Calcium in PDB 4llf: Crystal Structure of Cucumber Necrosis Virus

The structure of Crystal Structure of Cucumber Necrosis Virus, PDB code: 4llf was solved by T.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.31 / 2.89
Space group	I 2 3 3
Cell size a, b, c (Å), α, β, γ (°)	384.000, 384.000, 384.000, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 24.2

The structure of Crystal Structure of Cucumber Necrosis Virus also contains other interesting chemical elements:

Zinc

(Zn)

10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Cucumber Necrosis Virus (pdb code 4llf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Crystal Structure of Cucumber Necrosis Virus, PDB code: 4llf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:89.2 occ:1.00 OE1 B:GLN258 2.3 48.7 1.0 OD1 B:ASP145 2.7 47.7 1.0 OD1 A:ASP178 3.1 65.4 1.0 CD B:GLN258 3.2 51.2 1.0 OD2 A:ASP173 3.4 44.8 1.0 NE2 B:GLN258 3.4 50.4 1.0 CB A:ASP175 3.5 50.9 1.0 OD2 A:ASP175 3.5 59.2 1.0 CG B:ASP145 3.8 42.7 1.0 OD1 A:ASP173 3.9 42.7 1.0 CG A:ASP175 3.9 53.2 1.0 CG A:ASP178 3.9 63.5 1.0 CG A:ASP173 4.0 47.4 1.0 CB A:ASP178 4.1 60.6 1.0 OD2 B:ASP145 4.3 42.0 1.0 CA A:ASP178 4.3 54.0 1.0 CG B:GLN258 4.5 43.4 1.0 CD A:PRO179 4.7 53.8 1.0 CA A:ASP175 4.9 37.6 1.0 CB B:GLN258 4.9 42.7 1.0 OD2 A:ASP178 5.0 56.4 1.0

Calcium binding site 2 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:84.2 occ:1.00 OE1 D:GLN258 2.7 56.8 1.0 OD1 D:ASP145 2.8 60.0 1.0 CB B:ASP178 2.9 63.2 1.0 OD2 B:ASP173 3.0 45.7 1.0 CG B:ASP178 3.3 70.6 1.0 CD D:GLN258 3.4 56.2 1.0 OD2 D:ASP145 3.4 50.5 1.0 CB B:ASP175 3.4 51.3 1.0 CG D:ASP145 3.5 49.0 1.0 OD2 B:ASP175 3.5 47.6 1.0 NE2 D:GLN258 3.5 51.2 1.0 OD2 B:ASP178 3.6 73.3 1.0 CG B:ASP175 3.9 47.0 1.0 CG B:ASP173 3.9 49.0 1.0 OD1 B:ASP178 4.1 59.4 1.0 OD1 B:ASP173 4.1 50.8 1.0 CA B:ASP178 4.3 53.3 1.0 CG D:GLN258 4.6 41.6 1.0 CA B:ASP175 4.8 48.1 1.0 N B:ASP178 4.9 47.7 1.0 CB D:GLN258 4.9 42.1 1.0 O B:ASP175 4.9 48.4 1.0 CB D:ASP145 4.9 32.4 1.0

Calcium binding site 3 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:77.8 occ:1.00 OD1 D:ASP178 2.6 58.7 1.0 OD1 A:ASP145 2.7 46.9 1.0 OD2 D:ASP173 2.8 36.7 1.0 OE1 A:GLN258 3.0 48.2 1.0 CD A:GLN258 3.2 50.0 1.0 CG D:ASP178 3.3 47.5 1.0 CG D:ASP173 3.4 38.9 1.0 OD1 D:ASP173 3.4 47.2 1.0 NE2 A:GLN258 3.5 50.0 1.0 CB D:ASP178 3.5 41.3 1.0 CG A:ASP145 3.5 45.9 1.0 OD2 A:ASP145 3.7 45.5 1.0 CB D:ASP175 3.8 38.8 1.0 CB A:GLN258 3.8 35.2 1.0 CG A:GLN258 4.0 38.1 1.0 OD2 D:ASP175 4.1 40.0 1.0 O A:HOH402 4.2 33.0 1.0 CA D:ASP178 4.3 42.7 1.0 OD2 D:ASP178 4.3 48.0 1.0 CG D:ASP175 4.4 39.0 1.0 CB D:ASP173 4.7 35.7 1.0 CD D:PRO179 4.9 35.4 1.0 CB A:ASP145 5.0 32.9 1.0

