Manganese in PDB 4m5r: High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol

The structure of High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol, PDB code: 4m5r 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)	31.94 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.246, 102.978, 66.226, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.4

The binding sites of Manganese atom in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol (pdb code 4m5r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol, PDB code: 4m5r:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:16.9 occ:1.00 O A:ILE120 2.1 18.7 1.0 OE2 A:GLU119 2.1 30.1 1.0 OD2 A:ASP108 2.1 15.1 1.0 O A:HOH438 2.2 28.2 1.0 O A:HOH409 2.2 19.3 1.0 NE2 A:HIS41 2.2 14.8 1.0 CE1 A:HIS41 3.1 14.9 1.0 CG A:ASP108 3.1 14.1 1.0 CD A:GLU119 3.1 24.2 1.0 HE1 A:HIS41 3.2 17.9 1.0 C A:ILE120 3.2 18.9 1.0 CD2 A:HIS41 3.3 13.8 1.0 H A:ILE120 3.3 19.4 1.0 OD1 A:ASP108 3.4 18.5 1.0 HD2 A:HIS41 3.5 16.6 1.0 OE1 A:GLU119 3.6 26.2 1.0 HE3 A:LYS134 3.6 59.2 1.0 HB A:ILE120 3.7 22.6 1.0 N A:ILE120 3.7 16.2 1.0 O A:HOH463 3.9 34.3 1.0 HA2 A:GLY121 3.9 17.7 1.0 MN A:MN302 3.9 79.1 1.0 O A:HOH566 3.9 46.1 1.0 HZ3 A:LYS134 4.0 62.8 1.0 CA A:ILE120 4.0 18.5 1.0 HZ1 A:LYS134 4.1 62.8 1.0 HG3 A:GLU119 4.2 25.1 1.0 ND1 A:HIS41 4.3 16.7 1.0 N A:GLY121 4.3 17.1 1.0 CG A:GLU119 4.3 20.9 1.0 CB A:ILE120 4.4 18.8 1.0 NZ A:LYS134 4.4 52.3 1.0 CG A:HIS41 4.4 15.5 1.0 O A:HOH607 4.4 56.8 1.0 HA A:GLU119 4.4 20.6 1.0 CE A:LYS134 4.4 49.4 1.0 CB A:ASP108 4.5 14.3 1.0 O A:HOH404 4.6 18.0 1.0 C A:GLU119 4.6 16.9 1.0 CA A:GLY121 4.6 14.8 1.0 HB2 A:ASP108 4.6 17.2 1.0 HG22 A:ILE120 4.7 25.1 1.0 HB3 A:ASP108 4.8 17.2 1.0 HA A:ILE120 4.9 22.2 1.0 CA A:GLU119 4.9 17.1 1.0 HE2 A:LYS134 4.9 59.2 1.0 HG A:CYS45 5.0 19.2 1.0 HG2 A:GLU119 5.0 25.1 1.0

Manganese binding site 2 out of 4 in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:79.1 occ:1.00 O A:HOH431 2.2 23.9 1.0 OD1 A:ASP108 2.2 18.5 1.0 O A:HOH438 2.2 28.2 1.0 O A:HOH566 2.2 46.1 1.0 O A:HOH625 2.2 27.3 1.0 HE1 A:HIS41 3.2 17.9 1.0 CG A:ASP108 3.3 14.1 1.0 O A:HOH408 3.7 23.3 1.0 HB2 A:GLU80 3.7 24.6 1.0 OE1 A:GLU80 3.8 24.4 1.0 OD2 A:ASP108 3.8 15.1 1.0 CE1 A:HIS41 3.9 14.9 1.0 MN A:MN301 3.9 16.9 1.0 HA A:ASP108 3.9 18.0 1.0 O A:HOH463 3.9 34.3 1.0 MN A:MN303 4.0 24.9 1.0 O A:LEU106 4.0 21.4 1.0 O A:HOH607 4.2 56.8 1.0 O A:PRO107 4.3 15.8 1.0 NE2 A:HIS41 4.4 14.8 1.0 O A:HOH450 4.4 30.2 1.0 OE1 A:GLU119 4.4 26.2 1.0 CD A:GLU80 4.5 21.2 1.0 HA A:GLU80 4.5 20.2 1.0 O A:HOH541 4.5 43.6 1.0 CB A:ASP108 4.5 14.3 1.0 C A:PRO107 4.5 16.7 1.0 O A:HOH546 4.5 44.1 1.0 CA A:ASP108 4.5 15.0 1.0 CB A:GLU80 4.6 20.5 1.0 HB3 A:LEU106 4.6 28.8 1.0 N A:ASP108 4.7 17.7 1.0 OE2 A:GLU119 4.8 30.1 1.0 ND1 A:HIS41 4.9 16.7 1.0 HB3 A:ASP108 4.9 17.2 1.0 C A:LEU106 4.9 20.0 1.0 O A:HOH409 5.0 19.3 1.0 HA A:PRO107 5.0 21.3 1.0 HB2 A:LEU106 5.0 28.8 1.0

