Manganese in PDB 6qw5: Structure and Function of the Toscana Virus Cap Snatching Endonuclease

The structure of Structure and Function of the Toscana Virus Cap Snatching Endonuclease, PDB code: 6qw5 was solved by J.Reguera, R.Jones, G.Bragagniolo, S.Lessoued, M.Mate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.10 / 1.99
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.957, 106.209, 58.623, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.2

The binding sites of Manganese atom in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease (pdb code 6qw5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease, PDB code: 6qw5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure and Function of the Toscana Virus Cap Snatching Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:15.3 occ:1.00 O8 A:XI7303 2.1 16.8 1.0 O A:PHE128 2.1 14.0 1.0 O11 A:XI7303 2.2 20.0 1.0 OE2 A:GLU127 2.2 15.3 1.0 NE2 A:HIS78 2.2 16.6 1.0 OD2 A:ASP113 2.3 12.6 1.0 C10 A:XI7303 2.8 23.4 1.0 C9 A:XI7303 2.8 22.0 1.0 CG A:ASP113 3.1 12.8 1.0 CE1 A:HIS78 3.1 19.1 1.0 CD A:GLU127 3.1 13.8 1.0 CD2 A:HIS78 3.2 15.6 1.0 OD1 A:ASP113 3.2 14.0 1.0 C A:PHE128 3.2 12.7 1.0 MN A:MN302 3.7 8.6 0.7 N A:PHE128 3.7 10.9 1.0 OE1 A:GLU127 3.8 13.1 1.0 CA A:PHE128 3.9 12.9 1.0 O10 A:XI7303 4.0 28.9 1.0 CG A:GLU127 4.0 15.8 1.0 O A:HOH470 4.1 15.2 1.0 CB A:PHE128 4.1 10.3 1.0 O A:HOH416 4.2 19.0 1.0 C8 A:XI7303 4.2 21.4 1.0 ND1 A:HIS78 4.2 20.6 1.0 CG A:HIS78 4.3 22.5 1.0 N A:THR129 4.3 13.4 1.0 CB A:ASP113 4.5 13.7 1.0 O A:HOH431 4.5 22.1 1.0 CA A:THR129 4.5 12.7 1.0 O A:HOH419 4.6 28.2 1.0 CE A:LYS145 4.6 17.6 1.0 C A:GLU127 4.7 12.5 1.0 NZ A:LYS145 4.8 23.3 1.0 O14 A:XI7303 5.0 28.9 1.0 CB A:THR129 5.0 13.0 1.0

Manganese binding site 2 out of 4 in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure and Function of the Toscana Virus Cap Snatching Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:8.6 occ:0.71 O14 A:XI7303 2.0 28.9 1.0 OD1 A:ASP90 2.0 21.4 1.0 OD1 A:ASP113 2.0 14.0 1.0 O A:HOH431 2.0 22.1 1.0 O8 A:XI7303 2.1 16.8 1.0 O A:HOH470 2.2 15.2 1.0 C7 A:XI7303 2.9 27.5 1.0 CG A:ASP90 3.0 31.7 1.0 C9 A:XI7303 3.1 22.0 1.0 CG A:ASP113 3.2 12.8 1.0 OD2 A:ASP90 3.3 46.9 1.0 C8 A:XI7303 3.3 21.4 1.0 MN A:MN301 3.7 15.3 1.0 OD2 A:ASP113 3.8 12.6 1.0 O A:HOH433 4.0 28.9 1.0 CE1 A:HIS78 4.1 19.1 1.0 OG1 A:THR89 4.1 44.0 1.0 OE2 A:GLU127 4.1 15.3 1.0 CA A:ASP113 4.3 16.2 1.0 C1 A:XI7303 4.3 34.4 1.0 CB A:ASP113 4.3 13.7 1.0 C10 A:XI7303 4.3 23.4 1.0 NE2 A:HIS78 4.4 16.6 1.0 CB A:ASP90 4.4 27.2 1.0 O A:SER111 4.4 17.1 1.0 CB A:THR89 4.4 35.9 1.0 N A:ASP113 4.4 11.4 1.0 OE1 A:GLU127 4.5 13.1 1.0 N A:ASP90 4.5 35.6 1.0 CA A:ASP90 4.7 26.1 1.0 O A:HOH416 4.7 19.0 1.0 CD A:GLU127 4.7 13.8 1.0 C2 A:XI7303 4.8 30.0 1.0 O11 A:XI7303 4.8 20.0 1.0 C A:PRO112 4.9 12.5 1.0 ND1 A:HIS78 4.9 20.6 1.0

