Magnesium in PDB 5vrj: 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium

The structure of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium, PDB code: 5vrj 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)	38.91 / 2.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.924, 90.924, 133.913, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.7

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

Fluorine

(F)

3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:63.7 occ:1.00 O17 A:R07204 2.0 70.9 1.0 OD2 A:ASP108 2.0 57.6 1.0 OE2 A:GLU119 2.1 60.7 1.0 O A:ILE120 2.1 61.5 1.0 NE2 A:HIS41 2.3 60.0 1.0 O15 A:R07204 2.4 59.0 1.0 C01 A:R07204 2.8 66.7 1.0 CE1 A:HIS41 2.9 59.6 1.0 CG A:ASP108 2.9 65.5 1.0 CD A:GLU119 2.9 65.7 1.0 C08 A:R07204 2.9 62.3 1.0 OD1 A:ASP108 3.1 62.4 1.0 C A:ILE120 3.3 61.7 1.0 OE1 A:GLU119 3.4 60.6 1.0 CD2 A:HIS41 3.5 59.1 1.0 N A:ILE120 3.6 53.1 1.0 NZ A:LYS134 3.8 88.2 1.0 MG A:MG203 3.8 63.1 1.0 CA A:ILE120 3.9 55.0 1.0 O A:HOH302 3.9 51.6 1.0 CG A:GLU119 4.0 61.0 1.0 ND1 A:HIS41 4.1 53.2 1.0 C02 A:R07204 4.2 65.4 1.0 CB A:ILE120 4.2 63.7 1.0 CB A:ASP108 4.3 60.6 1.0 N A:GLY121 4.4 68.8 1.0 C A:GLU119 4.4 63.0 1.0 CG A:HIS41 4.4 57.9 1.0 C07 A:R07204 4.5 60.3 1.0 CA A:GLY121 4.7 59.7 1.0 CA A:GLU119 4.8 59.5 1.0 O A:HOH303 4.8 81.5 1.0 O18 A:R07204 4.8 64.3 1.0 OE1 A:GLU80 4.9 74.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2009 H1N1 Pa Endonuclease in Complex with Ro-7 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:63.1 occ:1.00 O18 A:R07204 1.9 64.3 1.0 O15 A:R07204 2.0 59.0 1.0 OE1 A:GLU80 2.0 74.0 1.0 OD1 A:ASP108 2.0 62.4 1.0 O A:HOH301 2.1 57.1 1.0 O A:HOH302 2.3 51.6 1.0 C14 A:R07204 3.0 64.6 1.0 C08 A:R07204 3.1 62.3 1.0 CD A:GLU80 3.2 80.6 1.0 CG A:ASP108 3.3 65.5 1.0 C07 A:R07204 3.6 60.3 1.0 MG A:MG202 3.8 63.7 1.0 OD2 A:ASP108 3.9 57.6 1.0 CE1 A:HIS41 3.9 59.6 1.0 OE2 A:GLU80 4.0 89.4 1.0 O A:PRO107 4.0 63.3 1.0 N13 A:R07204 4.1 67.5 1.0 CG A:GLU80 4.1 74.8 1.0 CB A:ASP108 4.4 60.6 1.0 C A:PRO107 4.4 64.1 1.0 OE1 A:GLU119 4.4 60.6 1.0 C01 A:R07204 4.4 66.7 1.0 C20 A:R07204 4.4 72.1 1.0 CA A:ASP108 4.5 59.8 1.0 OE2 A:GLU119 4.5 60.7 1.0 CB A:GLU80 4.5 63.7 1.0 F28 A:R07204 4.5 74.4 1.0 N A:ASP108 4.6 61.5 1.0 O A:LEU106 4.6 69.5 1.0 NE2 A:HIS41 4.7 60.0 1.0 ND1 A:HIS41 4.7 53.2 1.0 O17 A:R07204 4.8 70.9 1.0 CD A:GLU119 5.0 65.7 1.0 N06 A:R07204 5.0 65.4 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