Magnesium in PDB 7lar: Cryo-Em Structure of PCV2 Replicase Bound to Ssdna

The binding sites of Magnesium atom in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna (pdb code 7lar). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna, PDB code: 7lar:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of PCV2 Replicase Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:66.8 occ:1.00 OD2 A:ASP216 2.0 74.5 1.0 O3B A:ADP400 2.0 80.7 1.0 PB A:ADP400 2.4 80.7 1.0 O2B A:ADP400 2.7 80.7 1.0 O1B A:ADP400 2.7 80.7 1.0 CG A:ASP216 3.2 74.5 1.0 HH22 B:ARG277 3.3 61.8 1.0 OD2 A:ASP215 3.4 64.9 1.0 HB2 A:ASP216 3.4 74.5 1.0 NZ A:LYS180 3.8 78.7 1.0 CB A:ASP216 3.8 74.5 1.0 HH21 B:ARG277 3.8 61.8 1.0 NH2 B:ARG277 3.8 61.8 1.0 HD21 A:ASN256 3.9 81.4 1.0 O3A A:ADP400 3.9 80.7 1.0 HZ3 A:LYS180 4.0 78.7 1.0 HG A:SER181 4.0 73.1 1.0 HB3 A:SER181 4.1 73.1 1.0 OD1 A:ASP216 4.2 74.5 1.0 HZ1 A:LYS180 4.2 78.7 1.0 HA A:ASP216 4.3 74.5 1.0 HD2 A:LYS180 4.4 78.7 1.0 OG A:SER181 4.4 73.1 1.0 OD2 B:ASP231 4.5 61.2 1.0 CG A:ASP215 4.6 64.9 1.0 CA A:ASP216 4.6 74.5 1.0 HE3 A:LYS180 4.6 78.7 1.0 HB3 A:ASP216 4.6 74.5 1.0 CE A:LYS180 4.7 78.7 1.0 ND2 A:ASN256 4.7 81.4 1.0 H A:ASP216 4.7 74.5 1.0 CB A:SER181 4.8 73.1 1.0 HH21 B:ARG228 4.9 58.0 1.0 HH22 B:ARG276 4.9 67.3 1.0 HB2 A:LYS180 4.9 78.7 1.0 N A:ASP216 4.9 74.5 1.0 H A:SER181 5.0 73.1 1.0 OD1 A:ASP215 5.0 64.9 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of PCV2 Replicase Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:50.9 occ:1.00 HB3 B:SER181 1.8 55.5 1.0 HG B:SER181 2.4 55.5 1.0 OG B:SER181 2.4 55.5 1.0 CB B:SER181 2.4 55.5 1.0 HB2 B:SER181 2.8 55.5 1.0 OD2 B:ASP215 2.8 47.8 1.0 O3B B:ADP400 2.9 70.2 1.0 OD1 B:ASP215 3.0 47.8 1.0 CG B:ASP215 3.3 47.8 1.0 H B:SER181 3.7 55.5 1.0 CA B:SER181 3.8 55.5 1.0 OD2 C:ASP231 3.8 50.6 1.0 HD2 C:TYR233 3.9 49.5 1.0 OD2 B:ASP216 3.9 52.6 1.0 HA B:SER181 4.0 55.5 1.0 HG21 B:THR254 4.0 49.8 1.0 N B:SER181 4.1 55.5 1.0 HE2 C:TYR233 4.2 49.5 1.0 O1A B:ADP400 4.2 70.2 1.0 PB B:ADP400 4.4 70.2 1.0 HG22 B:THR254 4.5 49.8 1.0 HB2 B:ASP216 4.5 52.6 1.0 H B:ASP216 4.6 52.6 1.0 HB2 B:LYS180 4.6 57.0 1.0 HZ3 B:TRP195 4.6 42.7 1.0 HE2 B:LYS180 4.6 57.0 1.0 CD2 C:TYR233 4.6 49.5 1.0 HZ3 B:LYS180 4.7 57.0 1.0 CG C:ASP231 4.7 50.6 1.0 CG2 B:THR254 4.7 49.8 1.0 CG B:ASP216 4.8 52.6 1.0 CE2 C:TYR233 4.8 49.5 1.0 CB B:ASP215 4.8 47.8 1.0 O1B B:ADP400 4.9 70.2 1.0 C B:SER181 5.0 55.5 1.0 HZ1 