Calcium in PDB 1f2n: Rice Yellow Mottle Virus

The structure of Rice Yellow Mottle Virus, PDB code: 1f2n was solved by C.Qu, L.Liljas, N.Opalka, C.Brugidou, M.Yeager, R.N.Beachy, C.M.Fauquet, J.E.Johnson, T.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	283.500, 401.800, 284.000, 90.00, 89.40, 90.00
R / Rfree (%)	21.8 / 21.9

The binding sites of Calcium atom in the Rice Yellow Mottle Virus (pdb code 1f2n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Rice Yellow Mottle Virus, PDB code: 1f2n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Rice Yellow Mottle Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rice Yellow Mottle Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:18.5 occ:1.00 O B:VAL182 2.4 21.4 1.0 OD2 A:ASP126 2.4 30.5 1.0 O B:THR238 2.5 23.8 1.0 OD1 A:ASP129 2.5 28.9 1.0 OD1 B:ASN237 2.6 19.9 1.0 CG A:ASP129 3.2 26.7 1.0 OD2 A:ASP129 3.3 26.2 1.0 CG A:ASP126 3.3 22.4 1.0 C B:VAL182 3.6 18.2 1.0 CG B:ASN237 3.6 17.8 1.0 CB A:ASP126 3.6 18.7 1.0 C B:THR238 3.7 32.7 1.0 N B:THR238 3.7 28.0 1.0 CA B:THR183 4.3 24.6 1.0 ND2 B:ASN237 4.3 16.4 1.0 CA B:THR238 4.3 29.7 1.0 C B:ASN237 4.4 22.5 1.0 N B:THR183 4.4 23.6 1.0 CA B:ASN237 4.4 19.6 1.0 OD1 A:ASP126 4.5 26.6 1.0 CB A:ASP129 4.6 22.3 1.0 CA B:VAL182 4.6 10.7 1.0 CB B:ASN237 4.6 20.5 1.0 OXT B:THR238 4.6 33.7 1.0 O B:SER96 4.7 26.3 1.0 N B:VAL182 4.7 15.9 1.0 N A:ASP129 4.7 21.7 1.0 CB B:VAL182 4.8 4.5 1.0 CA A:ASP129 4.9 22.5 1.0 CG1 B:VAL182 5.0 2.6 1.0 CG2 B:THR183 5.0 22.2 1.0

Calcium binding site 2 out of 3 in the Rice Yellow Mottle Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rice Yellow Mottle Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:17.1 occ:1.00 O C:VAL182 2.4 17.2 1.0 OD1 B:ASP129 2.5 34.3 1.0 OD2 B:ASP126 2.5 27.4 1.0 O C:THR238 2.5 21.5 1.0 OD1 C:ASN237 2.6 23.9 1.0 CG B:ASP129 3.3 26.5 1.0 CG B:ASP126 3.4 21.6 1.0 OD2 B:ASP129 3.5 31.2 1.0 CG C:ASN237 3.5 20.9 1.0 N C:THR238 3.6 28.0 1.0 C C:VAL182 3.6 15.0 1.0 CB B:ASP126 3.6 19.5 1.0 C C:THR238 3.7 31.4 1.0 ND2 C:ASN237 4.1 22.9 1.0 CA C:ASN237 4.2 22.4 1.0 C C:ASN237 4.3 24.1 1.0 CA C:THR238 4.3 28.1 1.0 CA C:THR183 4.4 23.7 1.0 CB C:ASN237 4.4 20.6 1.0 N C:THR183 4.5 21.5 1.0 OD1 B:ASP126 4.5 26.5 1.0 CA C:VAL182 4.5 11.9 1.0 N C:VAL182 4.6 18.7 1.0 CB B:ASP129 4.6 22.2 1.0 N B:ASP129 4.6 24.3 1.0 CB C:VAL182 4.7 9.0 1.0 OXT C:THR238 4.7 31.0 1.0 O C:SER96 4.7 28.9 1.0 CA B:ASP129 4.8 20.2 1.0 CG1 C:VAL182 4.9 2.1 1.0 CB B:ALA128 4.9 28.0 1.0

Calcium binding site 3 out of 3 in the Rice Yellow Mottle Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rice Yellow Mottle Virus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:21.9 occ:1.00 O A:VAL182 2.4 17.1 1.0 O A:THR238 2.4 24.1 1.0 OD2 C:ASP126 2.4 25.1 1.0 OD1 A:ASN237 2.5 21.1 1.0 OD1 C:ASP129 2.5 27.5 1.0 CG C:ASP129 3.2 25.1 1.0 OD2 C:ASP129 3.2 28.6 1.0 CG C:ASP126 3.4 22.8 1.0 CG A:ASN237 3.5 19.3 1.0 C A:VAL182 3.6 18.3 1.0 C A:THR238 3.6 34.1 1.0 CB C:ASP126 3.6 19.6 1.0 N A:THR238 3.7 32.8 1.0 ND2 A:ASN237 4.0 17.9 1.0 CA A:THR238 4.3 31.3 1.0 C A:ASN237 4.4 26.3 1.0 O A:SER96 4.4 25.6 1.0 N A:VAL182 4.4 16.7 1.0 CA A:ASN237 4.4 23.7 1.0 CA A:THR183 4.5 21.8 1.0 CA A:VAL182 4.5 13.3 1.0 N A:THR183 4.5 22.7 1.0 OXT A:THR238 4.5 35.1 1.0 OD1 C:ASP126 4.6 30.8 1.0 CB A:ASN237 4.6 20.1 1.0 CB C:ASP129 4.6 19.0 1.0 CB A:VAL182 4.6 10.5 1.0 N C:ASP129 4.9 20.0 1.0 OG A:SER96 4.9 44.1 1.0 CA C:ASP129 5.0 16.5 1.0 CG1 A:VAL182 5.0 8.4 1.0

C.Qu, L.Liljas, N.Opalka, C.Brugidou, M.Yeager, R.N.Beachy, C.M.Fauquet, J.E.Johnson, T.Lin. 3D Domain Swapping Modulates the Stability of Members of An Icosahedral Virus Group. Structure Fold.Des. V. 8 1095 2000.
ISSN: ISSN 0969-2126
PubMed: 11080631
DOI: 10.1016/S0969-2126(00)00508-6