Calcium in PDB 2vq0: Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59)

The structure of Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59), PDB code: 2vq0 was solved by P.Anju, C.Subashchandrabose, P.S.Satheshkumar, H.S.Savithri, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.60
Space group	R 3 5
Cell size a, b, c (Å), α, β, γ (°)	288.793, 288.793, 288.793, 61.70, 61.70, 61.70
R / Rfree (%)	25.7 / 25.8

The binding sites of Calcium atom in the Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59) (pdb code 2vq0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59), PDB code: 2vq0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1269 b:18.0 occ:1.00 OD1 A:ASN267 2.1 16.4 1.0 OXT A:ASN268 2.2 49.4 1.0 OD1 C:ASP149 2.3 21.8 1.0 OD1 C:ASP146 2.4 15.1 1.0 O A:TYR207 2.4 24.2 1.0 CG C:ASP149 3.1 21.8 1.0 OD2 C:ASP149 3.2 21.8 1.0 CG A:ASN267 3.2 16.4 1.0 CG C:ASP146 3.2 15.1 1.0 CB C:ASP146 3.4 15.1 1.0 C A:ASN268 3.4 32.0 1.0 N A:ASN268 3.5 32.0 1.0 C A:TYR207 3.5 24.2 1.0 ND2 A:ASN267 3.9 16.4 1.0 N A:TYR207 4.0 24.2 1.0 CA A:ASN268 4.1 32.0 1.0 O A:SER116 4.1 10.5 1.0 CA A:TYR207 4.2 24.2 1.0 CD A:LYS208 4.2 20.1 1.0 C A:ASN267 4.3 10.5 1.0 CB A:TYR207 4.3 27.3 1.0 CA A:ASN267 4.4 10.5 1.0 CB A:ASN267 4.4 16.4 1.0 O A:ASN268 4.4 32.0 1.0 OD2 C:ASP146 4.4 15.1 1.0 CB C:ASP149 4.5 21.8 1.0 N A:LYS208 4.6 12.7 1.0 C A:PRO206 4.7 10.5 1.0 NZ A:LYS208 4.7 20.1 1.0 CD1 A:TYR207 4.7 27.3 1.0 CB A:PRO206 4.8 25.6 1.0 CA A:LYS208 4.8 12.7 1.0 CA C:ASP146 4.9 15.6 1.0 N C:ASP149 5.0 15.6 1.0 CE A:LYS208 5.0 20.1 1.0

Calcium binding site 2 out of 3 in the Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1269 b:18.0 occ:1.00 OD2 A:ASP146 2.0 63.1 1.0 OD1 B:ASN267 2.0 10.5 1.0 OD2 A:ASP149 2.3 33.0 1.0 OXT B:ASN268 2.3 48.2 1.0 O B:TYR207 2.5 10.5 1.0 CG A:ASP146 2.9 63.1 1.0 CG B:ASN267 3.1 10.5 1.0 CG A:ASP149 3.2 33.0 1.0 CB A:ASP146 3.2 63.1 1.0 N B:ASN268 3.4 44.3 1.0 OD1 A:ASP149 3.4 33.0 1.0 C B:ASN268 3.5 44.3 1.0 C B:TYR207 3.7 10.5 1.0 ND2 B:ASN267 3.9 10.5 1.0 OD1 A:ASP146 4.0 63.1 1.0 CA B:ASN267 4.1 22.9 1.0 CA B:ASN268 4.1 44.3 1.0 C B:ASN267 4.2 22.9 1.0 N B:TYR207 4.2 10.5 1.0 CB B:ASN267 4.2 10.5 1.0 CA B:TYR207 4.3 10.5 1.0 O B:SER116 4.4 10.5 1.0 CB B:TYR207 4.4 18.7 1.0 CD B:LYS208 4.4 36.6 1.0 O B:ASN268 4.5 44.3 1.0 CB A:ASP149 4.6 33.0 1.0 CA A:ASP146 4.6 40.7 1.0 NZ B:LYS208 4.6 36.6 1.0 N B:LYS208 4.7 10.5 1.0 CD1 B:TYR207 4.8 18.7 1.0 CA A:ASP149 4.9 24.7 1.0 N A:ASP149 4.9 24.7 1.0 CA B:LYS208 4.9 10.5 1.0 C B:PRO206 5.0 10.5 1.0 CE B:LYS208 5.0 36.6 1.0

Calcium binding site 3 out of 3 in the Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Capsid Structure of Sesbania Mosaic Virus Coat Protein Deletion Mutant Rcp(Delta 48 to 59) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1269 b:18.0 occ:1.00 OD2 B:ASP146 2.4 38.7 1.0 OD1 B:ASP149 2.4 28.3 1.0 OD1 C:ASN267 2.5 25.0 1.0 O C:ASN268 2.5 37.8 1.0 O C:TYR207 2.9 22.3 1.0 CG B:ASP146 3.3 38.7 1.0 CG B:ASP149 3.3 28.3 1.0 CG C:ASN267 3.4 25.0 1.0 CB B:ASP146 3.5 38.7 1.0 OD2 B:ASP149 3.6 28.3 1.0 C C:ASN268 3.7 37.8 1.0 N C:ASN268 3.8 37.8 1.0 O C:SER116 3.8 14.5 1.0 ND2 C:ASN267 4.0 25.0 1.0 C C:TYR207 4.0 22.3 1.0 CE C:LYS208 4.2 37.3 1.0 N C:TYR207 4.2 22.3 1.0 OD1 B:ASP146 4.4 38.7 1.0 CA C:ASN268 4.4 37.8 1.0 CA C:ASN267 4.5 24.2 1.0 C C:ASN267 4.5 24.2 1.0 CB C:ASN267 4.6 25.0 1.0 CB C:TYR207 4.6 20.2 1.0 CA C:TYR207 4.6 22.3 1.0 OG C:SER116 4.6 42.4 1.0 N B:ASP149 4.6 11.3 1.0 CB C:PRO206 4.6 10.5 1.0 CD C:LYS208 4.7 37.3 1.0 OXT C:ASN268 4.7 24.7 1.0 CB B:ASP149 4.7 28.3 1.0 C C:SER116 4.8 14.5 1.0 C C:PRO206 4.8 10.5 1.0 CB B:ALA148 4.8 24.7 1.0 CA C:SER116 4.8 14.5 1.0 CA B:ASP149 4.9 11.3 1.0 CA B:ASP146 5.0 19.2 1.0

P.Anju, C.Subashchandrabose, P.S.Satheshkumar, H.S.Savithri, M.R.N.Murthy. Structure of Recombinant Capsids Formed By the Beta-Annulus Deletion Mutant-Rcp (Delta 48-59) of Sesbania Mosaic Virus Virology V. 375 190 2008.
ISSN: ISSN 0042-6822
PubMed: 18295296
DOI: 10.1016/J.VIROL.2008.01.023