Calcium in PDB 2df7: Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle

The structure of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle, PDB code: 2df7 was solved by T.P.Ko, C.C.Lee, M.Y.Wang, A.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.60
Space group	P 21 3 2
Cell size a, b, c (Å), α, β, γ (°)	316.412, 316.412, 316.412, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.5

The structure of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Calcium atom in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle (pdb code 2df7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle, PDB code: 2df7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5903 b:34.4 occ:1.00 OD2 A:ASP174 2.1 36.9 1.0 OD2 A:ASP31 2.2 32.7 1.0 OD2 F:ASP31 2.4 38.4 1.0 OD2 F:ASP174 2.4 37.4 1.0 CG A:ASP31 3.2 32.2 1.0 CG A:ASP174 3.2 34.9 1.0 O F:HOH473 3.3 48.8 1.0 CG F:ASP31 3.4 36.2 1.0 CG F:ASP174 3.5 37.0 1.0 CB A:ASP31 3.6 30.4 1.0 OD1 A:ASP174 3.8 35.6 1.0 CB F:ASP31 3.8 34.9 1.0 OD1 F:ASP174 4.2 37.0 1.0 OD1 A:ASP31 4.3 31.9 1.0 CB A:ASP174 4.4 31.6 1.0 N A:ASP31 4.5 29.3 1.0 OD1 F:ASP31 4.5 35.5 1.0 CB F:ASP174 4.6 32.8 1.0 CA A:ASP31 4.7 30.1 1.0 O F:HOH535 4.9 38.0 1.0 N F:ASP31 4.9 32.1 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5901 b:33.8 occ:0.33 OD2 B:ASP174 2.2 39.0 1.0 OD2 B:ASP31 2.3 37.9 1.0 CG B:ASP174 3.4 38.0 1.0 CG B:ASP31 3.4 36.1 1.0 CB B:ASP31 3.8 32.6 1.0 OD1 B:ASP174 4.0 36.9 1.0 CB B:ASP174 4.4 33.5 1.0 OD1 B:ASP31 4.5 38.9 1.0 N B:ASP31 4.8 29.4 1.0 CA B:ASP31 5.0 29.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca5904 b:39.8 occ:1.00 OD2 C:ASP174 2.1 40.9 1.0 OD2 L:ASP31 2.2 38.4 1.0 OD2 E:ASP174 2.3 41.2 1.0 OD2 C:ASP31 2.3 39.1 1.0 OD2 L:ASP174 2.4 38.5 1.0 OD2 E:ASP31 2.5 42.4 1.0 CG C:ASP174 3.2 37.5 1.0 CG C:ASP31 3.3 38.4 1.0 CG L:ASP31 3.3 36.8 1.0 CG E:ASP174 3.4 38.5 1.0 CG L:ASP174 3.4 37.1 1.0 CG E:ASP31 3.5 39.9 1.0 CB C:ASP31 3.7 35.8 1.0 OD1 C:ASP174 3.8 35.9 1.0 CB L:ASP31 3.8 35.3 1.0 OD1 L:ASP174 3.9 33.8 1.0 O L:HOH469 3.9 51.0 1.0 CB E:ASP31 4.0 35.4 1.0 OD1 E:ASP174 4.0 39.6 1.0 CB C:ASP174 4.3 35.9 