Manganese in PDB 4mk1: 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease

The structure of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk1 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)	40.32 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.932, 101.655, 66.212, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.8

The structure of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Manganese atom in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease (pdb code 4mk1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease, PDB code: 4mk1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:26.1 occ:1.00 OD2 A:ASP108 2.2 27.6 1.0 O A:ILE120 2.2 27.4 1.0 OE2 A:GLU119 2.2 29.7 1.0 O01 A:27Y307 2.2 25.3 1.0 O09 A:27Y307 2.2 26.4 1.0 NE2 A:HIS41 2.3 25.1 1.0 C02 A:27Y307 2.9 31.2 1.0 C08 A:27Y307 2.9 25.6 1.0 CG A:ASP108 3.0 24.8 1.0 CD A:GLU119 3.2 34.4 1.0 CE1 A:HIS41 3.2 32.2 1.0 OD1 A:ASP108 3.3 26.1 1.0 HE1 A:HIS41 3.3 38.6 1.0 C A:ILE120 3.3 27.9 1.0 CD2 A:HIS41 3.3 24.4 1.0 H A:ILE120 3.3 28.1 1.0 HD2 A:HIS41 3.5 29.3 1.0 HB A:ILE120 3.6 30.8 1.0 HZ3 A:LYS134 3.6 48.4 1.0 HZ1 A:LYS134 3.7 48.4 1.0 N A:ILE120 3.7 23.4 1.0 OE1 A:GLU119 3.8 29.5 1.0 MN A:MN302 3.8 35.5 0.7 HE3 A:LYS134 3.8 45.9 1.0 HA2 A:GLY121 3.9 28.4 1.0 O A:HOH491 4.0 27.3 1.0 CA A:ILE120 4.0 23.7 1.0 HG3 A:GLU119 4.0 37.2 1.0 NZ A:LYS134 4.0 40.4 1.0 N07 A:27Y307 4.1 32.5 1.0 C03 A:27Y307 4.2 44.8 1.0 O A:HOH499 4.2 45.7 1.0 CG A:GLU119 4.2 31.0 1.0 CB A:ILE120 4.3 25.7 1.0 ND1 A:HIS41 4.3 25.3 1.0 O A:HOH404 4.3 31.9 1.0 CG A:HIS41 4.4 26.3 1.0 N A:GLY121 4.4 26.2 1.0 HG22 A:ILE120 4.4 33.3 1.0 CB A:ASP108 4.4 21.2 1.0 HA A:GLU119 4.4 30.8 1.0 CE A:LYS134 4.5 38.2 1.0 CA A:GLY121 4.6 23.7 1.0 HB2 A:ASP108 4.6 25.5 1.0 C A:GLU119 4.6 28.8 1.0 OE2 A:GLU80 4.8 28.6 1.0 HB3 A:ASP108 4.8 25.5 1.0 HG2 A:GLU119 4.9 37.2 1.0 HZ2 A:LYS134 4.9 48.4 1.0 HA A:ILE120 4.9 28.5 1.0 CG2 A:ILE120 4.9 27.7 1.0 CA A:GLU119 4.9 25.7 1.0

