Manganese in PDB 4qpx: Nv Polymerase Post-Incorporation-Like Complex

All present enzymatic activity of Nv Polymerase Post-Incorporation-Like Complex:
2.7.7.48;

The structure of Nv Polymerase Post-Incorporation-Like Complex, PDB code: 4qpx was solved by D.F.Zamyatkin, F.Parra, 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)	19.70 / 1.86
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.220, 81.220, 188.130, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.3

The binding sites of Manganese atom in the Nv Polymerase Post-Incorporation-Like Complex (pdb code 4qpx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Nv Polymerase Post-Incorporation-Like Complex, PDB code: 4qpx:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Nv Polymerase Post-Incorporation-Like Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Nv Polymerase Post-Incorporation-Like Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:44.7 occ:1.00 OD1 A:ASP242 1.9 50.4 1.0 OD1 A:ASP344 1.9 39.5 1.0 OP1 P:G8 1.9 48.4 1.0 OD1 A:ASP343 1.9 45.4 1.0 O P:HOH219 2.3 54.9 1.0 O3' P:G7 2.5 45.9 1.0 P P:G8 2.8 58.5 1.0 CG A:ASP343 2.8 46.4 1.0 CG A:ASP242 2.9 49.0 1.0 OD2 A:ASP343 3.1 46.7 1.0 CG A:ASP344 3.1 47.9 1.0 OD2 A:ASP242 3.2 55.0 1.0 MN A:MN603 3.6 51.2 1.0 C3' P:G7 3.8 44.0 1.0 OD2 A:ASP344 3.9 49.8 1.0 OP2 P:G8 3.9 42.5 1.0 O5' P:G8 4.0 45.1 1.0 N A:ASP344 4.0 38.5 1.0 C4' P:G7 4.1 42.1 1.0 C5' P:G8 4.2 46.0 1.0 O P:HOH210 4.2 51.2 1.0 CB A:ASP344 4.2 40.1 1.0 CB A:ASP242 4.2 49.4 1.0 C5' P:G7 4.3 42.4 1.0 CB A:ASP343 4.3 41.9 1.0 CA A:ASP344 4.3 36.3 1.0 C A:ASP343 4.4 37.8 1.0 O A:HOH960 4.7 48.9 1.0 CA A:ASP343 4.7 39.2 1.0 O2' P:G7 4.8 43.1 1.0 C2' P:G7 4.9 42.8 1.0 O A:HOH891 4.9 34.9 1.0 N A:ASP343 4.9 36.4 1.0 CA A:ASP242 4.9 47.7 1.0

Manganese binding site 2 out of 3 in the Nv Polymerase Post-Incorporation-Like Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Nv Polymerase Post-Incorporation-Like Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn603 b:51.2 occ:1.00 OD2 A:ASP242 1.9 55.0 1.0 OD2 A:ASP343 1.9 46.7 1.0 O A:TYR243 1.9 43.4 1.0 O A:HOH960 2.4 48.9 1.0 OP1 P:G8 2.6 48.4 1.0 CG A:ASP242 3.0 49.0 1.0 CG A:ASP343 3.1 46.4 1.0 C A:TYR243 3.1 45.2 1.0 O P:HOH220 3.2 37.5 1.0 OD1 A:ASP242 3.6 50.4 1.0 N A:TYR243 3.6 46.5 1.0 MN A:MN602 3.6 44.7 1.0 OD1 A:ASP343 3.6 45.4 1.0 P P:G8 3.9 58.5 1.0 CA A:TYR243 3.9 44.3 1.0 O5' P:G8 4.2 45.1 1.0 C5' P:G8 4.2 46.0 1.0 N A:SER244 4.2 45.3 1.0 NZ A:LYS374 4.2 50.6 1.0 CB A:ASP343 4.3 41.9 1.0 CB A:ASP242 4.3 49.4 1.0 CA A:SER244 4.5 43.6 1.0 CB A:TYR243 4.6 44.7 1.0 C A:ASP242 4.6 47.4 1.0 O P:HOH219 4.6 54.9 1.0 N A:ARG245 4.8 44.7 1.0 OP2 P:G8 4.8 42.5 1.0 CA A:ASP242 4.9 47.7 1.0 C A:SER244 4.9 43.3 1.0 CB A:TRP246 4.9 39.8 1.0 O3' P:G7 4.9 45.9 1.0 N A:TRP246 5.0 41.2 1.0

Manganese binding site 3 out of 3 in the Nv Polymerase Post-Incorporation-Like Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Nv Polymerase Post-Incorporation-Like Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn604 b:83.1 occ:1.00 OE2 A:GLU205 1.9 59.9 1.0 OD2 A:ASP99 1.9 72.1 1.0 NE2 A:HIS209 2.0 46.1 1.0 CE1 A:HIS209 2.9 48.1 1.0 CG A:ASP99 3.0 64.2 1.0 CD A:GLU205 3.1 55.4 1.0 CD2 A:HIS209 3.1 43.8 1.0 N A:ASP99 3.6 53.3 1.0 CB A:ASP99 3.6 60.0 1.0 OE1 A:GLU205 3.7 54.6 1.0 OD1 A:ASP99 4.0 67.5 1.0 ND1 A:HIS209 4.0 43.9 1.0 CG A:HIS209 4.2 42.7 1.0 CG A:GLU205 4.3 52.0 1.0 CA A:ASP99 4.3 57.8 1.0 CA A:ILE98 4.4 47.8 1.0 CG2 A:THR208 4.4 46.3 1.0 C A:ILE98 4.4 50.9 1.0 O A:THR97 4.5 45.1 1.0 CB A:THR208 4.9 41.9 1.0

D.Zamyatkin, C.Rao, E.Hoffarth, G.Jurca, H.Rho, F.Parra, P.Grochulski, K.K.Ng. Structure of A Backtracked State Reveals Conformational Changes Similar to the State Following Nucleotide Incorporation in Human Norovirus Polymerase. Acta Crystallogr.,Sect.D V. 70 3099 2014.
ISSN: ISSN 0907-4449
PubMed: 25478829
DOI: 10.1107/S1399004714021518