1.0 OD1 C:ASP31 4.4 39.3 1.0 CB E:ASP174 4.4 35.0 1.0 OD1 L:ASP31 4.4 38.4 1.0 N C:ASP31 4.5 32.2 1.0 CB L:ASP174 4.6 34.2 1.0 OD1 E:ASP31 4.6 41.1 1.0 CA C:ASP31 4.8 33.6 1.0 N L:ASP31 4.8 34.1 1.0 N E:ASP31 4.9 33.0 1.0 CA L:ASP31 5.0 33.5 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca5905 b:45.5 occ:1.00 OD2 M:ASP31 2.1 40.3 1.0 OD2 M:ASP174 2.2 39.5 1.0 OD2 K:ASP174 2.2 39.7 1.0 OD2 G:ASP31 2.2 39.5 1.0 OD2 G:ASP174 2.3 45.7 1.0 OD2 K:ASP31 2.4 45.2 1.0 CG M:ASP31 3.3 38.9 1.0 CG K:ASP31 3.3 42.6 1.0 CG G:ASP31 3.3 36.1 1.0 CG K:ASP174 3.4 39.7 1.0 CG M:ASP174 3.4 37.7 1.0 CG G:ASP174 3.5 44.4 1.0 CB M:ASP31 3.8 36.1 1.0 CB K:ASP31 3.8 40.5 1.0 CB G:ASP31 4.0 35.5 1.0 OD1 K:ASP174 4.1 40.2 1.0 OD1 M:ASP174 4.1 36.5 1.0 OD1 G:ASP174 4.2 46.9 1.0 OD1 G:ASP31 4.3 35.6 1.0 OD1 M:ASP31 4.4 41.5 1.0 OD1 K:ASP31 4.4 44.8 1.0 CB M:ASP174 4.4 34.3 1.0 CB G:ASP174 4.5 40.2 1.0 CB K:ASP174 4.5 36.3 1.0 N M:ASP31 4.7 32.5 1.0 N K:ASP31 4.8 37.0 1.0 CA M:ASP31 4.9 34.4 1.0 N G:ASP31 4.9 33.4 1.0 CA K:ASP31 4.9 37.5 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca5906 b:39.6 occ:1.00 OD2 O:ASP174 2.0 43.5 1.0 OD2 N:ASP174 2.1 41.2 1.0 OD2 H:ASP174 2.3 42.5 1.0 OD2 N:ASP31 2.3 39.2 1.0 OD2 O:ASP31 2.3 38.7 1.0 OD2 H:ASP31 2.4 36.6 1.0 CG O:ASP174 3.2 40.8 1.0 CG O:ASP31 3.4 37.9 1.0 CG H:ASP174 3.4 41.9 1.0 CG N:ASP174 3.4 38.8 1.0 CG H:ASP31 3.4 36.2 1.0 CG N:ASP31 3.4 38.7 1.0 O O:HOH469 3.6 40.3 1.0 CB O:ASP31 3.7 36.2 1.0 CB H:ASP31 3.8 34.6 1.0 CB N:ASP31 3.9 36.2 1.0 OD1 O:ASP174 3.9 39.1 1.0 OD1 H:ASP174 4.0 44.2 1.0 OD1 N:ASP174 4.2 38.5 1.0 CB O:ASP174 4.3 38.9 1.0 CB N:ASP174 4.4 35.6 1.0 CB H:ASP174 4.4 38.8 1.0 OD1 O:ASP31 4.5 42.0 1.0 OD1 N:ASP31 4.5 39.6 1.0 OD1 H:ASP31 4.6 36.7 1.0 N O:ASP31 4.6 33.1 1.0 N H:ASP31 4.8 37.1 1.0 CA O:ASP31 4.8 33.2 1.0 N N:ASP31 4.9 34.6 1.0 O N:HOH472 4.9 26.5 1.0 CA H:ASP31 5.0 35.5 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca5907 b:41.5 occ:1.00 OD2 Q:ASP174 2.1 44.9 1.0 OD2 J:ASP174 2.1 37.0 1.0 OD2 I:ASP174 2.1 40.0 1.0 OD2 J:ASP31 2.2 40.5 1.0 OD2 Q:ASP31 2.3 40.8 1.0 OD2 I:ASP31 2.3 38.0 1.0 CG Q:ASP174 