Manganese binding site 2 out of 4 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:35.5 occ:0.70 O09 A:27Y307 2.1 26.4 1.0 OE2 A:GLU80 2.1 28.6 1.0 OD1 A:ASP108 2.2 26.1 1.0 O A:HOH491 2.2 27.3 1.0 O A:HOH534 2.2 28.9 1.0 O A:HOH427 2.2 25.0 1.0 C08 A:27Y307 3.0 25.6 1.0 CD A:GLU80 3.2 28.3 1.0 N07 A:27Y307 3.2 32.5 1.0 HE1 A:HIS41 3.2 38.6 1.0 CG A:ASP108 3.3 24.8 1.0 HB2 A:GLU80 3.5 34.1 1.0 OD2 A:ASP108 3.8 27.6 1.0 MN A:MN301 3.8 26.1 1.0 HA A:ASP108 3.8 27.4 1.0 CE1 A:HIS41 3.9 32.2 1.0 OE1 A:GLU80 3.9 30.8 1.0 O A:HOH408 4.0 35.0 1.0 HG2 A:GLU80 4.0 34.7 1.0 CG A:GLU80 4.0 28.9 1.0 O09 A:27Y308 4.1 31.6 0.7 CB A:GLU80 4.2 28.4 1.0 O A:PRO107 4.2 27.2 1.0 O A:LEU106 4.3 29.0 1.0 C02 A:27Y307 4.3 31.2 1.0 O A:HOH501 4.3 43.0 1.0 OE1 A:GLU119 4.4 29.5 1.0 O A:HOH499 4.4 45.7 1.0 CB A:ASP108 4.4 21.2 1.0 C A:PRO107 4.4 29.6 1.0 HA A:GLU80 4.4 29.3 1.0 OE2 A:GLU119 4.4 29.7 1.0 CA A:ASP108 4.5 22.8 1.0 NE2 A:HIS41 4.5 25.1 1.0 N A:ASP108 4.5 24.7 1.0 C06 A:27Y307 4.5 44.5 1.0 MN A:MN303 4.8 34.6 0.6 O01 A:27Y307 4.8 25.3 1.0 HB3 A:ASP108 4.8 25.5 1.0 CD A:GLU119 4.9 34.4 1.0 CA A:GLU80 4.9 24.4 1.0 HA A:PRO107 4.9 38.7 1.0 H A:ASP108 4.9 29.6 1.0 HG3 A:GLU80 4.9 34.7 1.0 HB3 A:GLU80 5.0 34.1 1.0 ND1 A:HIS41 5.0 25.3 1.0

Manganese binding site 3 out of 4 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:34.6 occ:0.61 O01 A:27Y309 2.1 31.2 0.7 O09 A:27Y308 2.1 31.6 0.7 OE1 A:GLU80 2.1 30.8 1.0 O01 A:27Y308 2.2 43.3 0.7 O09 A:27Y309 2.2 34.7 0.7 O A:HOH408 2.2 35.0 1.0 C02 A:27Y309 2.8 31.9 0.7 C08 A:27Y308 2.8 31.5 0.7 C02 A:27Y308 2.8 27.6 0.7 C08 A:27Y309 2.9 32.4 0.7 CD A:GLU80 3.2 28.3 1.0 H A:GLY81 3.5 38.0 1.0 OE2 A:GLU80 3.6 28.6 1.0 HE2 A:TYR24 3.7 64.8 1.0 O A:HOH410 3.7 37.0 1.0 O A:HOH502 3.7 45.9 1.0 O A:HOH500 3.7 35.7 1.0 O A:HOH534 3.9 28.9 1.0 HA A:GLU80 4.0 29.3 1.0 N07 A:27Y308 4.1 40.7 0.7 HB1 A:ALA20 4.2 38.0 1.0 C03 A:27Y309 4.2 39.6 0.7 N07 A:27Y309 4.2 41.3 0.7 C03 A:27Y308 4.2 31.5 0.7 O A:HOH427 4.2 25.0 1.0 N A:GLY81 4.3 31.7 1.0 OH A:TYR24 4.4 66.5 1.0 HB2 A:ALA20 4.5 38.0 1.0 CE2 A:TYR24 4.5 54.0 1.0 CG A:GLU80 4.5 28.9 1.0 HG3 A:GLU80 4.6 34.7 1.0 O A:ARG82 4.8 31.2 1.0 MN A:MN302 4.8 35.5 0.7 CB A:ALA20 4.8 31.7 1.0 CA A:GLU80 4.8 24.4 1.0 CZ A:TYR24 4.9 63.6 1.0 N07 A:27Y307 5.0 32.5 1.0

Manganese binding site 4 out of 4 in the 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 5-Bromopyridine-2,3-Diol Bound to Influenza 2009 PH1N1 Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:0.2 occ:0.45 NE2 A:HIS74 2.2 71.6 1.0 CE1 A:HIS74 3.0 71.7 1.0 HE1 A:HIS74 3.1 86.0 1.0 CD2 A:HIS74 3.3 62.9 1.0 HD2 A:HIS74 3.6 75.5 1.0 HE1 A:PHE53 3.8 57.5 1.0 ND1 A:HIS74 4.2 60.1 1.0 HG3 A:PRO68 4.4 96.5 1.0 CG A:HIS74 4.4 55.5 1.0 HG2 A:PRO68 4.6 96.5 1.0 CE1 A:PHE53 4.7 47.9 1.0 HZ A:PHE53 4.7 60.2 1.0 HD1 A:HIS74 5.0 72.1 1.0 CG A:PRO68 5.0 80.4 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