 61.63
R / Rfree (%)	23.2 / 23.4

The binding sites of Calcium atom in the T=3 Recombinant Capsid of Semv Cp (pdb code 1x33). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the T=3 Recombinant Capsid of Semv Cp, PDB code: 1x33:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the T=3 Recombinant Capsid of Semv Cp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T=3 Recombinant Capsid of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca269 b:23.1 occ:1.00 OD1 C:ASN267 2.3 26.8 1.0 OD1 B:ASP149 2.3 30.1 1.0 OD2 B:ASP146 2.3 40.5 1.0 OXT C:ASN268 2.5 55.0 1.0 O C:TYR207 2.6 24.1 1.0 CG B:ASP149 3.2 30.1 1.0 CG B:ASP146 3.2 40.5 1.0 CG C:ASN267 3.3 26.8 1.0 CB B:ASP146 3.4 40.5 1.0 OD2 B:ASP149 3.4 30.1 1.0 C C:ASN268 3.7 39.6 1.0 C C:TYR207 3.7 24.1 1.0 N C:ASN268 3.7 39.6 1.0 ND2 C:ASN267 3.9 26.8 1.0 CE C:LYS208 4.1 39.1 1.0 N C:TYR207 4.2 24.1 1.0 CB C:TYR207 4.3 22.0 1.0 CA C:TYR207 4.3 24.1 1.0 O C:SER116 4.3 16.3 1.0 CA C:ASN268 4.4 39.6 1.0 OD1 B:ASP146 4.4 40.5 1.0 CA C:ASN267 4.4 26.0 1.0 C C:ASN267 4.4 26.0 1.0 CB C:ASN267 4.5 26.8 1.0 CB B:ASP149 4.6 30.1 1.0 O C:ASN268 4.6 39.6 1.0 CD1 C:TYR207 4.8 22.0 1.0 N C:LYS208 4.8 9.0 1.0 CA B:ASP146 4.9 21.1 1.0 C C:PRO206 4.9 9.0 1.0 N B:ASP149 5.0 13.1 1.0

Calcium binding site 2 out of 3 in the T=3 Recombinant Capsid of Semv Cp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T=3 Recombinant Capsid of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca270 b:23.1 occ:1.00 OD1 A:ASN267 2.2 18.2 1.0 OD1 C:ASP149 2.3 23.6 1.0 OD2 C:ASP146 2.4 16.9 1.0 OXT A:ASN268 2.4 51.2 1.0 O A:TYR207 2.4 26.1 1.0 CG C:ASP149 3.1 23.6 1.0 OD2 C:ASP149 3.3 23.6 1.0 CG C:ASP146 3.3 16.9 1.0 CG A:ASN267 3.4 18.2 1.0 CB C:ASP146 3.5 16.9 1.0 C A:TYR207 3.6 26.1 1.0 N A:ASN268 3.6 33.8 1.0 C A:ASN268 3.6 33.8 1.0 ND2 A:ASN267 4.1 18.2 1.0 N A:TYR207 4.1 26.1 1.0 CB A:TYR207 4.2 29.1 1.0 CA A:TYR207 4.2 26.1 1.0 CA A:ASN268 4.2 33.8 1.0 C A:ASN267 4.3 9.0 1.0 CA A:ASN267 4.3 9.0 1.0 CB A:ASN267 4.4 18.2 1.0 O A:SER116 4.5 9.0 1.0 OD1 C:ASP146 4.5 16.9 1.0 O A:ASN268 4.6 33.8 1.0 CB C:ASP149 4.6 23.6 1.0 CD A:LYS208 4.6 21.9 1.0 N A:LYS208 4.7 14.5 1.0 CD1 A:TYR207 4.8 29.1 1.0 NZ A:LYS208 4.8 21.9 1.0 C A:PRO206 4.9 9.0 1.0 CG A:TYR207 5.0 29.1 1.0 CA A:LYS208 5.0 14.5 1.0

Calcium binding site 3 out of 3 in the T=3 Recombinant Capsid of Semv Cp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of T=3 Recombinant Capsid of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca271 b:23.1 occ:1.00 OD1 B:ASN267 2.2 9.5 1.0 OD2 A:ASP146 2.2 65.0 1.0 OD2 A:ASP149 2.3 34.9 1.0 O B:TYR207 2.5 9.5 1.0 OXT B:ASN268 2.5 50.0 1.0 CG A:ASP146 3.1 65.0 1.0 CG A:ASP149 3.1 34.9 1.0 OD1 A:ASP149 3.2 34.9 1.0 CB A:ASP146 3.2 65.0 1.0 CG B:ASN267 3.3 9.5 1.0 N B:ASN268 3.6 46.1 1.0 C B:TYR207 3.6 9.5 1.0 C B:ASN268 3.7 46.1 1.0 ND2 B:ASN267 4.0 9.5 1.0 N B:TYR207 4.1 9.5 1.0 OD1 A:ASP146 4.2 65.0 1.0 CA B:TYR207 4.3 9.5 1.0 C B:ASN267 4.3 24.7 1.0 CA B:ASN268 4.3 46.1 1.0 CA B:ASN267 4.3 24.7 1.0 CB B:TYR207 4.3 20.5 1.0 O B:SER116 4.4 12.2 1.0 CB B:ASN267 4.4 9.5 1.0 CB A:ASP149 4.5 34.9 1.0 CD B:LYS208 4.5 38.4 1.0 O B:ASN268 4.7 46.1 1.0 NZ B:LYS208 4.7 38.4 1.0 CA A:ASP146 4.7 42.6 1.0 N B:LYS208 4.7 10.5 1.0 CD1 B:TYR207 4.8 20.5 1.0 C B:PRO206 5.0 9.0 1.0 CA B:LYS208 5.0 10.5 1.0 CA A:ASP149 5.0 26.5 1.0

V.Sangita, G.L.Lokesh, P.S.Satheshkumar, V.Saravanan, C.S.Vijay, H.S.Savithri, M.R.Murthy. Structural Studies on Recombinant T = 3 Capsids of Sesbania Mosaic Virus Coat Protein Mutants. Acta Crystallogr.,Sect.D V. 61 1402 2005.
ISSN: ISSN 0907-4449
PubMed: 16204893
DOI: 10.1107/S0907444905024029