3.2 43.4 1.0 CG J:ASP174 3.2 36.7 1.0 CG I:ASP174 3.2 38.6 1.0 CG J:ASP31 3.3 37.4 1.0 CG Q:ASP31 3.3 37.1 1.0 CG I:ASP31 3.4 37.7 1.0 CB J:ASP31 3.7 35.7 1.0 OD1 J:ASP174 3.8 37.7 1.0 CB I:ASP31 3.8 37.2 1.0 CB Q:ASP31 3.8 35.3 1.0 OD1 Q:ASP174 3.8 41.5 1.0 OD1 I:ASP174 3.8 38.5 1.0 O I:HOH5946 4.2 54.9 1.0 CB I:ASP174 4.3 36.1 1.0 CB Q:ASP174 4.3 40.4 1.0 CB J:ASP174 4.3 33.1 1.0 OD1 J:ASP31 4.4 38.6 1.0 OD1 Q:ASP31 4.4 39.0 1.0 OD1 I:ASP31 4.5 38.9 1.0 N J:ASP31 4.7 34.0 1.0 N Q:ASP31 4.8 32.8 1.0 N I:ASP31 4.8 35.5 1.0 CA J:ASP31 4.9 33.1 1.0 CA Q:ASP31 4.9 32.0 1.0 CA I:ASP31 5.0 35.5 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca5902 b:40.6 occ:0.33 OD2 P:ASP31 2.2 47.1 1.0 OD2 P:ASP174 2.3 40.7 1.0 CG P:ASP31 3.3 44.0 1.0 CG P:ASP174 3.4 41.3 1.0 CB P:ASP31 3.8 41.0 1.0 OD1 P:ASP174 3.9 44.5 1.0 OD1 P:ASP31 4.4 47.3 1.0 CB P:ASP174 4.6 38.5 1.0 N P:ASP31 4.8 37.9 1.0 CA P:ASP31 4.9 39.2 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range: probe atom residue distance (Å) B Occ R:Ca5908 b:36.4 occ:1.00 OD2 T:ASP174 2.1 34.1 1.0 OD2 S:ASP174 2.2 35.2 1.0 OD2 R:ASP174 2.2 36.4 1.0 OD2 S:ASP31 2.4 44.5 1.0 OD2 R:ASP31 2.4 39.8 1.0 OD2 T:ASP31 2.4 31.3 1.0 CG T:ASP174 3.1 33.3 1.0 CG S:ASP174 3.3 33.1 1.0 CG R:ASP174 3.3 34.0 1.0 CG S:ASP31 3.4 42.1 1.0 CG R:ASP31 3.4 37.3 1.0 CG T:ASP31 3.5 33.6 1.0 O S:HOH461 3.7 33.0 1.0 OD1 T:ASP174 3.7 32.3 1.0 CB T:ASP31 3.8 34.0 1.0 CB S:ASP31 3.8 38.9 1.0 CB R:ASP31 3.8 34.4 1.0 OD1 S:ASP174 4.0 34.2 1.0 OD1 R:ASP174 4.0 35.8 1.0 CB T:ASP174 4.2 31.9 1.0 CB R:ASP174 4.3 32.9 1.0 CB S:ASP174 4.3 32.7 1.0 OD1 S:ASP31 4.5 44.3 1.0 OD1 R:ASP31 4.5 39.9 1.0 OD1 T:ASP31 4.6 37.0 1.0 N T:ASP31 4.7 31.3 1.0 N S:ASP31 4.8 35.3 1.0 N R:ASP31 4.8 32.3 1.0 CA T:ASP31 4.9 32.0 1.0 CA S:ASP31 5.0 36.5 1.0 CA R:ASP31 5.0 32.2 1.0

C.C.Lee, T.P.Ko, C.C.Chou, M.Yoshimura, S.R.Doong, M.Y.Wang, A.H.Wang. Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle at 2.6A Resolution: Implications in Virion Assembly and Immunogenicity. J.Struct.Biol. V. 155 74 2006.
ISSN: ISSN 1047-8477
PubMed: 16677827
DOI: 10.1016/J.JSB.2006.02.014