Calcium in PDB 1x35: Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp

The structure of Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp, PDB code: 1x35 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)	20.00 / 4.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	471.500, 330.095, 351.474, 90.00, 131.05, 90.00
R / Rfree (%)	26.8 / 27

The binding sites of Calcium atom in the Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp (pdb code 1x35). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp, PDB code: 1x35:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Recombinant T=3 Capsid of A Site Specific Mutant 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 Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca269 b:39.8 occ:1.00 OD1 B:ASN267 2.1 27.1 1.0 OD2 A:ASP146 2.2 80.1 1.0 OD2 A:ASP149 2.3 31.1 1.0 O B:TYR207 2.3 38.4 1.0 OXT B:ASN268 2.6 92.0 1.0 O B:ASN268 2.7 79.1 1.0 CG A:ASP146 2.9 80.1 1.0 CB A:ASP146 3.0 80.1 1.0 CG A:ASP149 3.2 31.1 1.0 CG B:ASN267 3.2 27.1 1.0 OD1 A:ASP149 3.4 31.1 1.0 C B:TYR207 3.5 38.4 1.0 N B:ASN268 3.6 79.1 1.0 ND2 B:ASN267 3.8 27.1 1.0 C B:ASN268 3.8 79.1 1.0 N B:TYR207 3.9 38.4 1.0 OD1 A:ASP146 4.1 80.1 1.0 CA B:TYR207 4.1 38.4 1.0 CB B:TYR207 4.2 44.3 1.0 O B:SER116 4.2 13.5 1.0 CA B:ASN268 4.3 79.1 1.0 CB B:ASN267 4.4 27.1 1.0 CA B:ASN267 4.4 42.3 1.0 C B:ASN267 4.4 42.3 1.0 CA A:ASP146 4.5 41.0 1.0 CB A:ASP149 4.6 31.1 1.0 N B:LYS208 4.6 26.9 1.0 C B:PRO206 4.7 12.6 1.0 O A:ASP146 4.7 41.0 1.0 CA B:LYS208 4.8 26.9 1.0 N A:ASP149 4.9 34.0 1.0 CA A:ASP149 4.9 34.0 1.0 CB B:PRO206 4.9 95.9 1.0

Calcium binding site 2 out of 3 in the Recombinant T=3 Capsid of A Site Specific Mutant 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 Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca270 b:39.8 occ:1.00 OD2 B:ASP146 2.1 42.1 1.0 OD1 C:ASN267 2.2 50.5 1.0 O C:TYR207 2.4 27.9 1.0 OXT C:ASN268 2.4 96.9 1.0 O C:ASN268 2.4 64.5 1.0 OD1 B:ASP149 2.4 54.6 1.0 CG C:ASN267 2.9 50.5 1.0 CG B:ASP146 3.1 42.1 1.0 ND2 C:ASN267 3.2 50.5 1.0 CB B:ASP146 3.4 42.1 1.0 CG B:ASP149 3.4 54.6 1.0 C C:TYR207 3.5 27.9 1.0 C C:ASN268 3.6 64.5 1.0 N C:ASN268 3.6 64.5 1.0 OD2 B:ASP149 3.6 54.6 1.0 CB C:TYR207 4.0 43.3 1.0 CE C:LYS208 4.1 54.3 1.0 CB C:ASN267 4.1 50.5 1.0 CA C:TYR207 4.2 27.9 1.0 N C:TYR207 4.2 27.9 1.0 OD1 B:ASP146 4.2 42.1 1.0 CA C:ASN268 4.3 64.5 1.0 C C:ASN267 4.3 41.8 1.0 CA C:ASN267 4.3 41.8 1.0 O C:SER116 4.5 26.0 1.0 N C:LYS208 4.6 13.2 1.0 CD1 C:TYR207 4.7 43.3 1.0 CG C:TYR207 4.7 43.3 1.0 CB B:ASP149 4.8 54.6 1.0 CA C:LYS208 4.8 13.2 1.0 CA B:ASP146 4.9 25.1 1.0 C C:PRO206 5.0 17.4 1.0 O B:ASP146 5.0 25.1 1.0

Calcium binding site 3 out of 3 in the Recombinant T=3 Capsid of A Site Specific Mutant 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 Recombinant T=3 Capsid of A Site Specific Mutant of Semv Cp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca271 b:39.8 occ:1.00 OD1 A:ASN267 2.0 30.0 1.0 OD2 C:ASP146 2.2 37.9 1.0 OD1 C:ASP149 2.3 29.5 1.0 O A:TYR207 2.3 28.9 1.0 OXT A:ASN268 2.4 76.1 1.0 O A:ASN268 2.5 25.3 1.0 CG A:ASN267 3.0 30.0 1.0 CG C:ASP149 3.1 29.5 1.0 CG C:ASP146 3.1 37.9 1.0 OD2 C:ASP149 3.3 29.5 1.0 CB C:ASP146 3.4 37.9 1.0 ND2 A:ASN267 3.5 30.0 1.0 C A:TYR207 3.5 28.9 1.0 C A:ASN268 3.6 25.3 1.0 N A:ASN268 3.7 25.3 1.0 N A:TYR207 4.0 28.9 1.0 CA A:TYR207 4.1 28.9 1.0 O A:SER116 4.2 19.4 1.0 CB A:TYR207 4.2 43.4 1.0 CB A:ASN267 4.2 30.0 1.0 CD A:LYS208 4.3 21.6 1.0 OD1 C:ASP146 4.3 37.9 1.0 CA A:ASN268 4.3 25.3 1.0 CA A:ASN267 4.4 28.5 1.0 C A:ASN267 4.4 28.5 1.0 CB C:ASP149 4.6 29.5 1.0 N A:LYS208 4.6 21.8 1.0 NZ A:LYS208 4.7 21.6 1.0 C A:PRO206 4.8 10.1 1.0 CA A:LYS208 4.8 21.8 1.0 CD1 A:TYR207 4.8 43.4 1.0 CA C:ASP146 4.9 22.8 1.0 CE A:LYS208 4.9 21.6 1.0 N C:ASP149 4.9 39.3 1.0 O C:ASP146 4.9 22.8 1.0 CB A:PRO206 4.9 67.2 1.0 CA C:ASP149 5.0 39.3 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