Manganese in PDB 5cxr: Influenza Endonuclease Complexed with 4-Bromopyrazole

The structure of Influenza Endonuclease Complexed with 4-Bromopyrazole, PDB code: 5cxr was solved by J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.48 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.905, 102.451, 66.062, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.8

The structure of Influenza Endonuclease Complexed with 4-Bromopyrazole also contains other interesting chemical elements:

Bromine

(Br)

5 atoms

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

Manganese binding site 1 out of 3 in the Influenza Endonuclease Complexed with 4-Bromopyrazole


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Influenza Endonuclease Complexed with 4-Bromopyrazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:29.6 occ:1.00 OE2 A:GLU119 2.2 25.6 1.0 OD2 A:ASP108 2.2 21.2 1.0 O A:ILE120 2.3 24.6 1.0 NE2 A:HIS41 2.3 23.2 1.0 O A:HOH491 2.3 27.2 1.0 O A:HOH521 2.5 21.9 1.0 CE1 A:HIS41 3.1 19.8 1.0 CG A:ASP108 3.1 17.9 1.0 HE1 A:HIS41 3.2 23.7 1.0 CD A:GLU119 3.2 32.0 1.0 O A:HOH537 3.3 33.4 1.0 OD1 A:ASP108 3.3 21.9 1.0 CD2 A:HIS41 3.3 22.9 1.0 H A:ILE120 3.4 23.2 1.0 C A:ILE120 3.4 21.7 1.0 HD2 A:HIS41 3.6 27.5 1.0 HB A:ILE120 3.7 28.2 1.0 HZ1 A:LYS134 3.7 62.4 1.0 OE1 A:GLU119 3.8 25.7 1.0 MN A:MN302 3.8 34.9 1.0 HZ2 A:LYS134 3.8 62.4 1.0 N A:ILE120 3.8 19.4 1.0 O A:HOH424 4.0 26.9 1.0 CA A:ILE120 4.1 20.3 1.0 HG3 A:GLU119 4.1 38.1 1.0 HA2 A:GLY121 4.1 28.4 1.0 HE3 A:LYS134 4.2 55.6 1.0 NZ A:LYS134 4.2 52.0 1.0 ND1 A:HIS41 4.2 25.7 1.0 CG A:GLU119 4.3 31.7 1.0 O A:HOH526 4.3 48.9 1.0 CG A:HIS41 4.4 28.3 1.0 CB A:ILE120 4.4 23.5 1.0 HA A:GLU119 4.5 24.9 1.0 N A:GLY121 4.5 26.9 1.0 CB A:ASP108 4.5 16.9 1.0 HG22 A:ILE120 4.6 31.8 1.0 O A:HOH471 4.6 28.6 1.0 HB2 A:ASP108 4.7 20.3 1.0 C A:GLU119 4.7 22.9 1.0 CE A:LYS134 4.7 46.3 1.0 CA A:GLY121 4.8 23.6 1.0 OE1 A:GLU80 4.8 25.1 1.0 O A:HOH513 4.9 29.7 1.0 HB3 A:ASP108 4.9 20.3 1.0 HG2 A:GLU119 4.9 38.1 1.0 HZ3 A:LYS134 4.9 62.4 1.0 HD1 A:HIS41 5.0 30.8 1.0 HA A:ILE120 5.0 24.3 1.0

Manganese binding site 2 out of 3 in the Influenza Endonuclease Complexed with 4-Bromopyrazole


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Influenza Endonuclease Complexed with 4-Bromopyrazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:34.9 occ:1.00 O A:HOH451 1.9 22.2 1.0 O A:HOH521 2.0 21.9 1.0 O A:HOH513 2.1 29.7 1.0 OE1 A:GLU80 2.2 25.1 1.0 OD1 A:ASP108 2.2 21.9 1.0 O A:HOH424 2.2 26.9 1.0 HE1 A:HIS41 3.1 23.7 1.0 CG A:ASP108 3.2 17.9 1.0 CD A:GLU80 3.2 24.6 1.0 HB2 A:GLU80 3.5 38.8 1.0 HA A:ASP108 3.7 19.2 1.0 OD2 A:ASP108 3.8 21.2 1.0 O A:HOH529 3.8 52.3 1.0 MN A:MN301 3.8 29.6 1.0 CE1 A:HIS41 3.8 19.8 1.0 O A:HOH537 3.8 33.4 1.0 H041 A:BYZ308 4.0 1.0 1.0 OE2 A:GLU80 4.1 28.5 1.0 CG A:GLU80 4.1 22.1 1.0 O A:HOH429 4.1 47.9 1.0 HG2 A:GLU80 4.1 26.6 1.0 O A:PRO107 4.2 22.8 1.0 CB A:GLU80 4.2 32.3 1.0 O A:LEU106 4.3 25.1 1.0 HA A:GLU80 4.3 25.9 1.0 CB A:ASP108 4.4 16.9 1.0 CA A:ASP108 4.4 16.0 1.0 C A:PRO107 4.4 20.3 1.0 NE2 A:HIS41 4.4 23.2 1.0 OE1 A:GLU119 4.4 25.7 1.0 OE2 A:GLU119 4.5 25.6 1.0 N A:ASP108 4.5 18.2 1.0 O A:HOH526 4.6 48.9 1.0 O A:HOH481 4.6 42.1 1.0 HB3 A:ASP108 4.8 20.3 1.0 CA A:GLU80 4.8 21.6 1.0 ND1 A:HIS41 4.9 25.7 1.0 N2 A:BYZ308 4.9 0.8 1.0 CD A:GLU119 4.9 32.0 1.0 HA A:PRO107 4.9 29.0 1.0 HG3 A:GLU80 5.0 26.6 1.0 HB3 A:GLU80 5.0 38.8 1.0

Manganese binding site 3 out of 3 in the Influenza Endonuclease Complexed with 4-Bromopyrazole


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Influenza Endonuclease Complexed with 4-Bromopyrazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:75.7 occ:0.41 HE2 A:HIS74 2.4 82.9 1.0 NE2 A:HIS74 3.1 69.0 1.0 HG2 A:PRO68 3.3 99.5 1.0 HE1 A:PHE53 3.5 51.3 1.0 CD2 A:HIS74 3.9 60.9 1.0 CE1 A:HIS74 3.9 66.3 1.0 HD2 A:HIS74 4.0 73.0 1.0 HE1 A:HIS74 4.1 79.6 1.0 CG A:PRO68 4.2 83.0 1.0 HG3 A:PRO68 4.2 99.5 1.0 CE1 A:PHE53 4.3 42.8 1.0 HZ A:PHE53 4.4 50.2 1.0 CZ A:PHE53 4.8 41.8 1.0 HB2 A:PRO68 4.9 0.0 1.0 HD2 A:PRO68 4.9 0.0 1.0 ND1 A:HIS74 5.0 60.9 1.0 CG A:HIS74 5.0 55.1 1.0

J.D.Bauman, J.J.Harrison, E.Arnold. Rapid Experimental Sad Phasing and Hot-Spot Identification with Halogenated Fragments. Iucrj V. 3 51 2016.
ISSN: ESSN 2052-2525
PubMed: 26870381
DOI: 10.1107/S2052252515021259