Manganese in PDB 5tsn: Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex

The structure of Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex, PDB code: 5tsn was solved by M.M.Shaik, K.K.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.91 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.760, 81.760, 189.030, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22

The binding sites of Manganese atom in the Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex (pdb code 5tsn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex, PDB code: 5tsn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:39.7 occ:1.00 OD1 A:ASP344 2.2 50.1 1.0 OD1 A:ASP242 2.2 54.4 1.0 OP1 P:G8 2.3 43.5 1.0 O P:HOH108 2.3 35.3 1.0 OD1 A:ASP343 2.4 25.5 1.0 O3' P:G7 2.7 45.4 1.0 P P:G8 3.0 43.0 1.0 CG A:ASP242 3.1 48.1 1.0 CG A:ASP343 3.1 37.6 1.0 OD2 A:ASP343 3.2 34.6 1.0 OD2 A:ASP242 3.2 44.1 1.0 CG A:ASP344 3.4 50.2 1.0 MN A:MN602 3.5 59.4 1.0 C3' P:G7 4.0 40.9 1.0 N A:ASP344 4.1 22.7 1.0 OP2 P:G8 4.1 41.3 1.0 O5' P:G8 4.1 33.3 1.0 OD2 A:ASP344 4.2 52.9 1.0 C5' P:G8 4.2 36.0 1.0 C4' P:G7 4.3 36.8 1.0 CA A:ASP344 4.3 20.1 1.0 C5' P:G7 4.4 31.4 1.0 CB A:ASP344 4.4 30.6 1.0 C A:ASP343 4.4 24.5 1.0 CB A:ASP242 4.5 44.1 1.0 CB A:ASP343 4.5 30.5 1.0 O A:ASP343 4.8 22.9 1.0 O A:HOH709 4.9 48.0 1.0 O A:HOH891 4.9 27.2 1.0 CA A:ASP343 4.9 28.0 1.0 CA A:ASP242 5.0 48.3 1.0 O2' P:G7 5.0 25.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structures of Norwalk Virus Polymerase Bound to An Rna Primer- Template Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:59.4 occ:1.00 OD2 A:ASP343 2.4 34.6 1.0 O A:TYR243 2.5 41.3 1.0 OD2 A:ASP242 2.5 44.1 1.0 OP1 P:G8 2.5 43.5 1.0 O P:HOH113 2.6 41.9 1.0 O A:HOH922 3.1 21.1 1.0 CG A:ASP242 3.5 48.1 1.0 CG A:ASP343 3.5 37.6 1.0 MN A:MN601 3.5 39.7 1.0 C A:TYR243 3.6 37.1 1.0 N A:TYR243 3.9 37.9 1.0 P P:G8 3.9 43.0 1.0 OD1 A:ASP343 3.9 25.5 1.0 OD1 A:ASP242 3.9 54.4 1.0 O A:HOH873 4.0 41.1 1.0 NZ A:LYS374 4.1 48.5 1.0 C5' P:G8 4.2 36.0 1.0 O5' P:G8 4.2 33.3 1.0 CA A:TYR243 4.4 32.1 1.0 O P:HOH108 4.4 35.3 1.0 CB A:ASP242 4.6 44.1 1.0 N A:SER244 4.7 31.4 1.0 CB A:ASP343 4.8 30.5 1.0 CA A:SER244 4.8 32.6 1.0 OP2 P:G8 4.8 41.3 1.0 N A:ARG245 4.9 26.4 1.0 C A:ASP242 4.9 43.8 1.0 O3' P:G7 4.9 45.4 1.0

M.M.Shaik, N.Bhattacharjee, M.Feliks, K.K.Ng, M.J.Field. Norovirus Rna-Dependent Rna Polymerase: A Computational Study of Metal-Binding Preferences. Proteins V. 85 1435 2017.
ISSN: ESSN 1097-0134
PubMed: 28383118
DOI: 10.1002/PROT.25304