Calcium in PDB 3avy: Structure of Viral Rna Polymerase Complex 6

The structure of Structure of Viral Rna Polymerase Complex 6, PDB code: 3avy was solved by D.Takeshita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.62
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	140.070, 257.220, 101.310, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.2

The binding sites of Calcium atom in the Structure of Viral Rna Polymerase Complex 6 (pdb code 3avy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Viral Rna Polymerase Complex 6, PDB code: 3avy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Viral Rna Polymerase Complex 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Viral Rna Polymerase Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:42.7 occ:1.00 O A:LEU969 2.5 30.9 1.0 O2G A:CH12501 2.7 53.1 1.0 OD2 A:ASP968 2.7 43.8 1.0 OD1 A:ASP1053 2.7 34.6 1.0 OD1 A:ASP968 2.9 40.4 1.0 O3A A:CH12501 3.0 52.9 1.0 O1A A:CH12501 3.0 52.2 1.0 CG A:ASP968 3.1 41.9 1.0 CG A:ASP1053 3.4 32.2 1.0 PB A:CH12501 3.4 64.4 1.0 OD2 A:ASP1053 3.5 36.9 1.0 O2B A:CH12501 3.5 33.2 1.0 O3B A:CH12501 3.5 55.2 1.0 C A:LEU969 3.6 30.9 1.0 PA A:CH12501 3.6 50.2 1.0 PG A:CH12501 3.7 65.2 1.0 O A:SER970 3.7 54.0 1.0 CA A:CA3002 3.8 46.7 1.0 N A:LEU969 4.0 29.7 1.0 CA A:LEU969 4.4 29.5 1.0 O5' A:CH12501 4.4 57.9 1.0 CB A:ASP968 4.5 36.8 1.0 CB A:ALA972 4.6 29.4 1.0 N A:SER970 4.6 37.6 1.0 C A:SER970 4.6 42.6 1.0 CA A:SER970 4.6 38.2 1.0 O3G A:CH12501 4.7 50.9 1.0 O1G A:CH12501 4.7 47.3 1.0 C A:ASP968 4.7 26.1 1.0 C5' A:CH12501 4.8 55.3 1.0 CA A:ASP968 4.8 27.3 1.0 O2A A:CH12501 4.8 60.5 1.0 CB A:ASP1053 4.9 23.8 1.0 O1B A:CH12501 4.9 61.4 1.0

Calcium binding site 2 out of 2 in the Structure of Viral Rna Polymerase Complex 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Viral Rna Polymerase Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3002 b:46.7 occ:1.00 OD2 A:ASP968 2.8 43.8 1.0 O1A A:CH12501 2.8 52.2 1.0 OD2 A:ASP1053 2.8 36.9 1.0 OD1 A:ASP1054 3.1 44.5 1.0 C3' G:U2013 3.1 70.7 1.0 CG A:ASP1054 3.5 41.9 1.0 CG A:ASP1053 3.6 32.2 1.0 CA A:CA3001 3.8 42.7 1.0 OD2 A:ASP1054 3.8 50.9 1.0 OD1 A:ASP1053 3.8 34.6 1.0 C4' G:U2013 3.9 68.2 1.0 N A:ASP1054 3.9 22.3 1.0 CG A:ASP968 4.0 41.9 1.0 C A:ASP1053 4.1 24.1 1.0 PA A:CH12501 4.2 50.2 1.0 C5' G:U2013 4.2 64.2 1.0 CA A:ASP1054 4.2 23.2 1.0 C2' G:U2013 4.2 61.0 1.0 O A:ASP1053 4.2 24.1 1.0 O2' G:U2013 4.3 45.4 1.0 CB A:ASP1054 4.3 25.7 1.0 OP1 G:U2013 4.5 71.2 1.0 O2A A:CH12501 4.6 60.5 1.0 O5' G:U2013 4.8 81.3 1.0 OE2 A:GLU1089 4.8 44.0 1.0 O3A A:CH12501 4.8 52.9 1.0 CB A:ASP1053 4.8 23.8 1.0 OD1 A:ASP968 4.8 40.4 1.0 CA A:ASP1053 4.9 21.6 1.0 CB A:ASP968 4.9 36.8 1.0

D.Takeshita, K.Tomita. Molecular Basis For Rna Polymerization By Q Beta Replicase Nat.Struct.Mol.Biol. V. 19 229 2012.
ISSN: ISSN 1545-9993
PubMed: 22245970
DOI: 10.1038/NSMB.2204