Manganese in PDB 5vqn: E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7

The structure of E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn 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)	38.47 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.848, 89.848, 133.261, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of E119D 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 E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 (pdb code 5vqn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E119D Mutant of 2009 H1N1 Pa Endonuclease in Complex with Ro-7, PDB code: 5vqn:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the E119D 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 E119D 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:49.4 occ:1.00 O17 A:R07205 1.9 51.6 1.0 OD2 A:ASP108 2.1 41.7 1.0 O A:ILE120 2.1 51.5 1.0 NE2 A:HIS41 2.2 51.5 1.0 O15 A:R07205 2.5 54.8 1.0 C01 A:R07205 2.7 59.6 1.0 OD1 A:ASP119 2.7 70.3 1.0 C08 A:R07205 2.9 45.0 1.0 CG A:ASP108 3.0 54.3 1.0 CE1 A:HIS41 3.1 49.5 1.0 H20 A:R07205 3.1 66.0 1.0 HE1 A:HIS41 3.2 59.6 1.0 H A:ILE120 3.2 59.4 1.0 C A:ILE120 3.3 53.3 1.0 OD1 A:ASP108 3.3 53.6 1.0 CD2 A:HIS41 3.3 43.9 1.0 HD2 A:HIS41 3.5 52.9 1.0 N A:ILE120 3.6 49.3 1.0 MN A:MN202 3.7 53.5 1.0 HB A:ILE120 3.8 59.5 1.0 HZ2 A:LYS134 3.9 95.0 1.0 CA A:ILE120 3.9 43.3 1.0 O A:HOH301 3.9 59.8 1.0 HA2 A:GLY121 4.0 55.1 1.0 CG A:ASP119 4.0 70.3 1.0 HZ1 A:LYS134 4.0 95.0 1.0 C02 A:R07205 4.0 47.8 1.0 HA A:ASP119 4.2 67.8 1.0 ND1 A:HIS41 4.2 52.1 1.0 CB A:ILE120 4.3 49.4 1.0 N A:GLY121 4.3 55.2 1.0 CG A:HIS41 4.3 53.5 1.0 NZ A:LYS134 4.4 79.0 1.0 C A:ASP119 4.4 49.5 1.0 H1 A:R07205 4.4 57.5 1.0 CB A:ASP108 4.4 50.2 1.0 HE3 A:LYS134 4.4 0.9 1.0 HG22 A:ILE120 4.4 57.7 1.0 C07 A:R07205 4.5 53.1 1.0 HB2 A:ASP108 4.5 60.4 1.0 CA A:GLY121 4.6 45.8 1.0 CA A:ASP119 4.7 56.4 1.0 O A:HOH314 4.7 60.6 1.0 OD2 A:ASP119 4.7 80.5 1.0 HB3 A:ASP108 4.8 60.4 1.0 HA A:ILE120 4.8 52.1 1.0 HG A:CYS45 4.9 57.9 1.0 O18 A:R07205 4.9 58.7 1.0 HD1 A:HIS41 4.9 62.7 1.0 CG2 A:ILE120 5.0 47.9 1.0 CB A:ASP119 5.0 58.7 1.0 CE A:LYS134 5.0 85.6 1.0 OE1 A:GLU80 5.0 48.9 1.0

Manganese binding site 2 out of 2 in the E119D 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 E119D 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:53.5 occ:1.00 H20 A:R07205 1.8 66.0 1.0 O15 A:R07205 1.9 54.8 1.0 O18 A:R07205 2.1 58.7 1.0 OD1 A:ASP108 2.1 53.6 1.0 O A:HOH310 2.1 48.5 1.0 OE1 A:GLU80 2.2 48.9 1.0 O A:HOH301 2.4 59.8 1.0 C08 A:R07205 3.1 45.0 1.0 C14 A:R07205 3.1 55.3 1.0 HE1 A:HIS41 3.1 59.6 1.0 CG A:ASP108 3.2 54.3 1.0 CD A:GLU80 3.4 61.2 1.0 C07 A:R07205 3.6 53.1 1.0 MN A:MN201 3.7 49.4 1.0 OD2 A:ASP108 3.7 41.7 1.0 HB2 A:GLU80 3.8 66.4 1.0 CE1 A:HIS41 3.8 49.5 1.0 HA A:ASP108 3.9 54.2 1.0 H6 A:R07205 4.0 68.3 1.0 O A:PRO107 4.0 56.8 1.0 HG2 A:GLU80 4.2 77.6 1.0 N13 A:R07205 4.2 62.5 1.0 CG A:GLU80 4.2 64.6 1.0 OE2 A:GLU80 4.2 64.2 1.0 C01 A:R07205 4.3 59.6 1.0 F28 A:R07205 4.4 62.3 1.0 NE2 A:HIS41 4.4 51.5 1.0 CB A:ASP108 4.4 50.2 1.0 CB A:GLU80 4.4 55.2 1.0 C A:PRO107 4.4 57.9 1.0 O A:LEU106 4.5 64.7 1.0 CA A:ASP108 4.5 45.0 1.0 HA A:GLU80 4.5 61.8 1.0 C20 A:R07205 4.6 56.8 1.0 O17 A:R07205 4.6 51.6 1.0 N A:ASP108 4.6 47.6 1.0 H16 A:R07205 4.7 66.0 1.0 OD1 A:ASP119 4.7 70.3 1.0 HB3 A:LEU106 4.8 63.5 1.0 HB3 A:ASP108 4.8 60.4 1.0 ND1 A:HIS41 4.9 52.1 1.0 N06 A:R07205 5.0 58.2 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