Manganese in PDB 3h5y: Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2

All present enzymatic activity of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2:
2.7.7.48;

The structure of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2, PDB code: 3h5y was solved by D.F.Zamyatkin, F.Parra, A.Machin, P.Grochulski, K.K.S.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.200, 93.600, 96.300, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.9

The binding sites of Manganese atom in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2 (pdb code 3h5y). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2, PDB code: 3h5y:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn511 b:33.1 occ:1.00 OD1 A:ASP343 2.1 29.7 1.0 OD1 A:ASP344 2.1 34.5 1.0 OD1 A:ASP242 2.2 37.8 1.0 O1A A:CTP515 2.2 34.6 1.0 O A:HOH670 2.2 36.7 1.0 O3' P:G8 2.3 32.5 1.0 CG A:ASP343 3.1 31.4 1.0 CG A:ASP242 3.2 35.8 1.0 OD2 A:ASP343 3.3 32.9 1.0 CG A:ASP344 3.4 35.0 1.0 PA A:CTP515 3.4 35.1 1.0 OD2 A:ASP242 3.6 35.1 1.0 C3' P:G8 3.6 30.2 1.0 MN A:MN512 3.7 36.2 1.0 O2A A:CTP515 3.9 32.5 1.0 N A:ASP344 3.9 24.9 1.0 O5' A:CTP515 4.0 29.5 1.0 C5' A:CTP515 4.2 28.6 1.0 C4' P:G8 4.2 27.4 1.0 OD2 A:ASP344 4.2 35.9 1.0 CA A:ASP344 4.3 25.9 1.0 CB A:ASP344 4.3 28.2 1.0 C A:ASP343 4.3 25.4 1.0 C5' P:G8 4.3 24.7 1.0 CB A:ASP343 4.4 28.1 1.0 CB A:ASP242 4.5 37.5 1.0 O P:HOH563 4.7 35.9 1.0 O3A A:CTP515 4.8 36.3 1.0 CA A:ASP343 4.8 25.5 1.0 C2' P:G8 4.8 27.0 1.0 O A:HOH737 4.8 55.8 1.0 O A:ASP343 4.9 26.1 1.0 O2' P:G8 4.9 27.4 1.0 MN A:MN513 4.9 48.3 1.0 OP1 P:G8 4.9 33.1 1.0 N A:ASP343 4.9 24.8 1.0 O5' P:G8 5.0 25.4 1.0

Manganese binding site 2 out of 4 in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn512 b:36.2 occ:1.00 OD2 A:ASP343 2.2 32.9 1.0 O3G A:CTP515 2.2 48.0 1.0 OD2 A:ASP242 2.2 35.1 1.0 O A:TYR243 2.2 33.0 1.0 O2B A:CTP515 2.2 34.8 1.0 O1A A:CTP515 2.4 34.6 1.0 PB A:CTP515 3.1 36.9 1.0 CG A:ASP242 3.1 35.8 1.0 CG A:ASP343 3.2 31.4 1.0 O3A A:CTP515 3.3 36.3 1.0 PA A:CTP515 3.3 35.1 1.0 PG A:CTP515 3.4 52.8 1.0 C A:TYR243 3.4 31.9 1.0 OD1 A:ASP242 3.5 37.8 1.0 O3B A:CTP515 3.6 43.0 1.0 MN A:MN511 3.7 33.1 1.0 OD1 A:ASP343 3.7 29.7 1.0 N A:TYR243 3.7 34.5 1.0 C5' A:CTP515 4.1 28.6 1.0 CA A:TYR243 4.2 32.9 1.0 O5' A:CTP515 4.2 29.5 1.0 O1G A:CTP515 4.3 47.9 1.0 O A:HOH737 4.4 55.8 1.0 CB A:ASP242 4.4 37.5 1.0 N A:SER244 4.4 31.5 1.0 O2G A:CTP515 4.4 50.3 1.0 CB A:ASP343 4.5 28.1 1.0 O1B A:CTP515 4.5 39.8 1.0 CA A:SER244 4.6 30.9 1.0 O2A A:CTP515 4.6 32.5 1.0 O A:HOH670 4.6 36.7 1.0 C A:ASP242 4.7 36.2 1.0 N A:ARG245 4.8 30.1 1.0 CB A:TYR243 4.8 31.4 1.0 C A:SER244 4.9 30.0 1.0 N A:TRP246 4.9 25.1 1.0 CB A:TRP246 4.9 23.9 1.0 CA A:ASP242 4.9 36.2 1.0