Manganese binding site 3 out of 4 in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:24.9 occ:1.00 OE1 A:GLU80 2.0 24.4 1.0 NFE A:MSR306 2.2 24.7 1.0 O A:HOH565 2.2 26.8 1.0 O A:HOH408 2.2 23.3 1.0 O A:HOH625 2.2 27.3 1.0 NFE A:MSR304 2.3 20.5 1.0 CD A:GLU80 3.1 21.2 1.0 C2 A:MSR306 3.1 28.7 1.0 C5 A:MSR304 3.1 21.8 1.0 C5 A:MSR306 3.1 21.2 1.0 H5 A:MSR304 3.3 26.1 1.0 H2 A:MSR306 3.3 34.5 1.0 C2 A:MSR304 3.3 22.0 1.0 H5 A:MSR306 3.3 25.4 1.0 OE2 A:GLU80 3.4 27.1 1.0 H A:GLY81 3.6 18.0 1.0 H2 A:MSR304 3.6 26.4 1.0 MN A:MN302 4.0 79.1 1.0 HA A:GLU80 4.0 20.2 1.0 O A:HOH590 4.1 41.7 1.0 O A:HOH431 4.1 23.9 1.0 O A:HOH450 4.2 30.2 1.0 N3 A:MSR306 4.3 29.1 1.0 O A:HOH411 4.3 20.2 1.0 C4 A:MSR306 4.3 24.2 1.0 C4 A:MSR304 4.4 19.8 1.0 N A:GLY81 4.4 15.0 1.0 CG A:GLU80 4.4 24.0 1.0 N3 A:MSR304 4.4 23.4 1.0 HE1 A:HIS41 4.5 17.9 1.0 HB2 A:GLU80 4.5 24.6 1.0 O A:HOH477 4.5 26.6 1.0 HD1 A:HIS41 4.6 20.0 1.0 HB1 A:ALA20 4.6 21.4 1.0 HB2 A:ALA20 4.7 21.4 1.0 CA A:GLU80 4.7 16.8 1.0 CB A:GLU80 4.8 20.5 1.0 HG3 A:GLU80 4.8 28.8 1.0 O A:HOH546 4.8 44.1 1.0 HG23 A:ILE38 4.9 21.5 1.0 O A:HOH463 4.9 34.3 1.0 CE1 A:HIS41 5.0 14.9 1.0 HA2 A:GLY81 5.0 17.5 1.0 HD21 A:LEU42 5.0 32.0 1.0 ND1 A:HIS41 5.0 16.7 1.0 HG A:LEU42 5.0 22.3 1.0

Manganese binding site 4 out of 4 in the High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of High-Resolution Influenza 2009 H1N1 Endonuclease Bound to 4-(1H- Imidazol-1-Yl)Phenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn307 b:33.5 occ:0.37 O A:HOH481 2.2 37.3 1.0 NE2 A:HIS74 2.2 39.8 1.0 O A:HOH606 2.2 61.5 1.0 CE1 A:HIS74 3.0 46.1 1.0 HE1 A:HIS74 3.0 55.3 1.0 CD2 A:HIS74 3.3 42.0 1.0 HD2 A:HIS74 3.6 50.4 1.0 HE1 A:PHE53 3.8 35.4 1.0 HG3 A:PRO68 4.0 87.6 1.0 ND1 A:HIS74 4.2 40.2 1.0 O A:HOH598 4.3 53.5 1.0 HG2 A:PRO68 4.3 87.6 1.0 CG A:HIS74 4.4 33.6 1.0 CG A:PRO68 4.6 73.0 1.0 HZ A:PHE53 4.7 37.3 1.0 CE1 A:PHE53 4.7 29.5 1.0 HD1 A:HIS74 4.9 48.2 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