Manganese in PDB 3bso: Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna

All present enzymatic activity of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna:
2.7.7.48;

The structure of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna, PDB code: 3bso was solved by D.F.Zamyatkin, K.K.S.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.100, 93.473, 96.538, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.2

The binding sites of Manganese atom in the Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna (pdb code 3bso). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna, PDB code: 3bso:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn511 b:36.9 occ:1.00 OD1 A:ASP344 2.1 37.0 1.0 OD1 A:ASP242 2.1 41.0 1.0 OD1 A:ASP343 2.1 34.3 1.0 O1A A:CTP514 2.2 39.8 1.0 O3' P:G8 2.2 38.1 1.0 O A:HOH658 2.4 36.6 1.0 CG A:ASP343 3.0 35.9 1.0 CG A:ASP242 3.2 41.3 1.0 OD2 A:ASP343 3.2 37.0 1.0 CG A:ASP344 3.4 40.2 1.0 PA A:CTP514 3.4 44.0 1.0 OD2 A:ASP242 3.5 41.8 1.0 C3' P:G8 3.6 32.8 1.0 MN A:MN512 3.7 40.5 1.0 O2A A:CTP514 3.9 35.0 1.0 N A:ASP344 3.9 27.5 1.0 O5' A:CTP514 4.0 32.4 1.0 C5' A:CTP514 4.2 32.7 1.0 OD2 A:ASP344 4.2 38.3 1.0 C4' P:G8 4.2 29.0 1.0 CA A:ASP344 4.3 28.9 1.0 CB A:ASP344 4.3 29.2 1.0 C A:ASP343 4.3 27.2 1.0 C5' P:G8 4.4 28.0 1.0 CB A:ASP343 4.4 28.1 1.0 O A:HOH722 4.5 57.0 1.0 CB A:ASP242 4.5 41.8 1.0 O3A A:CTP514 4.7 42.5 1.0 CA A:ASP343 4.8 25.9 1.0 C2' P:G8 4.8 33.0 1.0 O A:HOH561 4.8 39.2 1.0 O A:ASP343 4.8 28.6 1.0 O2' P:G8 4.9 33.5 1.0 O A:HOH582 4.9 29.3 1.0 OP1 P:G8 4.9 36.7 1.0 N A:ASP343 4.9 24.9 1.0 O5' P:G8 5.0 29.8 1.0

Manganese binding site 2 out of 3 in the Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn512 b:40.5 occ:1.00 O2B A:CTP514 2.1 40.8 1.0 OD2 A:ASP343 2.1 37.0 1.0 OD2 A:ASP242 2.1 41.8 1.0 O3G A:CTP514 2.2 53.9 1.0 O A:TYR243 2.2 35.0 1.0 O1A A:CTP514 2.4 39.8 1.0 PB A:CTP514 3.1 46.1 1.0 CG A:ASP242 3.1 41.3 1.0 CG A:ASP343 3.2 35.9 1.0 O3A A:CTP514 3.3 42.5 1.0 PG A:CTP514 3.4 72.1 1.0 PA A:CTP514 3.4 44.0 1.0 C A:TYR243 3.4 36.0 1.0 O3B A:CTP514 3.5 52.2 1.0 OD1 A:ASP242 3.6 41.0 1.0 MN A:MN511 3.7 36.9 1.0 OD1 A:ASP343 3.7 34.3 1.0 N A:TYR243 3.7 39.6 1.0 O A:HOH722 4.0 57.0 1.0 C5' A:CTP514 4.2 32.7 1.0 CA A:TYR243 4.2 35.9 1.0 O5' A:CTP514 4.3 32.4 1.0 O1G A:CTP514 4.3 63.8 1.0 CB A:ASP242 4.4 41.8 1.0 CB A:ASP343 4.4 28.1 1.0 N A:SER244 4.4 30.6 1.0 O2G A:CTP514 4.4 67.5 1.0 O1B A:CTP514 4.4 41.4 1.0 CA A:SER244 4.6 34.0 1.0 O A:HOH658 4.6 36.6 1.0 O2A A:CTP514 4.6 35.0 1.0 C A:ASP242 4.7 40.5 1.0 N A:ARG245 4.7 32.1 1.0 CB A:TRP246 4.8 29.1 1.0 CB A:TYR243 4.8 35.5 1.0 N A:TRP246 4.8 28.1 1.0 C A:SER244 4.9 32.4 1.0 CA A:ASP242 4.9 40.2 1.0

Manganese binding site 3 out of 3 in the Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn513 b:29.2 occ:1.00 OE2 A:GLU205 2.1 34.8 1.0 NE2 A:HIS209 2.1 29.5 1.0 OD2 A:ASP99 2.1 33.7 1.0 CD A:GLU205 2.9 34.9 1.0 CD2 A:HIS209 3.0 27.7 1.0 CE1 A:HIS209 3.1 33.0 1.0 CG A:ASP99 3.2 35.5 1.0 OE1 A:GLU205 3.2 34.0 1.0 CB A:ASP99 3.6 35.7 1.0 N A:ASP99 3.8 33.6 1.0 CG A:HIS209 4.2 26.5 1.0 ND1 A:HIS209 4.2 28.2 1.0 OD1 A:ASP99 4.2 38.3 1.0 CG A:GLU205 4.3 32.5 1.0 CA A:ASP99 4.3 33.8 1.0 CA A:ILE98 4.4 31.7 1.0 C A:ILE98 4.5 32.5 1.0 CG2 A:THR208 4.5 32.6 1.0 O A:THR97 4.6 30.5 1.0 CB A:THR208 4.9 29.9 1.0 O A:GLU205 4.9 28.1 1.0

D.F.Zamyatkin, F.Parra, J.M.Alonso, D.A.Harki, B.R.Peterson, P.Grochulski, K.K.Ng. Structural Insights Into Mechanisms of Catalysis and Inhibition in Norwalk Virus Polymerase. J.Biol.Chem. V. 283 7705 2008.
ISSN: ISSN 0021-9258
PubMed: 18184655
DOI: 10.1074/JBC.M709563200