Manganese in PDB 5jhv: Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000

The structure of Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000, PDB code: 5jhv was solved by S.Fudo, N.Yamamoto, M.Nukaga, T.Odagiri, M.Tashiro, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.49 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.243, 87.404, 66.497, 90.00, 94.31, 90.00
R / Rfree (%)	19.7 / 23.4

The binding sites of Manganese atom in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000 (pdb code 5jhv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000, PDB code: 5jhv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:37.8 occ:1.00 OE2 A:GLU119 2.0 35.6 1.0 O A:ILE120 2.1 35.2 1.0 OD2 A:ASP108 2.3 31.3 1.0 NE2 A:HIS41 2.3 32.8 1.0 O A:HOH421 2.4 29.1 1.0 CD A:GLU119 3.1 37.3 1.0 CE1 A:HIS41 3.2 31.6 1.0 CG A:ASP108 3.3 32.6 1.0 CD2 A:HIS41 3.3 30.8 1.0 C A:ILE120 3.3 34.2 1.0 OD1 A:ASP108 3.5 37.5 1.0 OE1 A:GLU119 3.8 41.0 1.0 N A:ILE120 4.0 31.9 1.0 MN A:MN302 4.1 55.3 1.0 CG A:GLU119 4.1 36.5 1.0 CA A:ILE120 4.2 32.6 1.0 NZ A:LYS134 4.2 49.3 1.0 ND1 A:HIS41 4.3 34.1 1.0 N A:GLY121 4.3 35.4 1.0 CG A:HIS41 4.3 29.4 1.0 CA A:GLY121 4.4 31.6 1.0 O A:HOH406 4.4 30.1 1.0 CE A:LYS134 4.6 44.1 1.0 CB A:ASP108 4.6 27.5 1.0 CB A:ILE120 4.7 34.5 1.0 C A:GLU119 4.8 35.7 1.0

Manganese binding site 2 out of 4 in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:55.3 occ:1.00 O A:HOH406 2.0 30.1 1.0 OE2 A:GLU80 2.3 49.6 1.0 OD1 A:ASP108 2.4 37.5 1.0 O A:HOH421 2.5 29.1 1.0 CD A:GLU80 2.9 39.8 1.0 O A:HOH420 3.0 23.9 1.0 CG A:GLU80 3.2 40.5 1.0 CG A:ASP108 3.5 32.6 1.0 CE1 A:HIS41 3.5 31.6 1.0 OE1 A:GLU80 3.9 44.9 1.0 OD2 A:ASP108 4.0 31.3 1.0 MN A:MN301 4.1 37.8 1.0 NE2 A:HIS41 4.3 32.8 1.0 ND1 A:HIS41 4.4 34.1 1.0 CB A:GLU80 4.5 36.8 1.0 CB A:ASP108 4.6 27.5 1.0 OE2 A:GLU119 4.8 35.6 1.0 O A:LEU106 4.8 39.1 1.0 CA A:ASP108 4.9 30.7 1.0 CA A:GLU80 4.9 33.6 1.0 O A:HOH415 5.0 31.9 1.0

Manganese binding site 3 out of 4 in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:53.7 occ:1.00 OD2 B:ASP108 1.8 45.4 1.0 O B:ILE120 1.9 49.2 1.0 O B:HOH405 1.9 44.6 1.0 OE2 B:GLU119 1.9 50.6 1.0 NE2 B:HIS41 2.1 43.9 1.0 CG B:ASP108 2.8 45.8 1.0 CE1 B:HIS41 2.9 40.0 1.0 CD B:GLU119 2.9 46.0 1.0 C B:ILE120 3.0 39.0 1.0 OD1 B:ASP108 3.0 53.4 1.0 CD2 B:HIS41 3.3 42.7 1.0 N B:ILE120 3.4 44.4 1.0 OE1 B:GLU119 3.6 46.4 1.0 CA B:ILE120 3.7 41.5 1.0 CG B:GLU119 4.0 40.6 1.0 MN B:MN302 4.1 63.0 1.0 CB B:ILE120 4.1 40.2 1.0 ND1 B:HIS41 4.1 38.0 1.0 N B:GLY121 4.1 37.9 1.0 CB B:ASP108 4.1 41.2 1.0 C B:GLU119 4.3 43.7 1.0 CG B:HIS41 4.3 37.1 1.0 CE B:LYS134 4.4 58.2 1.0 CA B:GLY121 4.5 42.5 1.0 NZ B:LYS134 4.5 52.7 1.0 OE2 B:GLU80 4.5 48.6 1.0 CA B:GLU119 4.7 49.0 1.0 SG B:CYS45 4.9 29.1 1.0 CB B:GLU119 4.9 45.5 1.0 CG2 B:ILE120 5.0 37.6 1.0

Manganese binding site 4 out of 4 in the Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Apo Form of Influenza Strain H1N1 Polymerase Acidic Subunit N-Terminal Region Crystallized with Polyethylene Glycol 8000 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:63.0 occ:1.00 OE2 B:GLU80 2.1 48.6 1.0 OD1 B:ASP108 2.2 53.4 1.0 OE1 B:GLU80 2.3 58.0 1.0 CD B:GLU80 2.5 53.3 1.0 O B:HOH412 2.6 29.6 1.0 O B:HOH405 3.4 44.6 1.0 CG B:ASP108 3.5 45.8 1.0 O B:LEU106 3.5 53.6 1.0 OE1 B:GLU119 3.8 46.4 1.0 CG B:GLU80 3.9 41.6 1.0 MN B:MN301 4.1 53.7 1.0 O B:PRO107 4.1 49.8 1.0 OE2 B:GLU119 4.1 50.6 1.0 OD2 B:ASP108 4.1 45.4 1.0 C B:PRO107 4.2 48.5 1.0 CE1 B:HIS41 4.3 40.0 1.0 CD B:GLU119 4.4 46.0 1.0 N B:ASP108 4.4 46.6 1.0 C B:LEU106 4.5 51.2 1.0 CA B:ASP108 4.5 45.9 1.0 CB B:ASP108 4.6 41.2 1.0 CB B:GLU80 4.6 43.9 1.0 CA B:PRO107 4.8 46.7 1.0 NE2 B:HIS41 4.8 43.9 1.0

S.Fudo, Q.Fei, M.Nukaga, T.Hoshino. Influence of Precipitants on Molecular Arrangements and Space Groups of Protein Crystals Cryst.Growth Des. V. 17 534 2017.
ISSN: ISSN 1528-7483
DOI: 10.1021/ACS.CGD.6B01385