Calcium in PDB 3avx: Structure of Viral Rna Polymerase Complex 5

The structure of Structure of Viral Rna Polymerase Complex 5, PDB code: 3avx 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)	19.93 / 2.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.310, 256.580, 101.590, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.6

The binding sites of Calcium atom in the Structure of Viral Rna Polymerase Complex 5 (pdb code 3avx). 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 5, PDB code: 3avx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Viral Rna Polymerase Complex 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:42.7 occ:1.00 O A:LEU969 2.3 40.1 1.0 O1A A:GH32501 2.5 46.4 1.0 OD1 A:ASP1053 2.5 46.8 1.0 O1G A:GH32501 2.5 47.9 1.0 O2B A:GH32501 2.5 44.6 1.0 OD2 A:ASP968 2.7 56.3 1.0 OD1 A:ASP968 3.1 55.3 1.0 CG A:ASP968 3.2 53.3 1.0 CG A:ASP1053 3.3 43.7 1.0 C A:LEU969 3.5 41.3 1.0 PB A:GH32501 3.5 43.0 1.0 OD2 A:ASP1053 3.5 46.4 1.0 PG A:GH32501 3.7 44.1 1.0 PA A:GH32501 3.7 54.9 1.0 N A:LEU969 3.9 35.2 1.0 O3B A:GH32501 3.9 42.1 1.0 O3A A:GH32501 3.9 42.0 1.0 CA A:LEU969 4.2 39.9 1.0 O5' A:GH32501 4.3 36.3 1.0 C5' A:GH32501 4.4 43.9 1.0 O A:SER970 4.4 50.9 1.0 N A:SER970 4.5 48.1 1.0 N A:ALA972 4.5 38.1 1.0 C A:ASP968 4.5 34.9 1.0 CB A:ASP968 4.5 43.2 1.0 CB A:ALA972 4.5 42.2 1.0 C A:SER970 4.6 47.0 1.0 O3G A:GH32501 4.6 43.3 1.0 CA A:SER970 4.6 46.7 1.0 CB A:ASP1053 4.6 38.6 1.0 O2G A:GH32501 4.7 52.7 1.0 CA A:ASP968 4.8 41.1 1.0 O1B A:GH32501 4.8 41.2 1.0 CB A:LEU969 4.9 36.6 1.0 O2A A:GH32501 4.9 48.6 1.0

Calcium binding site 2 out of 2 in the Structure of Viral Rna Polymerase Complex 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3002 b:80.0 occ:1.00 OE2 A:GLU1089 2.8 58.3 1.0 OD2 A:ASP1054 2.8 46.3 1.0 OD2 A:ASP968 3.0 56.3 1.0 CG A:ASP1054 3.8 46.4 1.0 CB A:ASP968 3.8 43.2 1.0 CG A:ASP968 3.8 53.3 1.0 CD A:GLU1089 4.0 60.5 1.0 OD2 A:ASP1053 4.2 46.4 1.0 CA A:ASP1054 4.3 35.0 1.0 O A:VAL967 4.4 39.6 1.0 NZ A:LYS1080 4.4 69.3 1.0 CB A:ASP1054 4.4 41.9 1.0 CA A:ASP968 4.5 41.1 1.0 CE A:LYS1080 4.6 74.3 1.0 OD1 A:ASP1054 4.6 51.2 1.0 O A:ASP1053 4.7 37.4 1.0 O A:HOH3524 4.7 32.8 1.0 OP1 G:C2009 4.7 61.8 1.0 C5' G:C2009 4.8 48.5 1.0 N A:ASP1054 4.8 33.0 1.0 OE1 A:GLU1089 4.9 53.6 1.0 C A:ASP1053 5.0 33.8 1.0 CG A:GLU1089 5.0 46.7 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