Calcium in PDB 3avt: Structure of Viral Rna Polymerase Complex 1

The structure of Structure of Viral Rna Polymerase Complex 1, PDB code: 3avt 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 / 2.61
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.120, 255.990, 101.370, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28.8

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

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3001 b:59.6 occ:1.00 O A:LEU969 2.5 37.6 1.0 O3A A:GH32502 2.7 72.4 1.0 OD1 A:ASP968 2.8 50.3 1.0 O2G A:GH32502 2.8 61.2 1.0 OD2 A:ASP968 3.0 50.9 1.0 CG A:ASP968 3.2 47.5 1.0 OD2 A:ASP1053 3.2 38.0 1.0 O3B A:GH32502 3.2 71.8 1.0 PB A:GH32502 3.4 77.0 1.0 OD1 A:ASP1053 3.5 55.0 1.0 PG A:GH32502 3.5 80.1 1.0 CA A:CA3002 3.6 69.6 1.0 C A:LEU969 3.7 39.9 1.0 CG A:ASP1053 3.7 44.6 1.0 O A:SER970 3.8 64.2 1.0 PA A:GH32502 3.8 76.9 1.0 O5' A:GH32502 3.9 67.2 1.0 O2B A:GH32502 4.0 57.4 1.0 O1G A:GH32502 4.1 76.7 1.0 O1A A:GH32502 4.2 82.0 1.0 N A:LEU969 4.3 41.3 1.0 CB A:ASP968 4.6 45.4 1.0 CA A:LEU969 4.6 36.7 1.0 N A:SER970 4.6 45.1 1.0 C A:SER970 4.7 56.0 1.0 CA A:SER970 4.7 48.4 1.0 C A:ASP968 4.7 36.5 1.0 C5' A:GH32502 4.8 72.5 1.0 O1B A:GH32502 4.8 78.9 1.0 O3G A:GH32502 4.8 68.7 1.0 CA A:ASP968 4.9 36.4 1.0 CB A:ALA972 5.0 47.9 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3002 b:69.6 occ:1.00 OD2 A:ASP968 2.5 50.9 1.0 OD2 A:ASP1054 2.9 55.9 1.0 C3' T:GH32501 3.1 76.7 1.0 OD1 A:ASP1053 3.2 55.0 1.0 CA A:CA3001 3.6 59.6 1.0 CG A:ASP968 3.7 47.5 1.0 C5' T:GH32501 3.7 80.8 1.0 C4' T:GH32501 3.8 75.6 1.0 CG A:ASP1054 3.8 49.5 1.0 O1A A:GH32502 3.8 82.0 1.0 O5' T:GH32501 3.9 92.9 1.0 CG A:ASP1053 4.0 44.6 1.0 OD2 A:ASP1053 4.2 38.0 1.0 OD1 A:ASP968 4.4 50.3 1.0 O5' A:GH32502 4.4 67.2 1.0 OE2 A:GLU1089 4.4 51.9 1.0 OD1 A:ASP1054 4.4 48.4 1.0 C2' T:GH32501 4.4 83.2 1.0 PA A:GH32502 4.5 76.9 1.0 N A:ASP1054 4.5 32.4 1.0 CA A:ASP1054 4.5 33.6 1.0 CB A:ASP1054 4.6 36.3 1.0 O A:ASP1053 4.7 32.5 1.0 CB A:ASP968 4.7 45.4 1.0 O3A A:GH32502 4.7 72.4 1.0 C A:ASP1053 4.7 28.1 1.0 O2' T:GH32501 4.8 66.0 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