Calcium in PDB 3avv: Structure of Viral Rna Polymerase Complex 3

The structure of Structure of Viral Rna Polymerase Complex 3, PDB code: 3avv 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)	20.00 / 3.12
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	138.990, 255.090, 101.060, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 29.8

The binding sites of Calcium atom in the Structure of Viral Rna Polymerase Complex 3 (pdb code 3avv). 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 3, PDB code: 3avv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Viral Rna Polymerase Complex 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:65.1 occ:1.00 O A:LEU969 2.9 42.5 1.0 OD2 A:ASP968 3.1 55.8 1.0 OP1 G:U2008 3.5 71.1 1.0 OD1 A:ASP968 3.5 52.5 1.0 OD2 A:ASP1053 3.6 53.4 1.0 O A:SER970 3.6 65.1 1.0 CG A:ASP968 3.7 55.3 1.0 O5' G:U2008 3.7 63.9 1.0 C5' G:U2008 3.8 66.2 1.0 C A:LEU969 4.0 48.1 1.0 P G:U2008 4.1 81.7 1.0 CA A:SER970 4.3 46.0 1.0 C A:SER970 4.3 55.4 1.0 OP2 G:U2008 4.5 63.1 1.0 N A:SER970 4.6 45.0 1.0 NZ A:LYS908 4.6 50.8 1.0 CG A:ASP1053 4.8 56.9 1.0 CA A:CA3002 4.8 45.8 1.0

Calcium binding site 2 out of 2 in the Structure of Viral Rna Polymerase Complex 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3002 b:45.8 occ:1.00 OP1 G:U2008 2.6 71.1 1.0 OD2 A:ASP1053 3.0 53.4 1.0 OD2 A:ASP968 3.1 55.8 1.0 OD2 A:ASP1054 3.3 47.0 1.0 CG A:ASP968 3.6 55.3 1.0 CG A:ASP1054 3.6 52.7 1.0 P G:U2008 3.6 81.7 1.0 CG A:ASP1053 3.6 56.9 1.0 O3' G:A2007 3.6 71.4 1.0 CB A:ASP968 3.7 47.8 1.0 CA A:ASP968 3.8 50.2 1.0 OD1 A:ASP1054 3.9 50.6 1.0 O5' G:U2008 4.0 63.9 1.0 N A:ASP1054 4.1 47.7 1.0 CB A:ASP1053 4.1 53.5 1.0 CA A:ASP1054 4.1 43.1 1.0 C A:ASP1053 4.2 49.0 1.0 O A:ASP1053 4.2 49.6 1.0 OD1 A:ASP1053 4.3 51.7 1.0 CB A:ASP1054 4.4 44.8 1.0 O A:VAL967 4.4 41.4 1.0 OD1 A:ASP968 4.5 52.5 1.0 N A:LEU969 4.6 46.5 1.0 N A:ASP968 4.8 49.6 1.0 C A:ASP968 4.8 45.0 1.0 CA A:CA3001 4.8 65.1 1.0 CA A:ASP1053 4.8 39.6 1.0 C3' G:A2007 4.9 64.8 1.0 OP2 G:U2008 5.0 63.1 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