Calcium binding site 4 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:82.5 occ:1.00 OD1 E:ASP145 2.4 61.4 1.0 OE1 E:GLN258 2.8 44.8 1.0 CD E:GLN258 2.8 48.7 1.0 OD1 G:ASP178 2.9 59.4 1.0 OD2 G:ASP173 3.0 44.2 1.0 NE2 E:GLN258 3.1 46.8 1.0 CG E:ASP145 3.3 54.3 1.0 OD1 G:ASP173 3.5 54.0 1.0 CB E:GLN258 3.6 45.1 1.0 OD2 E:ASP145 3.6 51.5 1.0 CG G:ASP173 3.6 45.5 1.0 CG E:GLN258 3.6 39.2 1.0 CG G:ASP178 3.7 53.3 1.0 CB G:ASP178 4.0 50.5 1.0 CB G:ASP175 4.0 47.8 1.0 OD2 G:ASP175 4.3 47.2 1.0 CG G:ASP175 4.7 42.2 1.0 CB E:ASP145 4.7 38.2 1.0 OD2 G:ASP178 4.7 55.9 1.0 CA G:ASP178 4.7 54.1 1.0 CB G:ASP173 4.9 37.7 1.0 CA E:ASP145 5.0 35.2 1.0

Calcium binding site 5 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca402 b:93.3 occ:1.00 OE1 F:GLN258 2.1 65.2 1.0 OD1 E:ASP178 2.2 80.7 1.0 OD2 E:ASP173 2.6 52.6 1.0 CG E:ASP178 3.0 73.9 1.0 OD1 F:ASP145 3.0 52.1 1.0 CD F:GLN258 3.2 50.1 1.0 CG E:ASP173 3.4 46.8 1.0 CB E:ASP178 3.4 61.7 1.0 OD1 E:ASP173 3.6 48.6 1.0 CB E:ASP175 3.7 53.3 1.0 NE2 F:GLN258 3.7 49.7 1.0 CA E:ASP178 3.9 47.2 1.0 CG F:ASP145 4.0 43.7 1.0 OD2 E:ASP175 4.0 47.1 1.0 OD2 E:ASP178 4.1 56.2 1.0 CG E:ASP175 4.2 49.7 1.0 OD2 F:ASP145 4.2 45.9 1.0 CD E:PRO179 4.4 54.1 1.0 CG F:GLN258 4.4 41.0 1.0 CB F:GLN258 4.6 37.6 1.0 CB E:ASP173 4.7 39.0 1.0 N E:ASP178 4.8 49.1 1.0 CA E:ASP175 4.9 38.5 1.0 C E:ASP178 5.0 52.5 1.0 O E:ASP175 5.0 44.3 1.0

Calcium binding site 6 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:82.5 occ:1.00 CB F:ASP178 2.8 71.3 1.0 OE1 G:GLN258 2.8 69.1 1.0 OD1 G:ASP145 2.9 56.3 1.0 OD2 F:ASP175 3.3 53.5 1.0 OD2 F:ASP173 3.4 46.3 1.0 CG F:ASP178 3.4 83.5 1.0 CD G:GLN258 3.5 54.9 1.0 NE2 G:GLN258 3.5 50.7 1.0 CB F:ASP175 3.5 59.2 1.0 OD2 F:ASP178 3.6 84.0 1.0 CG G:ASP145 3.8 47.1 1.0 OD2 G:ASP145 3.8 41.4 1.0 CG F:ASP175 3.8 55.0 1.0 CA F:ASP178 4.2 58.9 1.0 OD1 F:ASP178 4.3 71.5 1.0 CG F:ASP173 4.3 50.2 1.0 OD1 F:ASP173 4.5 54.9 1.0 N F:ASP178 4.8 52.6 1.0 CG G:GLN258 4.8 45.3 1.0 OG G:SER261 4.8 49.1 1.0 CA F:ASP175 5.0 52.2 1.0 OD1 F:ASP175 5.0 51.6 1.0

Calcium binding site 7 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:77.1 occ:1.00 OD1 H:ASP145 2.4 47.1 1.0 OD1 J:ASP178 2.8 51.2 1.0 OE1 H:GLN258 2.8 52.9 1.0 OD2 J:ASP173 2.9 39.9 1.0 CD H:GLN258 3.0 48.7 1.0 OD1 J:ASP173 3.3 58.9 1.0 CG H:ASP145 3.3 44.1 1.0 NE2 H:GLN258 3.4 55.3 1.0 CG J:ASP173 3.4 42.9 1.0 OD2 H:ASP145 3.5 46.2 1.0 CG J:ASP178 3.5 50.9 1.0 CB H:GLN258 3.5 40.6 1.0 CG H:GLN258 3.7 38.0 1.0 CB J:ASP178 3.8 52.1 1.0 CB J:ASP175 3.9 53.6 1.0 OD2 J:ASP175 4.3 53.2 1.0 OD2 J:ASP178 4.5 61.0 1.0 CA J:ASP178 4.6 50.2 1.0 CG J:ASP175 4.6 49.4 1.0 CB H:ASP145 4.7 35.2 1.0 CB J:ASP173 4.8 34.8 1.0

