Calcium in PDB 3vnu: Complex Structure of Viral Rna Polymerase I

The structure of Complex Structure of Viral Rna Polymerase I, PDB code: 3vnu 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 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.005, 255.506, 101.425, 90.00, 90.00, 90.00
R / Rfree (%)	27.4 / 31.6

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

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


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 I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2502 b:52.4 occ:1.00 OD1 A:ASP968 2.5 60.1 1.0 O2A A:ATP2501 2.5 64.3 1.0 O2B A:ATP2501 2.6 70.8 1.0 O A:LEU969 2.7 70.0 1.0 OD2 A:ASP1053 2.9 62.3 1.0 O2G A:ATP2501 3.0 83.5 1.0 CG A:ASP1053 3.1 64.1 1.0 CG A:ASP968 3.1 58.6 1.0 O3B A:ATP2501 3.2 72.9 1.0 OD1 A:ASP1053 3.3 68.7 1.0 OD2 A:ASP968 3.3 59.4 1.0 PB A:ATP2501 3.3 65.4 1.0 C A:LEU969 3.3 61.5 1.0 N A:LEU969 3.6 55.6 1.0 PG A:ATP2501 3.7 78.9 1.0 PA A:ATP2501 3.8 66.7 1.0 O3A A:ATP2501 3.9 64.3 1.0 CA A:LEU969 4.0 58.0 1.0 CB A:ASP1053 4.0 57.0 1.0 N A:SER970 4.1 59.0 1.0 C A:SER970 4.2 53.8 1.0 O A:SER970 4.3 55.5 1.0 C A:ASP968 4.3 55.9 1.0 CA A:SER970 4.4 55.5 1.0 CB A:LEU969 4.4 55.1 1.0 CB A:ASP968 4.4 59.8 1.0 O1G A:ATP2501 4.4 75.4 1.0 C5' A:ATP2501 4.5 66.1 1.0 CA A:ASP968 4.6 59.2 1.0 O5' A:ATP2501 4.6 63.4 1.0 CB A:ALA972 4.6 65.8 1.0 N A:ALA972 4.7 60.9 1.0 N A:ALA971 4.7 52.2 1.0 O1B A:ATP2501 4.7 67.8 1.0 CA A:CA2503 4.8 34.0 1.0 O3G A:ATP2501 4.9 79.3 1.0

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


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 I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2503 b:34.0 occ:1.00 OD1 A:ASP968 2.8 60.1 1.0 OD1 A:ASP1053 2.8 68.7 1.0 CG A:ASP968 3.6 58.6 1.0 C3' G:C2008 3.7 0.7 1.0 CG A:ASP1053 3.7 64.1 1.0 CG A:ASP1054 3.8 65.1 1.0 CB A:ASP968 3.8 59.8 1.0 OD2 A:ASP1054 3.9 56.6 1.0 OD2 A:ASP1053 3.9 62.3 1.0 C5' G:C2008 3.9 0.1 1.0 CB A:ASP1054 3.9 62.3 1.0 O2A A:ATP2501 4.0 64.3 1.0 CA A:ASP1054 4.0 57.4 1.0 C4' G:C2008 4.1 0.7 1.0 N A:ASP1054 4.3 53.4 1.0 OD1 A:ASP1054 4.3 69.5 1.0 O5' G:C2008 4.6 0.3 1.0 OE2 A:GLU1089 4.6 77.2 1.0 OD2 A:ASP968 4.6 59.4 1.0 CA A:ASP968 4.6 59.2 1.0 C A:ASP1053 4.6 53.8 1.0 O A:ASP1053 4.7 58.8 1.0 CA A:CA2502 4.8 52.4 1.0 O A:VAL967 4.9 62.3 1.0 C5' A:ATP2501 4.9 66.1 1.0 OP1 G:C2008 5.0 0.5 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