Manganese binding site 3 out of 4 in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure and Function of the Toscana Virus Cap Snatching Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:13.3 occ:1.00 OE2 B:GLU127 2.2 13.4 1.0 OD2 B:ASP113 2.2 11.6 1.0 O B:PHE128 2.2 11.9 1.0 O8 B:XI7303 2.3 13.5 1.0 O10 B:XI7303 2.3 14.9 1.0 NE2 B:HIS78 2.3 16.4 1.0 C10 B:XI7303 3.0 22.4 1.0 CG B:ASP113 3.0 10.3 1.0 C9 B:XI7303 3.0 23.0 1.0 OD1 B:ASP113 3.1 12.4 1.0 CD B:GLU127 3.1 15.4 1.0 CE1 B:HIS78 3.2 14.9 1.0 CD2 B:HIS78 3.3 14.3 1.0 C B:PHE128 3.3 12.6 1.0 MN B:MN302 3.7 15.6 1.0 N B:PHE128 3.7 7.8 1.0 OE1 B:GLU127 3.8 11.0 1.0 CA B:PHE128 3.9 11.2 1.0 CG B:GLU127 4.1 13.8 1.0 O B:HOH450 4.1 13.1 1.0 O11 B:XI7303 4.2 28.4 1.0 CB B:PHE128 4.2 11.1 1.0 ND1 B:HIS78 4.2 19.8 1.0 O B:HOH429 4.3 12.7 1.0 CG B:HIS78 4.3 15.9 1.0 C8 B:XI7303 4.4 19.3 1.0 N B:THR129 4.4 11.3 1.0 CB B:ASP113 4.4 8.6 1.0 O B:HOH417 4.6 23.8 1.0 CA B:THR129 4.7 12.0 1.0 CE B:LYS145 4.7 19.1 1.0 C B:GLU127 4.7 11.6 1.0 O B:HOH461 4.8 20.5 1.0 NZ B:LYS145 4.8 19.2 1.0

Manganese binding site 4 out of 4 in the Structure and Function of the Toscana Virus Cap Snatching Endonuclease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure and Function of the Toscana Virus Cap Snatching Endonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:15.6 occ:1.00 O8 B:XI7303 2.1 13.5 1.0 O14 B:XI7303 2.1 23.8 1.0 OD2 B:ASP90 2.1 16.7 1.0 OD1 B:ASP113 2.2 12.4 1.0 O B:HOH461 2.2 20.5 1.0 O B:HOH450 2.3 13.1 1.0 C7 B:XI7303 3.0 25.9 1.0 CG B:ASP90 3.1 20.6 1.0 C9 B:XI7303 3.1 23.0 1.0 CG B:ASP113 3.3 10.3 1.0 OD1 B:ASP90 3.4 20.4 1.0 C8 B:XI7303 3.4 19.3 1.0 MN B:MN301 3.7 13.3 1.0 OD2 B:ASP113 3.9 11.6 1.0 O B:HOH426 4.0 23.1 1.0 CE1 B:HIS78 4.2 14.9 1.0 OE2 B:GLU127 4.2 13.4 1.0 CA B:ASP113 4.3 11.2 1.0 C10 B:XI7303 4.3 22.4 1.0 O B:SER111 4.4 13.9 1.0 CB B:ASP113 4.4 8.6 1.0 C1 B:XI7303 4.4 28.8 1.0 CB B:ASP90 4.5 15.5 1.0 N B:ASP113 4.5 9.0 1.0 OE1 B:GLU127 4.5 11.0 1.0 NE2 B:HIS78 4.5 16.4 1.0 O10 B:XI7303 4.7 14.9 1.0 O B:HOH460 4.7 35.2 1.0 CD B:GLU127 4.8 15.4 1.0 O B:HOH429 4.8 12.7 1.0 C B:PRO112 4.8 12.7 1.0 C2 B:XI7303 4.9 25.3 1.0 O B:HOH527 4.9 25.6 1.0

R.Jones, S.Lessoued, K.Meier, S.Devignot, S.Barata-Garcia, M.Mate, G.Bragagnolo, F.Weber, M.Rosenthal, J.Reguera. Structure and Function of the Toscana Virus Cap-Snatching Endonuclease. Nucleic Acids Res. V. 47 10914 2019.
ISSN: ESSN 1362-4962
PubMed: 31584100
DOI: 10.1093/NAR/GKZ838