Calcium in PDB 2gsy: The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles

The structure of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles, PDB code: 2gsy was solved by D.Garriga, J.Querol-Audi, F.Abaitua, I.Saugar, J.Pous, N.Verdaguer, J.R.Caston, J.F.Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.60
Space group	P 21 3 2
Cell size a, b, c (Å), α, β, γ (°)	326.300, 326.300, 326.300, 90.00, 90.00, 90.00
R / Rfree (%)	25.4 / 26.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles (pdb code 2gsy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles, PDB code: 2gsy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:10.5 occ:0.66 OD2 E:ASP174 1.9 12.7 1.0 OD2 E:ASP31 2.0 11.8 1.0 OD2 A:ASP31 2.0 11.9 1.0 OD2 A:ASP174 2.0 12.8 1.0 CG E:ASP31 3.1 10.8 1.0 CG A:ASP31 3.1 10.9 1.0 CG E:ASP174 3.1 12.2 1.0 CG A:ASP174 3.2 12.2 1.0 CB E:ASP31 3.8 9.9 1.0 CB A:ASP31 3.8 9.9 1.0 OD1 E:ASP174 3.9 12.2 1.0 OD1 A:ASP174 3.9 12.2 1.0 OD1 E:ASP31 4.1 9.3 1.0 OD1 A:ASP31 4.1 9.2 1.0 CB E:ASP174 4.2 11.2 1.0 CB A:ASP174 4.2 11.2 1.0 N E:ASP31 4.6 9.8 1.0 N A:ASP31 4.7 9.9 1.0 CA E:ASP31 4.9 9.9 1.0 CA A:ASP31 4.9 9.9 1.0

Calcium binding site 2 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:12.6 occ:0.33 OD2 B:ASP31 2.0 11.9 1.0 OD2 B:ASP174 2.1 12.8 1.0 CG B:ASP31 3.2 10.9 1.0 CG B:ASP174 3.2 12.2 1.0 CB B:ASP31 3.8 9.9 1.0 OD1 B:ASP174 4.0 12.2 1.0 OD1 B:ASP31 4.2 9.2 1.0 CB B:ASP174 4.3 11.2 1.0 N B:ASP31 4.8 9.9 1.0 CA B:ASP31 4.9 9.9 1.0

Calcium binding site 3 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:2.0 occ:0.66 OD2 J:ASP174 1.9 12.8 1.0 OD2 C:ASP174 2.0 12.8 1.0 OD2 J:ASP31 2.0 11.9 1.0 OD2 C:ASP31 2.0 11.9 1.0 CG J:ASP31 3.1 10.9 1.0 CG J:ASP174 3.1 12.2 1.0 CG C:ASP174 3.2 12.2 1.0 CG C:ASP31 3.2 10.9 1.0 CB J:ASP31 3.7 9.9 1.0 CB C:ASP31 3.8 9.9 1.0 OD1 J:ASP174 3.9 12.2 1.0 OD1 C:ASP174 3.9 12.2 1.0 OD1 J:ASP31 4.1 9.2 1.0 CB C:ASP174 4.2 11.2 1.0 CB J:ASP174 4.2 11.2 1.0 OD1 C:ASP31 4.2 9.2 1.0 N J:ASP31 4.7 9.9 1.0 N C:ASP31 4.7 9.9 1.0 CA J:ASP31 4.8 9.9 1.0 CA C:ASP31 4.9 9.9 1.0

Calcium binding site 4 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca504 b:2.0 occ:0.33 OD2 D:ASP174 1.9 12.8 1.0 OD2 D:ASP31 2.2 11.9 1.0 CG D:ASP174 3.0 12.2 1.0 CG D:ASP31 3.3 10.9 1.0 CB D:ASP31 3.8 9.9 1.0 OD1 D:ASP174 3.8 12.2 1.0 CB D:ASP174 4.0 11.2 1.0 OD1 D:ASP31 4.3 9.2 1.0 N D:ASP31 4.7 9.9 1.0 CA D:ASP31 4.9 9.9 1.0

