Calcium in PDB 3vnv: Complex Structure of Viral Rna Polymerase II

The structure of Complex Structure of Viral Rna Polymerase II, PDB code: 3vnv 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)	19.94 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.730, 256.040, 101.720, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.9

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Structure of Viral Rna Polymerase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2502 b:31.9 occ:1.00 O A:LEU969 2.3 30.6 1.0 O3G A:CH12501 2.5 43.1 1.0 O2A A:CH12501 2.6 49.4 1.0 O2B A:CH12501 2.6 35.6 1.0 OD2 A:ASP968 2.7 38.6 1.0 OD2 A:ASP1053 2.7 30.7 1.0 O3A A:CH12501 3.2 48.6 1.0 OD1 A:ASP968 3.3 44.3 1.0 CG A:ASP968 3.3 35.8 1.0 PB A:CH12501 3.3 43.0 1.0 CG A:ASP1053 3.4 31.1 1.0 OD1 A:ASP1053 3.5 33.4 1.0 PA A:CH12501 3.5 42.4 1.0 C A:LEU969 3.5 32.4 1.0 PG A:CH12501 3.7 53.2 1.0 O3B A:CH12501 3.8 46.4 1.0 O A:SER970 3.9 45.2 1.0 O5' A:CH12501 4.1 43.2 1.0 N A:LEU969 4.1 28.4 1.0 CA A:CA2503 4.3 53.6 1.0 CB A:ALA972 4.4 38.9 1.0 C A:SER970 4.4 40.5 1.0 CA A:LEU969 4.4 30.0 1.0 N A:SER970 4.4 39.7 1.0 CA A:SER970 4.5 36.3 1.0 O2G A:CH12501 4.6 41.8 1.0 C5' A:CH12501 4.6 44.9 1.0 CB A:ASP968 4.6 31.2 1.0 O1B A:CH12501 4.6 42.6 1.0 N A:ALA972 4.7 31.6 1.0 O1G A:CH12501 4.7 48.6 1.0 CB A:ASP1053 4.7 32.5 1.0 O1A A:CH12501 4.7 44.1 1.0 C A:ASP968 4.8 28.6 1.0 CA A:ASP968 5.0 27.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Structure of Viral Rna Polymerase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2503 b:53.6 occ:1.00 OD2 A:ASP1054 2.7 50.6 1.0 O3' G:C2007 2.7 58.4 1.0 OD2 A:ASP968 2.7 38.6 1.0 OD1 A:ASP1053 2.9 33.4 1.0 CG A:ASP1054 3.3 42.8 1.0 O2A A:CH12501 3.4 49.4 1.0 OD1 A:ASP1054 3.8 43.4 1.0 CG A:ASP1053 3.8 31.1 1.0 CG A:ASP968 3.8 35.8 1.0 C3' G:C2007 4.1 60.9 1.0 OD2 A:ASP1053 4.1 30.7 1.0 O A:ASP1053 4.2 30.7 1.0 N A:ASP1054 4.2 28.2 1.0 CA A:ASP1054 4.2 28.1 1.0 CB A:ASP968 4.2 31.2 1.0 CA A:CA2502 4.3 31.9 1.0 C A:ASP1053 4.3 27.5 1.0 CB A:ASP1054 4.3 32.1 1.0 C4' G:C2007 4.8 55.5 1.0 PA A:CH12501 4.8 42.4 1.0 CA A:ASP968 4.8 27.6 1.0 OE2 A:GLU1089 4.8 66.0 1.0 OD1 A:ASP968 4.9 44.3 1.0

D.Takeshita, S.Yamashita, K.Tomita. Mechanism For Template-Independent Terminal Adenylation Activity of Q Beta Replicase Structure V. 20 1661 2012.
ISSN: ISSN 0969-2126
PubMed: 22884418
DOI: 10.1016/J.STR.2012.07.004