Calcium in PDB 4rfu: Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A

The structure of Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A, PDB code: 4rfu was solved by N.C.Chen, C.J.Chen, M.Yoshimura, H.H.Guan, T.Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.76 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.982, 83.458, 85.577, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 18.1

The binding sites of Calcium atom in the Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A (pdb code 4rfu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A, PDB code: 4rfu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A


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 Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:8.1 occ:1.00 O A:VAL61 2.3 8.6 1.0 OD1 A:ASP62 2.3 9.3 1.0 O B:HOH301 2.4 8.2 1.0 OD2 C:ASP60 2.4 10.5 1.0 OD2 A:ASP60 2.5 9.8 1.0 OD1 A:ASP60 2.5 10.4 1.0 O C:HOH301 2.5 8.4 1.0 OD1 C:ASP60 2.6 10.1 1.0 CG A:ASP60 2.8 9.0 1.0 CG C:ASP60 2.9 9.1 1.0 C A:VAL61 3.3 8.1 1.0 CG A:ASP62 3.5 8.3 1.0 CA B:CA201 3.7 8.0 1.0 N A:ASP62 4.0 7.8 1.0 O C:VAL61 4.0 10.9 1.0 O A:HOH312 4.1 12.5 1.0 N A:VAL61 4.1 8.1 1.0 OD2 A:ASP62 4.2 9.3 1.0 CA A:ASP62 4.2 8.1 1.0 CB A:ASP60 4.3 10.1 1.0 CA A:VAL61 4.3 8.4 1.0 O B:HOH319 4.3 12.1 1.0 OD1 B:ASP62 4.4 9.3 1.0 CB C:ASP60 4.4 10.7 1.0 CB A:ASP62 4.4 8.5 1.0 O A:HOH370 4.5 19.7 1.0 C A:ASP60 4.6 8.5 1.0 OD2 B:ASP60 4.6 12.7 1.0 OD1 B:ASP60 4.7 10.3 1.0 N C:VAL61 4.8 9.8 1.0 O B:HOH335 4.8 13.9 1.0 O A:HOH309 4.8 9.6 1.0 O B:HOH442 4.9 21.5 1.0 CA A:ASP60 5.0 9.1 1.0 C C:VAL61 5.0 9.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A


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 Truncated P-Domain From Grouper Nervous Necrosis Virus Capsid Protein at 1.2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:8.0 occ:1.00 OD1 C:ASP60 2.3 10.1 1.0 O B:VAL61 2.3 8.5 1.0 OD1 B:ASP60 2.4 10.3 1.0 OD1 C:ASP62 2.4 9.0 1.0 O C:HOH304 2.4 9.7 1.0 O B:HOH301 2.5 8.2 1.0 O C:HOH301 2.5 8.4 1.0 CG B:ASP60 3.4 10.8 1.0 C B:VAL61 3.4 7.8 1.0 CG C:ASP62 3.4 9.2 1.0 CG C:ASP60 3.5 9.1 1.0 N B:VAL61 3.6 9.2 1.0 CA A:CA201 3.7 8.1 1.0 OD2 C:ASP62 3.8 9.9 1.0 OD2 B:ASP60 3.9 12.7 1.0 CA B:VAL61 4.0 8.9 1.0 OD1 B:ASP62 4.1 9.3 1.0 O C:HOH321 4.2 12.3 1.0 OD2 C:ASP60 4.4 10.5 1.0 CB C:ASP60 4.4 10.7 1.0 CB B:VAL61 4.4 9.4 1.0 O C:VAL61 4.4 10.9 1.0 C B:ASP60 4.4 9.9 1.0 O B:HOH319 4.5 12.1 1.0 N B:ASP62 4.6 8.1 1.0 CB B:ASP60 4.7 10.3 1.0 O C:HOH381 4.7 24.6 1.0 CA B:ASP60 4.7 10.1 1.0 CB C:ASP62 4.8 9.8 1.0 O A:VAL61 4.8 8.6 1.0 CG B:ASP62 4.9 8.9 1.0 OD1 A:ASP60 4.9 10.4 1.0 C C:VAL61 4.9 9.2 1.0 CA B:ASP62 5.0 7.6 1.0 CA C:ASP62 5.0 9.2 1.0

N.C.Chen, M.Yoshimura, H.H.Guan, T.Y.Wang, Y.Misumi, C.C.Lin, P.Chuankhayan, A.Nakagawa, S.I.Chan, T.Tsukihara, T.Y.Chen, C.J.Chen. Crystal Structures of A Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection Plos Pathog. V. 11 05203 2015.
ISSN: ISSN 1553-7366
PubMed: 26491970
DOI: 10.1371/JOURNAL.PPAT.1005203