Calcium binding site 5 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca505 b:2.0 occ:1.00 OD2 K:ASP174 1.9 12.8 1.0 OD2 K:ASP31 1.9 11.9 1.0 OD2 I:ASP31 1.9 11.9 1.0 OD2 F:ASP174 2.0 12.8 1.0 OD2 F:ASP31 2.1 11.9 1.0 OD2 I:ASP174 2.1 12.8 1.0 CG I:ASP31 3.1 10.9 1.0 CG K:ASP31 3.1 10.9 1.0 CG K:ASP174 3.1 12.2 1.0 CG F:ASP174 3.2 12.2 1.0 CG F:ASP31 3.2 10.9 1.0 CG I:ASP174 3.2 12.2 1.0 CB K:ASP31 3.7 9.9 1.0 CB I:ASP31 3.7 9.9 1.0 OD1 K:ASP174 3.8 12.2 1.0 CB F:ASP31 3.8 9.9 1.0 OD1 I:ASP174 3.9 12.2 1.0 OD1 F:ASP174 3.9 12.2 1.0 OD1 I:ASP31 4.1 9.2 1.0 OD1 K:ASP31 4.1 9.2 1.0 CB K:ASP174 4.1 11.2 1.0 CB F:ASP174 4.2 11.2 1.0 OD1 F:ASP31 4.2 9.2 1.0 CB I:ASP174 4.3 11.2 1.0 N K:ASP31 4.6 9.9 1.0 N I:ASP31 4.7 9.9 1.0 N F:ASP31 4.8 9.9 1.0 CA K:ASP31 4.8 9.9 1.0 CA I:ASP31 4.8 9.9 1.0 CA F:ASP31 5.0 9.9 1.0

Calcium binding site 6 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca506 b:2.0 occ:1.00 OD2 G:ASP31 1.8 11.9 1.0 OD2 N:ASP174 1.9 12.8 1.0 OD2 G:ASP174 1.9 12.8 1.0 OD2 N:ASP31 2.0 11.9 1.0 OD2 H:ASP31 2.1 11.9 1.0 OD2 H:ASP174 2.1 12.8 1.0 CG G:ASP31 3.0 10.9 1.0 CG G:ASP174 3.1 12.2 1.0 CG N:ASP174 3.1 12.2 1.0 CG N:ASP31 3.2 10.9 1.0 CG H:ASP31 3.2 10.9 1.0 CG H:ASP174 3.3 12.2 1.0 CB G:ASP31 3.6 9.9 1.0 OD1 G:ASP174 3.8 12.2 1.0 CB N:ASP31 3.8 9.9 1.0 CB H:ASP31 3.8 9.9 1.0 OD1 N:ASP174 3.9 12.2 1.0 OD1 G:ASP31 4.0 9.2 1.0 OD1 H:ASP174 4.1 12.2 1.0 CB N:ASP174 4.1 11.2 1.0 CB G:ASP174 4.2 11.2 1.0 OD1 H:ASP31 4.2 9.2 1.0 OD1 N:ASP31 4.2 9.2 1.0 CB H:ASP174 4.3 11.2 1.0 N G:ASP31 4.5 9.9 1.0 N N:ASP31 4.7 9.9 1.0 CA G:ASP31 4.7 9.9 1.0 N H:ASP31 4.8 9.9 1.0 CA N:ASP31 4.9 9.9 1.0

Calcium binding site 7 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca507 b:2.8 occ:0.33 OD2 L:ASP31 2.0 11.9 1.0 OD2 L:ASP174 2.1 12.8 1.0 CG L:ASP31 3.1 10.9 1.0 CG L:ASP174 3.3 12.2 1.0 CB L:ASP31 3.8 9.9 1.0 OD1 L:ASP174 4.0 12.2 1.0 OD1 L:ASP31 4.1 9.2 1.0 CB L:ASP174 4.3 11.2 1.0 N L:ASP31 4.7 9.9 1.0 CA L:ASP31 4.9 9.9 1.0