B:LYS180 5.0 57.0 1.0 HB B:THR254 5.0 49.8 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of PCV2 Replicase Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:42.1 occ:1.00 OG C:SER181 2.1 50.8 1.0 OD1 C:ASP215 2.4 42.0 1.0 OD2 C:ASP216 2.5 43.9 1.0 O1B C:ADP400 3.2 66.7 1.0 CG C:ASP215 3.3 42.0 1.0 CB C:SER181 3.4 50.8 1.0 OD2 C:ASP215 3.5 42.0 1.0 CG C:ASP216 3.7 43.9 1.0 HZ3 C:LYS180 3.7 52.4 1.0 HB3 C:SER181 3.7 50.8 1.0 HB2 C:ASP216 3.9 43.9 1.0 HB2 C:SER181 3.9 50.8 1.0 HZ1 C:LYS180 4.1 52.4 1.0 H C:SER181 4.1 50.8 1.0 HG21 C:THR254 4.1 44.1 1.0 HG22 C:THR254 4.2 44.1 1.0 H C:ASP216 4.2 43.9 1.0 CB C:ASP216 4.3 43.9 1.0 NZ C:LYS180 4.3 52.4 1.0 PB C:ADP400 4.3 66.7 1.0 CA C:SER181 4.4 50.8 1.0 HA C:SER181 4.4 50.8 1.0 OD2 D:ASP231 4.4 46.7 1.0 N C:SER181 4.5 50.8 1.0 HA C:ASP216 4.6 43.9 1.0 HB2 C:LYS180 4.6 52.4 1.0 N C:ASP216 4.6 43.9 1.0 CG2 C:THR254 4.6 44.1 1.0 HZ2 C:LYS180 4.7 52.4 1.0 OD1 C:ASP216 4.7 43.9 1.0 CB C:ASP215 4.7 42.0 1.0 CA C:ASP216 4.8 43.9 1.0 O3B C:ADP400 4.8 66.7 1.0 O2B C:ADP400 4.8 66.7 1.0 HB3 C:ASP215 4.8 42.0 1.0 HZ3 C:TRP195 4.9 38.3 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of PCV2 Replicase Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of PCV2 Replicase Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:47.4 occ:1.00 HG D:SER181 2.1 48.6 1.0 OG D:SER181 2.6 48.6 1.0 O1B D:ADP400 3.2 69.2 1.0 HZ2 D:LYS180 3.3 51.2 1.0 HZ3 D:LYS180 3.4 51.2 1.0 OD1 D:ASP215 3.4 40.3 1.0 OD2 E:ASP231 3.5 59.8 1.0 HB2 D:ASP216 3.6 45.4 1.0 HB2 D:SER181 3.8 48.6 1.0 CB D:SER181 3.8 48.6 1.0 NZ D:LYS180 3.8 51.2 1.0 H D:SER181 4.1 48.6 1.0 OD2 D:ASP216 4.1 45.4 1.0 HB3 D:SER181 4.3 48.6 1.0 CG D:ASP215 4.4 40.3 1.0 HZ1 D:LYS180 4.4 51.2 1.0 HG21 D:THR254 4.4 41.5 1.0 HE2 D:LYS180 4.5 51.2 1.0 CB D:ASP216 4.5 45.4 1.0 HG22 D:THR254 4.5 41.5 1.0 HB3 D:LYS180 4.6 51.2 1.0 PB D:ADP400 4.6 69.2 1.0 OD2 D:ASP215 4.7 40.3 1.0 N D:SER181 4.7 48.6 1.0 HB2 D:LYS180 4.7 51.2 1.0 CG E:ASP231 4.7 59.8 1.0 CE D:LYS180 4.8 51.2 1.0 CA D:SER181 4.8 48.6 1.0 CG D:ASP216 4.8 45.4 1.0 HH11 E:ARG228 4.9 53.8 1.0 CG2 D:THR254 5.0 41.5 1.0 HB3 D:ASP216 5.0 45.4 1.0 HA D:SER181 5.0 48.6 1.0

E.Tarasova, S.Dhindwal, M.Popp, S.Hussain, R.Khayat. Mechanism of Dna Interaction and Translocation By the Replicase of A Circular Rep-Encoding Single-Stranded Dna Virus. Mbio 76321 2021.
ISSN: ESSN 2150-7511
PubMed: 34311576
DOI: 10.1128/MBIO.00763-21