Manganese in PDB 3bsn: Norwalk Virus Polymerase Bound to 5-Nitrocytidine Triphosphate and Primer-Template Rna

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

The structure of Norwalk Virus Polymerase Bound to 5-Nitrocytidine Triphosphate and Primer-Template Rna, PDB code: 3bsn 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)	19.71 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.310, 93.850, 96.030, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.6

The binding sites of Manganese atom in the Norwalk Virus Polymerase Bound to 5-Nitrocytidine Triphosphate and Primer-Template Rna (pdb code 3bsn). 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 5-Nitrocytidine Triphosphate and Primer-Template Rna, PDB code: 3bsn:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Norwalk Virus Polymerase Bound to 5-Nitrocytidine 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 5-Nitrocytidine Triphosphate and Primer-Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn511 b:35.4 occ:0.80 O A:HOH664 2.2 35.2 1.0 OD1 A:ASP343 2.2 27.5 1.0 OD1 A:ASP242 2.2 39.5 1.0 O3' P:G8 2.2 30.8 1.0 O1A A:N5C514 2.2 32.9 1.0 OD1 A:ASP344 2.5 31.5 1.0 CG A:ASP343 3.1 24.5 1.0 CG A:ASP242 3.3 38.8 1.0 PA A:N5C514 3.3 39.4 1.0 OD2 A:ASP343 3.4 27.3 1.0 C3' P:G8 3.5 27.0 1.0 MN A:MN512 3.7 29.4 1.0 OD2 A:ASP242 3.7 38.2 1.0 CG A:ASP344 3.7 26.6 1.0 O2A A:N5C514 3.8 34.6 1.0 O5' A:N5C514 3.8 29.4 1.0 C5' A:N5C514 3.9 28.1 1.0 N A:ASP344 4.1 21.1 1.0 C4' P:G8 4.2 19.5 1.0 C5' P:G8 4.3 25.4 1.0 OD2 A:ASP344 4.5 29.8 1.0 CB A:ASP343 4.5 23.6 1.0 C A:ASP343 4.5 20.7 1.0 CB A:ASP242 4.6 36.1 1.0 CA A:ASP344 4.6 20.9 1.0 CB A:ASP344 4.6 20.8 1.0 O P:HOH13 4.6 32.7 1.0 C2' P:G8 4.7 20.6 1.0 O3A A:N5C514 4.8 34.0 1.0 CA A:ASP343 4.9 21.8 1.0 OP1 P:G8 4.9 27.5 1.0 O2' P:G8 4.9 27.9 1.0 O5' P:G8 4.9 23.1 1.0 O2B A:N5C514 5.0 31.6 1.0 N A:ASP343 5.0 21.6 1.0

Manganese binding site 2 out of 3 in the Norwalk Virus Polymerase Bound to 5-Nitrocytidine 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 5-Nitrocytidine Triphosphate and Primer-Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn512 b:29.4 occ:1.00 OD2 A:ASP343 2.1 27.3 1.0 O A:TYR243 2.1 27.1 1.0 O2B A:N5C514 2.1 31.6 1.0 OD2 A:ASP242 2.2 38.2 1.0 O3G A:N5C514 2.2 37.9 1.0 O1A A:N5C514 2.2 32.9 1.0 CG A:ASP242 3.1 38.8 1.0 PB A:N5C514 3.2 31.8 1.0 CG A:ASP343 3.2 24.5 1.0 C A:TYR243 3.3 29.9 1.0 PA A:N5C514 3.3 39.4 1.0 O3A A:N5C514 3.4 34.0 1.0 PG A:N5C514 3.4 48.7 1.0 OD1 A:ASP242 3.4 39.5 1.0 O3B A:N5C514 3.6 37.2 1.0 OD1 A:ASP343 3.6 27.5 1.0 N A:TYR243 3.6 32.8 1.0 MN A:MN511 3.7 35.4 0.8 CA A:TYR243 4.0 29.6 1.0 O A:HOH635 4.1 41.6 1.0 C5' A:N5C514 4.2 28.1 1.0 O5' A:N5C514 4.2 29.4 1.0 N A:SER244 4.3 27.5 1.0 O1G A:N5C514 4.3 47.9 1.0 CB A:ASP242 4.4 36.1 1.0 O2G A:N5C514 4.4 46.3 1.0 CB A:ASP343 4.5 23.6 1.0 O2A A:N5C514 4.5 34.6 1.0 CA A:SER244 4.5 28.3 1.0 O1B A:N5C514 4.6 31.9 1.0 C A:ASP242 4.6 34.1 1.0 O A:HOH664 4.7 35.2 1.0 CB A:TYR243 4.7 30.7 1.0 N A:ARG245 4.8 29.5 1.0 CB A:TRP246 4.8 20.6 1.0 N A:TRP246 4.9 23.8 1.0 C A:SER244 4.9 26.9 1.0 CA A:ASP242 4.9 34.9 1.0

Manganese binding site 3 out of 3 in the Norwalk Virus Polymerase Bound to 5-Nitrocytidine 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 5-Nitrocytidine Triphosphate and Primer-Template Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn513 b:22.1 occ:1.00 OE2 A:GLU205 2.1 28.9 1.0 NE2 A:HIS209 2.1 18.1 1.0 OD1 A:ASP99 2.2 33.0 1.0 OD2 A:ASP99 2.4 51.4 1.0 CG A:ASP99 2.5 35.0 1.0 CD2 A:HIS209 3.0 21.7 1.0 CD A:GLU205 3.1 32.3 1.0 CE1 A:HIS209 3.1 24.6 1.0 N A:ASP99 3.6 25.7 1.0 OE1 A:GLU205 3.6 29.7 1.0 CB A:ASP99 3.8 29.2 1.0 CG A:HIS209 4.2 18.5 1.0 ND1 A:HIS209 4.2 18.6 1.0 CA A:ASP99 4.3 26.9 1.0 CG A:GLU205 4.3 24.4 1.0 C A:ILE98 4.4 24.6 1.0 CA A:ILE98 4.4 26.0 1.0 CG2 A:THR208 4.6 30.8 1.0 O A:THR97 4.6 26.6 1.0 O A:GLU205 4.9 23.7 1.0 CB A:THR208 4.9 26.6 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