Magnesium in PDB 6whm: The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak)

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak), PDB code: 6whm was solved by M.G.Cuypers, G.Kumar, T.Webb, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.35 / 1.92
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.885, 89.885, 134.295, 90, 90, 90
R / Rfree (%)	17.7 / 21.7

The structure of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak) also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Magnesium atom in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak) (pdb code 6whm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak), PDB code: 6whm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:31.1 occ:0.70 MN A:MN204 0.3 34.9 0.3 OE2 A:GLU119 1.8 49.0 1.0 O B:HOH102 2.1 41.7 1.0 O A:ILE120 2.1 41.8 1.0 OD2 A:ASP108 2.2 40.8 1.0 NE2 A:HIS41 2.5 46.2 1.0 MG A:MG207 2.9 63.1 1.0 CD A:GLU119 2.9 51.0 1.0 CG A:ASP108 3.1 41.5 1.0 C A:ILE120 3.3 40.1 1.0 CE1 A:HIS41 3.3 40.5 1.0 OD1 A:ASP108 3.4 46.5 1.0 OE1 A:GLU119 3.4 54.4 1.0 N A:ILE120 3.5 37.4 1.0 CD2 A:HIS41 3.5 41.5 1.0 CA A:ILE120 3.9 36.4 1.0 OP2 B:DA2 4.1 107.1 1.0 CG A:GLU119 4.1 40.9 1.0 N A:GLY121 4.3 35.6 1.0 C A:GLU119 4.4 38.3 1.0 ND1 A:HIS41 4.5 41.8 1.0 CB A:ASP108 4.5 35.6 1.0 CB A:ILE120 4.5 37.9 1.0 CA A:GLY121 4.6 38.7 1.0 CG A:HIS41 4.6 44.1 1.0 CA A:GLU119 4.7 36.9 1.0 CE A:LYS134 4.7 79.3 1.0 OP1 B:DT1 4.7 147.3 1.0 CB A:GLU119 5.0 40.4 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the 2009/H1N1/California Pa Endonuclease Wild Type Bound to Dna Oligomer Tagc (Cleaved Ttagcatt, 5MM Overnight Dna Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:63.1 occ:1.00 OD1 A:ASP108 2.0 46.5 1.0 MN A:MN204 2.7 34.9 0.3 OP1 B:DT1 2.9 147.3 1.0 CG A:ASP108 2.9 41.5 1.0 MG A:MG203 2.9 31.1 0.7 OD2 A:ASP108 3.1 40.8 1.0 CE1 A:HIS41 3.2 40.5 1.0 O A:HOH335 3.2 47.1 1.0 OE1 A:GLU80 3.4 60.8 1.0 NE2 A:HIS41 3.5 46.2 1.0 OE2 A:GLU119 3.8 49.0 1.0 OE1 A:GLU119 3.9 54.4 1.0 O B:HOH102 3.9 41.7 1.0 O A:LEU106 4.2 48.8 1.0 P B:DT1 4.3 150.3 1.0 CB A:ASP108 4.3 35.6 1.0 CD A:GLU119 4.3 51.0 1.0 CD A:GLU80 4.3 60.3 1.0 ND1 A:HIS41 4.3 41.8 1.0 C A:PRO107 4.6 38.6 1.0 CA A:ASP108 4.6 37.1 1.0 O A:PRO107 4.6 39.5 1.0 N A:ASP108 4.7 33.0 1.0 C5' B:DT1 4.7 126.7 1.0 CD2 A:HIS41 4.8 41.5 1.0 O A:ILE120 4.9 41.8 1.0 OE2 A:GLU80 4.9 67.1 1.0

G.Kumar, M.Cuypers, R.R.Webby, T.R.Webb, S.W.White. Structural Insights Into the Substrate Specificity of the Endonuclease Activity of the Influenza Virus Cap-Snatching Mechanism. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33469660
DOI: 10.1093/NAR/GKAA1294