Manganese in PDB 7kaf: The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kaf was solved by M.G.Cuypers, G.Kumar, J.Slavish, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.06 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.824, 89.824, 133.773, 90, 90, 90
R / Rfree (%)	19.2 / 23.5

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid (pdb code 7kaf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kaf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:43.1 occ:1.00 O1 A:E4Z201 2.0 49.9 1.0 OD2 A:ASP108 2.1 38.9 1.0 O A:ILE120 2.2 55.8 1.0 NE2 A:HIS41 2.2 49.0 1.0 OE2 A:GLU119 2.3 47.5 1.0 O2 A:E4Z201 2.4 48.4 1.0 CE1 A:HIS41 2.7 41.4 1.0 C1 A:E4Z201 2.7 51.8 1.0 C5 A:E4Z201 3.0 40.7 1.0 CG A:ASP108 3.0 54.5 1.0 CD A:GLU119 3.2 55.8 1.0 OD1 A:ASP108 3.3 49.5 1.0 CD2 A:HIS41 3.3 42.9 1.0 C A:ILE120 3.3 40.1 1.0 OE1 A:GLU119 3.7 50.5 1.0 N A:ILE120 3.8 38.6 1.0 MN A:MN204 3.8 50.5 1.0 O A:HOH308 3.9 52.4 1.0 ND1 A:HIS41 3.9 38.2 1.0 CA A:ILE120 4.0 41.2 1.0 C2 A:E4Z201 4.1 53.1 1.0 O A:HOH304 4.1 46.6 1.0 CG A:HIS41 4.2 47.0 1.0 C4 A:E4Z201 4.3 44.5 1.0 CG A:GLU119 4.4 48.3 1.0 N A:GLY121 4.4 52.9 1.0 CB A:ILE120 4.4 40.7 1.0 CB A:ASP108 4.4 43.7 1.0 H1 A:E4Z201 4.4 63.9 1.0 NZ A:LYS134 4.5 68.7 1.0 CE A:LYS134 4.5 64.1 1.0 O3 A:E4Z201 4.6 54.4 1.0 CA A:GLY121 4.7 33.6 1.0 C A:GLU119 4.7 51.9 1.0 C6 A:E4Z201 4.9 51.1 1.0 CG2 A:ILE120 5.0 37.6 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease I38T (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:50.5 occ:1.00 O3 A:E4Z201 1.9 54.4 1.0 OD1 A:ASP108 2.1 49.5 1.0 O2 A:E4Z201 2.1 48.4 1.0 O A:HOH306 2.3 38.7 1.0 OE2 A:GLU80 2.3 49.9 1.0 O A:HOH304 2.4 46.6 1.0 C6 A:E4Z201 3.0 51.1 1.0 CD A:GLU80 3.2 45.1 1.0 CG A:ASP108 3.2 54.5 1.0 C5 A:E4Z201 3.3 40.7 1.0 C4 A:E4Z201 3.6 44.5 1.0 OD2 A:ASP108 3.7 38.9 1.0 CE1 A:HIS41 3.8 41.4 1.0 OE1 A:GLU80 3.8 70.2 1.0 MN A:MN203 3.8 43.1 1.0 H18 A:E4Z201 3.8 68.5 1.0 CG A:GLU80 4.0 51.7 1.0 N3 A:E4Z201 4.1 46.3 1.0 O A:PRO107 4.1 52.9 1.0 CB A:GLU80 4.3 48.3 1.0 CB A:ASP108 4.3 43.7 1.0 CA A:ASP108 4.3 50.0 1.0 OE1 A:GLU119 4.4 50.5 1.0 C10 A:E4Z201 4.4 57.0 1.0 C A:PRO107 4.4 51.1 1.0 C1 A:E4Z201 4.5 51.8 1.0 O A:LEU106 4.6 55.7 1.0 N A:ASP108 4.6 48.0 1.0 OE2 A:GLU119 4.6 47.5 1.0 NE2 A:HIS41 4.6 49.0 1.0 ND1 A:HIS41 4.7 38.2 1.0 O1 A:E4Z201 4.8 49.9 1.0 H9 A:E4Z201 4.8 49.0 1.0 O A:HOH307 4.9 64.8 1.0 CA A:GLU80 4.9 55.0 1.0 H12 A:E4Z201 5.0 59.6 1.0 H15 A:E4Z201 5.0 61.1 1.0 CD A:GLU119 5.0 55.8 1.0

G.Kumar, M.Cuypers, R.R.Webby, T.R.Webb, S.W.White. Structural Insights Into the Substrate Specificity of the Endonuclease Activity of the Influenza Virus Cap-Snatching Mechanism. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33469660
DOI: 10.1093/NAR/GKAA1294