Manganese in PDB 5vpx: I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpx 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)	38.82 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.672, 90.672, 134.165, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.4

The structure of I38T Mutant 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 I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vpx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vpx:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the I38T Mutant of 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 I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:60.5 occ:1.00 O17 A:R07205 2.0 66.7 1.0 OE1 A:GLU119 2.2 64.4 1.0 OD2 A:ASP108 2.2 56.4 1.0 O A:ILE120 2.2 65.4 1.0 NE2 A:HIS41 2.2 66.5 1.0 O15 A:R07205 2.3 61.2 1.0 C01 A:R07205 2.7 62.2 1.0 C08 A:R07205 2.9 58.3 1.0 CE1 A:HIS41 2.9 63.5 1.0 CG A:ASP108 3.0 60.9 1.0 CD A:GLU119 3.1 66.5 1.0 OD1 A:ASP108 3.2 62.4 1.0 CD2 A:HIS41 3.4 63.3 1.0 C A:ILE120 3.4 62.6 1.0 OE2 A:GLU119 3.5 62.3 1.0 N A:ILE120 3.7 56.9 1.0 MN A:MN202 3.7 65.0 1.0 O A:HOH302 3.9 46.8 1.0 CA A:ILE120 4.0 56.5 1.0 ND1 A:HIS41 4.1 60.1 1.0 C02 A:R07205 4.1 65.6 1.0 CG A:GLU119 4.2 60.9 1.0 NZ A:LYS134 4.3 93.6 1.0 CG A:HIS41 4.3 62.5 1.0 O A:HOH306 4.4 62.2 1.0 C07 A:R07205 4.4 61.9 1.0 CB A:ILE120 4.5 65.3 1.0 CB A:ASP108 4.5 58.8 1.0 N A:GLY121 4.5 67.1 1.0 C A:GLU119 4.6 61.2 1.0 CE A:LYS134 4.7 93.6 1.0 CA A:GLY121 4.8 62.5 1.0 O18 A:R07205 4.8 70.7 1.0 CA A:GLU119 4.9 59.5 1.0 CG2 A:ILE120 4.9 67.3 1.0

Manganese binding site 2 out of 2 in the I38T Mutant of 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 I38T Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:65.0 occ:1.00 O15 A:R07205 2.0 61.2 1.0 O18 A:R07205 2.0 70.7 1.0 OD1 A:ASP108 2.1 62.4 1.0 O A:HOH304 2.3 54.9 1.0 OE1 A:GLU80 2.4 55.9 1.0 O A:HOH302 2.4 46.8 1.0 C14 A:R07205 3.1 66.2 1.0 C08 A:R07205 3.2 58.3 1.0 CG A:ASP108 3.2 60.9 1.0 CD A:GLU80 3.5 66.4 1.0 C07 A:R07205 3.6 61.9 1.0 MN A:MN201 3.7 60.5 1.0 CE1 A:HIS41 3.8 63.5 1.0 OD2 A:ASP108 3.9 56.4 1.0 N13 A:R07205 4.1 71.9 1.0 O A:PRO107 4.2 66.2 1.0 CG A:GLU80 4.2 65.4 1.0 OE2 A:GLU80 4.3 78.1 1.0 CB A:ASP108 4.4 58.8 1.0 CB A:GLU80 4.4 59.9 1.0 F28 A:R07205 4.4 79.6 1.0 C01 A:R07205 4.5 62.2 1.0 CA A:ASP108 4.5 62.6 1.0 NE2 A:HIS41 4.5 66.5 1.0 C20 A:R07205 4.5 75.8 1.0 C A:PRO107 4.5 65.7 1.0 OE2 A:GLU119 4.5 62.3 1.0 O A:LEU106 4.5 63.1 1.0 N A:ASP108 4.7 58.2 1.0 OE1 A:GLU119 4.7 64.4 1.0 ND1 A:HIS41 4.7 60.1 1.0 O17 A:R07205 4.8 66.7 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