Calcium binding site 8 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


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 Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca401 b:99.1 occ:1.00 OE1 I:GLN258 2.0 58.4 1.0 OD1 I:ASP145 2.4 51.0 1.0 CD I:GLN258 2.9 51.6 1.0 OD1 H:ASP178 3.0 70.2 1.0 OD2 H:ASP173 3.0 49.0 1.0 NE2 I:GLN258 3.3 54.6 1.0 CG I:ASP145 3.5 38.6 1.0 CB H:ASP175 3.5 47.0 1.0 OD1 H:ASP173 3.6 52.8 1.0 CG H:ASP173 3.7 51.3 1.0 OD2 H:ASP175 3.8 51.1 1.0 CG H:ASP178 3.8 60.7 1.0 OD2 I:ASP145 3.9 46.0 1.0 CB H:ASP178 4.1 56.2 1.0 CG H:ASP175 4.1 48.0 1.0 CG I:GLN258 4.2 38.0 1.0 CA H:ASP178 4.5 51.0 1.0 CB I:GLN258 4.5 37.9 1.0 CB I:ASP145 4.8 30.5 1.0 OD2 H:ASP178 4.8 54.3 1.0 CA H:ASP175 4.9 38.8 1.0 CD H:PRO179 5.0 50.9 1.0

Calcium binding site 9 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca402 b:91.9 occ:1.00 OD1 J:ASP145 2.9 60.7 1.0 OD2 I:ASP175 2.9 73.4 1.0 CB I:ASP178 3.0 67.9 1.0 OE1 J:GLN258 3.2 50.9 1.0 CB I:ASP175 3.5 52.5 1.0 NE2 J:GLN258 3.5 46.8 1.0 CG I:ASP175 3.6 56.8 1.0 CD J:GLN258 3.6 50.8 1.0 CG I:ASP178 3.8 82.4 1.0 CG J:ASP145 3.8 46.3 1.0 OD2 I:ASP173 3.9 49.6 1.0 OD2 J:ASP145 4.0 41.0 1.0 OD2 I:ASP178 4.0 81.2 1.0 CA I:ASP178 4.2 57.8 1.0 OD1 I:ASP178 4.7 73.9 1.0 CG I:ASP173 4.7 56.3 1.0 OG J:SER261 4.7 42.9 1.0 N I:ASP178 4.7 58.1 1.0 OD1 I:ASP175 4.7 50.4 1.0 OD1 I:ASP173 4.9 56.0 1.0 CA I:ASP175 5.0 48.8 1.0

Calcium binding site 10 out of 15 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca401 b:78.0 occ:1.00 OD1 K:ASP145 2.6 50.6 1.0 OE1 K:GLN258 2.6 54.3 1.0 OD1 M:ASP178 2.7 58.5 1.0 CD K:GLN258 2.8 48.7 1.0 OD2 M:ASP173 3.1 43.8 1.0 NE2 K:GLN258 3.2 53.7 1.0 CG K:ASP145 3.5 45.5 1.0 CG M:ASP178 3.6 55.3 1.0 OD1 M:ASP173 3.6 52.7 1.0 CB K:GLN258 3.6 40.5 1.0 CG M:ASP173 3.7 40.1 1.0 CG K:GLN258 3.7 38.9 1.0 OD2 K:ASP145 3.8 34.1 1.0 CB M:ASP178 3.9 51.3 1.0 CB M:ASP175 4.1 42.3 1.0 OD2 M:ASP175 4.3 48.1 1.0 OD2 M:ASP178 4.6 55.9 1.0 CA M:ASP178 4.6 47.7 1.0 CG M:ASP175 4.7 44.2 1.0 CB K:ASP145 4.9 34.7 1.0 CD M:PRO179 4.9 37.1 1.0 CB M:ASP173 5.0 36.6 1.0

M.Li, K.Kakani, U.Katpally, S.Johnson, D.Rochon, T.J.Smith. Atomic Structure of Cucumber Necrosis Virus and the Role of the Capsid in Vector Transmission. J.Virol. V. 87 12166 2013.
ISSN: ISSN 0022-538X
PubMed: 24006433
DOI: 10.1128/JVI.01965-13