Calcium binding site 8 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca508 b:2.0 occ:0.66 OD2 M:ASP31 1.9 11.8 1.0 OD2 R:ASP31 1.9 11.8 1.0 OD2 R:ASP174 2.0 12.7 1.0 OD2 M:ASP174 2.1 12.7 1.0 CG M:ASP31 3.1 10.8 1.0 CG R:ASP31 3.1 10.8 1.0 CG R:ASP174 3.3 12.1 1.0 CG M:ASP174 3.3 12.2 1.0 CB M:ASP31 3.7 9.9 1.0 CB R:ASP31 3.8 9.9 1.0 OD1 R:ASP174 4.0 12.1 1.0 OD1 M:ASP174 4.0 12.2 1.0 OD1 M:ASP31 4.0 9.2 1.0 OD1 R:ASP31 4.1 9.3 1.0 CB R:ASP174 4.3 11.2 1.0 CB M:ASP174 4.3 11.2 1.0 N R:ASP31 4.7 9.9 1.0 N M:ASP31 4.7 9.9 1.0 CA M:ASP31 4.9 9.9 1.0 CA R:ASP31 4.9 9.9 1.0

Calcium binding site 9 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca509 b:2.0 occ:1.00 OD2 O:ASP31 1.8 11.9 1.0 OD2 O:ASP174 1.9 12.8 1.0 OD2 Q:ASP174 1.9 12.8 1.0 OD2 P:ASP31 2.1 11.9 1.0 OD2 Q:ASP31 2.1 11.9 1.0 OD2 P:ASP174 2.2 12.8 1.0 CG O:ASP31 3.0 10.9 1.0 CG O:ASP174 3.1 12.2 1.0 CG Q:ASP174 3.2 12.2 1.0 CG P:ASP31 3.2 10.9 1.0 CG Q:ASP31 3.2 10.9 1.0 CG P:ASP174 3.4 12.2 1.0 CB O:ASP31 3.6 9.9 1.0 OD1 O:ASP174 3.8 12.2 1.0 CB P:ASP31 3.9 9.9 1.0 CB Q:ASP31 3.9 9.9 1.0 OD1 Q:ASP174 3.9 12.2 1.0 OD1 O:ASP31 4.0 9.2 1.0 OD1 P:ASP174 4.1 12.2 1.0 CB O:ASP174 4.2 11.2 1.0 CB Q:ASP174 4.2 11.2 1.0 OD1 P:ASP31 4.2 9.2 1.0 OD1 Q:ASP31 4.2 9.2 1.0 CB P:ASP174 4.4 11.2 1.0 N O:ASP31 4.5 9.9 1.0 CA O:ASP31 4.7 9.9 1.0 N Q:ASP31 4.7 9.9 1.0 N P:ASP31 4.9 9.8 1.0 CA Q:ASP31 5.0 9.9 1.0

Calcium binding site 10 out of 11 in the The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The 2.6A Structure of Infectious Bursal Virus Derived T=1 Particles within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca510 b:5.3 occ:0.33 OD2 S:ASP31 2.0 11.9 1.0 OD2 S:ASP174 2.0 12.7 1.0 CG S:ASP31 3.1 10.9 1.0 CG S:ASP174 3.2 12.2 1.0 CB S:ASP31 3.8 9.8 1.0 OD1 S:ASP174 3.9 12.1 1.0 OD1 S:ASP31 4.1 9.3 1.0 CB S:ASP174 4.3 11.2 1.0 N S:ASP31 4.7 9.9 1.0 CA S:ASP31 4.9 9.9 1.0

D.Garriga, J.Querol-Audi, F.Abaitua, I.Saugar, J.Pous, N.Verdaguer, J.R.Caston, J.F.Rodriguez. The 2.6-Angstrom Structure of Infectious Bursal Disease Virus-Derived T=1 Particles Reveals New Stabilizing Elements of the Virus Capsid. J.Virol. V. 80 6895 2006.
ISSN: ISSN 0022-538X
PubMed: 16809295
DOI: 10.1128/JVI.00368-06