Manganese binding site 3 out of 4 in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn513 b:48.3 occ:1.00 O A:HOH637 2.3 26.1 1.0 O A:ALA241 3.0 34.2 1.0 CG A:ASP344 3.4 35.0 1.0 OD2 A:ASP344 3.5 35.9 1.0 OD1 A:ASP242 3.6 37.8 1.0 C A:ALA241 3.7 35.7 1.0 OD1 A:ASP344 3.7 34.5 1.0 CB A:ASP242 3.8 37.5 1.0 CB A:PRO372 3.9 51.1 1.0 CA A:ASP344 4.0 25.9 1.0 CB A:ASP344 4.0 28.2 1.0 N A:ASP242 4.1 36.4 1.0 CA A:ASP242 4.1 36.2 1.0 CG A:ASP242 4.2 35.8 1.0 O P:HOH563 4.2 35.9 1.0 N A:GLU345 4.2 25.6 1.0 O A:THR389 4.3 32.9 1.0 OG1 A:THR389 4.4 39.5 1.0 CG A:PRO372 4.5 50.2 1.0 CA A:PRO372 4.5 50.7 1.0 C A:ASP344 4.6 24.7 1.0 O A:GLU345 4.7 29.4 1.0 CA A:ALA241 4.7 36.4 1.0 N A:ALA241 4.7 37.5 1.0 CA A:PHE390 4.8 30.4 1.0 C A:THR389 4.9 32.6 1.0 MN A:MN511 4.9 33.1 1.0

Manganese binding site 4 out of 4 in the Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Norovirus Polymerase+Primer/Template+Ctp Complex at 6 Mm MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn514 b:33.7 occ:1.00 NE2 A:HIS209 2.1 32.3 1.0 OD2 A:ASP99 2.1 34.6 1.0 OE2 A:GLU205 2.1 30.1 1.0 CD2 A:HIS209 3.0 29.4 1.0 CD A:GLU205 3.0 32.8 1.0 CE1 A:HIS209 3.1 32.1 1.0 CG A:ASP99 3.2 32.1 1.0 OE1 A:GLU205 3.3 31.9 1.0 CB A:ASP99 3.7 31.4 1.0 N A:ASP99 3.9 30.1 1.0 CG2 A:THR208 4.0 35.8 1.0 CG A:HIS209 4.2 28.3 1.0 ND1 A:HIS209 4.2 31.2 1.0 CB A:THR208 4.2 30.8 1.0 OD1 A:ASP99 4.3 39.4 1.0 CG A:GLU205 4.3 28.8 1.0 CA A:ASP99 4.5 30.7 1.0 O A:GLU205 4.6 24.4 1.0 CA A:ILE98 4.7 28.6 1.0 C A:ILE98 4.7 28.8 1.0 OG1 A:THR208 5.0 35.6 1.0

D.F.Zamyatkin, F.Parra, A.Machin, P.Grochulski, K.K.Ng. Binding of 2'-Amino-2'-Deoxycytidine-5'-Triphosphate to Norovirus Polymerase Induces Rearrangement of the Active Site. J.Mol.Biol. V. 390 10 2009.
ISSN: ISSN 0022-2836
PubMed: 19426741
DOI: 10.1016/J.JMB.2009.04.069