Manganese in PDB 5vpt: 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpt was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 2.10
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.881, 89.881, 133.731, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22

The structure of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Manganese atom in the 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vpt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:52.7 occ:1.00 O17 A:R07204 1.9 55.9 1.0 OD2 A:ASP108 2.1 44.5 1.0 OE2 A:GLU119 2.1 57.5 1.0 NE2 A:HIS41 2.2 54.2 1.0 O A:ILE120 2.2 59.2 1.0 O15 A:R07204 2.4 49.1 1.0 C01 A:R07204 2.6 58.3 1.0 C08 A:R07204 2.9 53.1 1.0 CE1 A:HIS41 2.9 54.7 1.0 CG A:ASP108 3.0 55.9 1.0 CD A:GLU119 3.1 58.2 1.0 OD1 A:ASP108 3.2 56.7 1.0 CD2 A:HIS41 3.3 51.4 1.0 C A:ILE120 3.4 57.8 1.0 OE1 A:GLU119 3.6 57.2 1.0 N A:ILE120 3.7 53.5 1.0 MN A:MN202 3.8 59.6 1.0 O A:HOH303 3.8 46.5 1.0 CA A:ILE120 4.0 53.6 1.0 C02 A:R07204 4.0 53.4 1.0 ND1 A:HIS41 4.1 50.7 1.0 NZ A:LYS134 4.2 93.0 1.0 O A:HOH316 4.2 53.1 1.0 CB A:ILE120 4.3 59.5 1.0 CG A:HIS41 4.3 57.8 1.0 CG A:GLU119 4.3 54.7 1.0 CB A:ASP108 4.4 52.6 1.0 C07 A:R07204 4.4 53.3 1.0 N A:GLY121 4.5 56.1 1.0 CE A:LYS134 4.5 87.2 1.0 C A:GLU119 4.6 57.2 1.0 CA A:GLY121 4.8 54.5 1.0 O18 A:R07204 4.9 55.0 1.0 CA A:GLU119 4.9 54.8 1.0 OE1 A:GLU80 4.9 46.2 1.0

Manganese binding site 2 out of 2 in the 2009 H1N1 Pa Endonuclease in Complex with Ro-7


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:59.6 occ:1.00 O15 A:R07204 2.0 49.1 1.0 O18 A:R07204 2.1 55.0 1.0 OD1 A:ASP108 2.1 56.7 1.0 OE1 A:GLU80 2.2 46.2 1.0 O A:HOH303 2.4 46.5 1.0 O A:HOH301 2.4 46.5 1.0 C14 A:R07204 3.1 54.2 1.0 C08 A:R07204 3.2 53.1 1.0 CG A:ASP108 3.3 55.9 1.0 CD A:GLU80 3.3 51.3 1.0 C07 A:R07204 3.6 53.3 1.0 CE1 A:HIS41 3.8 54.7 1.0 MN A:MN201 3.8 52.7 1.0 OD2 A:ASP108 3.8 44.5 1.0 O A:PRO107 4.1 56.3 1.0 CG A:GLU80 4.2 54.1 1.0 N13 A:R07204 4.2 60.6 1.0 OE2 A:GLU80 4.2 55.8 1.0 F29 A:R07204 4.4 66.6 1.0 CB A:ASP108 4.4 52.6 1.0 C01 A:R07204 4.4 58.3 1.0 CB A:GLU80 4.4 55.2 1.0 C A:PRO107 4.5 58.7 1.0 NE2 A:HIS41 4.5 54.2 1.0 CA A:ASP108 4.5 49.5 1.0 C20 A:R07204 4.5 66.1 1.0 OE1 A:GLU119 4.5 57.2 1.0 OE2 A:GLU119 4.6 57.5 1.0 N A:ASP108 4.7 46.1 1.0 ND1 A:HIS41 4.7 50.7 1.0 O17 A:R07204 4.7 55.9 1.0 O A:LEU106 4.7 63.2 1.0

J.C.Jones, G.Kumar, S.Barman, I.Najera, S.W.White, R.J.Webby, E.A.Govorkova. Identification of the I38T Pa Substitution As A Resistance Marker For Next-Generation Influenza Virus Endonuclease Inhibitors. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 29691337
DOI: 10.1128/MBIO.00430-18