Manganese in PDB 4m5q: High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure

The structure of High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure, PDB code: 4m5q was solved by J.D.Bauman, D.Patel, K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 1.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.400, 101.490, 66.000, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.4

The binding sites of Manganese atom in the High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure (pdb code 4m5q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure, PDB code: 4m5q:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:19.3 occ:1.00 OE2 A:GLU119 2.1 23.1 1.0 OD2 A:ASP108 2.2 17.1 1.0 O A:ILE120 2.2 20.2 1.0 NE2 A:HIS41 2.2 19.9 1.0 O A:HOH409 2.2 22.3 1.0 O A:HOH435 2.3 22.5 1.0 CE1 A:HIS41 3.1 18.4 1.0 CG A:ASP108 3.1 18.6 1.0 CD A:GLU119 3.1 24.9 1.0 HE1 A:HIS41 3.2 22.1 1.0 CD2 A:HIS41 3.3 17.6 1.0 OD1 A:ASP108 3.4 18.7 1.0 C A:ILE120 3.4 18.6 1.0 H A:ILE120 3.4 22.9 1.0 O A:HOH458 3.4 26.4 1.0 HD2 A:HIS41 3.5 21.1 1.0 HB A:ILE120 3.6 21.6 1.0 OE1 A:GLU119 3.7 21.7 1.0 HZ3 A:LYS134 3.8 49.7 1.0 N A:ILE120 3.8 19.1 1.0 MN A:MN302 3.9 22.6 1.0 HA2 A:GLY121 3.9 23.4 1.0 HZ1 A:LYS134 3.9 49.7 1.0 HG3 A:GLU119 4.0 24.8 1.0 HE3 A:LYS134 4.0 44.4 1.0 CA A:ILE120 4.0 17.8 1.0 O A:HOH509 4.1 22.9 1.0 O A:HOH518 4.2 37.3 1.0 CG A:GLU119 4.2 20.6 1.0 NZ A:LYS134 4.2 41.4 1.0 ND1 A:HIS41 4.2 19.3 1.0 CB A:ILE120 4.3 18.0 1.0 CG A:HIS41 4.3 18.7 1.0 N A:GLY121 4.4 19.5 1.0 HG22 A:ILE120 4.4 26.4 1.0 HA A:GLU119 4.4 23.3 1.0 CB A:ASP108 4.5 16.0 1.0 O A:HOH404 4.5 21.4 1.0 CA A:GLY121 4.6 19.5 1.0 HB2 A:ASP108 4.6 19.2 1.0 CE A:LYS134 4.6 37.0 1.0 C A:GLU119 4.7 19.4 1.0 OE1 A:GLU80 4.8 23.6 1.0 HG2 A:GLU119 4.8 24.8 1.0 HB3 A:ASP108 4.9 19.2 1.0 CG2 A:ILE120 4.9 22.0 1.0 HA3 A:GLY121 4.9 23.4 1.0 HA A:ILE120 4.9 21.3 1.0 CA A:GLU119 5.0 19.4 1.0 HD1 A:HIS41 5.0 23.1 1.0 O A:HOH521 5.0 25.9 1.0

Manganese binding site 2 out of 3 in the High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:22.6 occ:1.00 OE1 A:GLU80 2.1 23.6 1.0 OD1 A:ASP108 2.1 18.7 1.0 O A:HOH435 2.2 22.5 1.0 O A:HOH428 2.2 22.2 1.0 O A:HOH509 2.2 22.9 1.0 O A:HOH521 2.2 25.9 1.0 HE1 A:HIS41 3.2 22.1 1.0 CG A:ASP108 3.2 18.6 1.0 CD A:GLU80 3.2 21.6 1.0 HB2 A:GLU80 3.5 26.3 1.0 OD2 A:ASP108 3.7 17.1 1.0 HA A:ASP108 3.8 18.6 1.0 O A:HOH458 3.8 26.4 1.0 MN A:MN301 3.9 19.3 1.0 CE1 A:HIS41 3.9 18.4 1.0 O A:HOH408 3.9 30.9 1.0 OE2 A:GLU80 4.0 24.1 1.0 CG A:GLU80 4.1 21.9 1.0 HG2 A:GLU80 4.1 26.2 1.0 O A:PRO107 4.1 19.4 1.0 CB A:GLU80 4.2 21.9 1.0 O A:LEU106 4.3 25.3 1.0 HA A:GLU80 4.4 23.0 1.0 CB A:ASP108 4.4 16.0 1.0 OE1 A:GLU119 4.4 21.7 1.0 CA A:ASP108 4.4 15.4 1.0 C A:PRO107 4.4 19.6 1.0 NE2 A:HIS41 4.4 19.9 1.0 N A:ASP108 4.5 17.9 1.0 O A:HOH503 4.5 36.5 1.0 OE2 A:GLU119 4.5 23.1 1.0 O A:HOH518 4.5 37.3 1.0 O A:HOH589 4.6 46.3 1.0 HB3 A:ASP108 4.8 19.2 1.0 CA A:GLU80 4.8 19.1 1.0 CD A:GLU119 4.9 24.9 1.0 H A:ASP108 4.9 21.5 1.0 HA A:PRO107 4.9 23.6 1.0 HG A:CYS45 5.0 24.1 1.0 HG3 A:GLU80 5.0 26.2 1.0

Manganese binding site 3 out of 3 in the High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High-Resolution Apo Influenza 2009 H1N1 Endonuclease Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:31.0 occ:0.29 NE2 A:HIS74 2.2 42.5 1.0 O A:HOH473 2.3 50.3 1.0 CE1 A:HIS74 3.1 46.5 1.0 HE1 A:HIS74 3.2 55.8 1.0 CD2 A:HIS74 3.2 37.5 1.0 HD2 A:HIS74 3.4 45.0 1.0 HE1 A:PHE53 3.6 48.1 1.0 HG3 A:PRO68 4.0 83.7 1.0 HG2 A:PRO68 4.1 83.7 1.0 ND1 A:HIS74 4.2 43.2 1.0 CG A:HIS74 4.3 35.9 1.0 CE1 A:PHE53 4.4 40.1 1.0 HZ A:PHE53 4.5 43.7 1.0 CG A:PRO68 4.5 69.8 1.0 CZ A:PHE53 4.9 36.4 1.0 HD1 A:HIS74 5.0 51.8 1.0

J.D.Bauman, D.Patel, S.F.Baker, R.S.Vijayan, A.Xiang, A.K.Parhi, L.Martinez-Sobrido, E.J.Lavoie, K.Das, E.Arnold. Crystallographic Fragment Screening and Structure-Based Optimization Yields A New Class of Influenza Endonuclease Inhibitors. Acs Chem.Biol. V. 8 2501 2013.
ISSN: ISSN 1554-8929
PubMed: 23978130
DOI: 10.1021/CB400400J