Calcium in PDB 1qhd: Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus

The structure of Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus, PDB code: 1qhd was solved by M.Mathieu, I.Petitpas, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.00 / 1.95
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	157.780, 157.780, 157.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22

The structure of Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus (pdb code 1qhd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus, PDB code: 1qhd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus


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 VP6, the Major Capsid Protein of Group A Rotavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:39.3 occ:0.33 O A:HOH874 2.0 77.4 1.0 O A:HOH890 2.6 35.6 0.3 O A:HOH766 3.3 60.6 1.0 O A:HOH873 4.2 89.6 1.0 O A:HOH889 4.4 88.8 1.0 CG A:PRO235 4.4 26.4 1.0 OD1 A:ASN250 4.5 29.7 1.0 O A:HOH686 4.9 33.0 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus


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 VP6, the Major Capsid Protein of Group A Rotavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:32.5 occ:0.50 O A:HOH794 1.4 41.6 1.0 OD1 A:ASN266 2.2 24.8 1.0 OD2 A:ASP286 2.4 32.3 1.0 CG A:ASN266 3.4 20.1 1.0 CG A:ASP286 3.5 22.8 1.0 N A:ASN266 4.2 20.9 1.0 ND2 A:ASN266 4.2 19.6 1.0 CA A:ASN266 4.2 23.0 1.0 CB A:ASP286 4.3 20.4 1.0 CB A:ASN266 4.3 22.0 1.0 OD1 A:ASP286 4.4 25.7 1.0 O A:HOH800 4.6 47.7 1.0 CD1 A:LEU265 4.9 17.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus


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 VP6, the Major Capsid Protein of Group A Rotavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:34.6 occ:1.00 O A:HOH767 2.2 46.6 1.0 O A:HOH845 2.3 65.8 1.0 O A:HOH668 2.3 28.4 1.0 OE2 A:GLU379 2.5 20.5 1.0 O A:HOH652 3.0 28.0 1.0 O A:HOH789 3.1 72.9 1.0 CD A:GLU379 3.3 19.4 1.0 OE1 A:GLU379 3.8 22.3 1.0 O A:HOH620 4.0 18.6 1.0 CG A:GLU379 4.2 19.2 1.0 OG A:SER333 4.3 16.9 1.0 OE1 A:GLN383 4.6 22.7 1.0 O A:GLU332 4.7 22.1 1.0 OD1 A:ASP380 4.7 28.8 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus


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 VP6, the Major Capsid Protein of Group A Rotavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:51.4 occ:1.00 OE1 A:GLN47 2.6 34.2 1.0 O A:HOH783 2.6 62.8 1.0 O A:HOH681 2.7 32.5 1.0 CD A:GLN47 3.6 30.1 1.0 NE2 A:GLN47 4.0 31.1 1.0 ND2 A:ASN58 4.2 30.0 1.0 OD1 A:ASN58 4.8 29.2 1.0 CG A:GLN47 4.9 26.9 1.0 CG A:ASN58 4.9 24.2 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of VP6, the Major Capsid Protein of Group A Rotavirus


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 VP6, the Major Capsid Protein of Group A Rotavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:73.5 occ:1.00 OE2 A:GLU340 2.1 50.9 1.0 O A:HOH628 2.4 22.3 1.0 O A:THR151 2.4 17.8 1.0 O A:HOH886 2.5 0.0 1.0 O A:HOH847 3.2 52.0 1.0 CD A:GLU340 3.2 44.5 1.0 C A:THR151 3.6 17.8 1.0 CG A:GLU340 3.8 34.5 1.0 O A:HOH710 3.9 30.2 1.0 OD2 A:ASP337 4.1 16.7 1.0 CA A:PHE152 4.3 16.6 1.0 OE1 A:GLU340 4.3 47.6 1.0 N A:PHE152 4.4 16.3 1.0 CD1 A:PHE152 4.5 15.1 1.0 OE1 A:GLU134 4.5 51.2 1.0 CA A:THR151 4.6 17.5 1.0 O A:HOH872 4.6 94.3 1.0 CB A:THR151 4.7 18.6 1.0 N A:THR151 4.8 17.4 1.0

M.Mathieu, I.Petitpas, J.Navaza, J.Lepault, E.Kohli, P.Pothier, B.V.Prasad, J.Cohen, F.A.Rey. Atomic Structure of the Major Capsid Protein of Rotavirus: Implications For the Architecture of the Virion. Embo J. V. 20 1485 2001.
ISSN: ISSN 0261-4189
PubMed: 11285213
DOI: 10.1093/EMBOJ/20.7.1485