Manganese in PDB 7kbc: The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kbc 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)	44.98 / 2.25
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.963, 89.963, 133.943, 90, 90, 90
R / Rfree (%)	19.5 / 22.8

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Mutant E119D (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 Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid (pdb code 7kbc). 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 Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid, PDB code: 7kbc:
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 Mutant E119D (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 Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn208 b:49.1 occ:1.00 OD2 A:ASP108 2.0 41.7 1.0 O1 A:E4Z201 2.0 61.1 1.0 O A:ILE120 2.1 62.3 1.0 NE2 A:HIS41 2.2 48.3 1.0 O2 A:E4Z201 2.3 61.8 1.0 CE1 A:HIS41 2.7 56.2 1.0 C1 A:E4Z201 2.8 60.8 1.0 CG A:ASP108 2.9 52.0 1.0 C5 A:E4Z201 3.0 48.7 1.0 OD1 A:ASP108 3.1 52.3 1.0 OD1 A:ASP119 3.2 69.9 1.0 C A:ILE120 3.3 45.4 1.0 CD2 A:HIS41 3.4 51.9 1.0 N A:ILE120 3.7 42.9 1.0 MN A:MN209 3.7 61.7 1.0 O A:HOH301 3.8 50.2 1.0 CA A:ILE120 3.9 45.9 1.0 ND1 A:HIS41 3.9 35.7 1.0 C2 A:E4Z201 4.2 61.4 1.0 CB A:ASP108 4.3 47.7 1.0 CG A:HIS41 4.3 50.7 1.0 C4 A:E4Z201 4.3 59.8 1.0 CB A:ILE120 4.3 41.0 1.0 N A:GLY121 4.4 57.4 1.0 NZ A:LYS134 4.4 72.2 1.0 CG A:ASP119 4.4 64.2 1.0 O A:HOH328 4.5 70.3 1.0 C A:ASP119 4.5 56.4 1.0 H1 A:E4Z201 4.5 73.7 1.0 O3 A:E4Z201 4.6 61.2 1.0 CA A:GLY121 4.7 47.1 1.0 CA A:ASP119 4.9 55.0 1.0 CE A:LYS134 4.9 76.8 1.0 C6 A:E4Z201 4.9 59.0 1.0 CG2 A:ILE120 5.0 41.4 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Mutant E119D (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 Mutant E119D (Construct with Truncated Loop 51-72) in Complex with Baloxavir Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn209 b:61.7 occ:1.00 O3 A:E4Z201 1.9 61.2 1.0 O2 A:E4Z201 2.1 61.8 1.0 OD1 A:ASP108 2.1 52.3 1.0 O A:HOH305 2.2 47.2 1.0 OE2 A:GLU80 2.4 55.4 1.0 O A:HOH301 2.5 50.2 1.0 C6 A:E4Z201 3.0 59.0 1.0 CG A:ASP108 3.2 52.0 1.0 CD A:GLU80 3.2 46.6 1.0 C5 A:E4Z201 3.2 48.7 1.0 CG A:GLU80 3.3 48.0 1.0 C4 A:E4Z201 3.6 59.8 1.0 OD2 A:ASP108 3.7 41.7 1.0 CE1 A:HIS41 3.7 56.2 1.0 MN A:MN208 3.7 49.1 1.0 H18 A:E4Z201 3.9 71.0 1.0 C1 A:GOL206 4.0 67.1 1.0 O A:PRO107 4.1 58.9 1.0 N3 A:E4Z201 4.2 49.5 1.0 CA A:ASP108 4.3 45.4 1.0 CB A:ASP108 4.3 47.7 1.0 OE1 A:GLU80 4.3 54.7 1.0 O3 A:GOL206 4.4 70.1 1.0 C A:PRO107 4.4 53.9 1.0 C1 A:E4Z201 4.5 60.8 1.0 C10 A:E4Z201 4.5 59.1 1.0 O A:LEU106 4.5 51.3 1.0 ND1 A:HIS41 4.6 35.7 1.0 N A:ASP108 4.6 53.3 1.0 H9 A:E4Z201 4.6 64.1 1.0 NE2 A:HIS41 4.6 48.3 1.0 CB A:GLU80 4.7 49.4 1.0 O1 A:E4Z201 4.7 61.1 1.0 O1 A:GOL206 4.8 64.0 1.0 H15 A:E4Z201 5.0 67.5 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