Magnesium in PDB 7las: 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 7las). 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: 7las:
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:94.9 occ:1.00 OD2 A:ASP216 1.8 89.4 1.0 O3B A:ADP400 2.0 98.3 1.0 PB A:ADP400 2.4 98.3 1.0 O2B A:ADP400 2.7 98.3 1.0 O1B A:ADP400 2.7 98.3 1.0 CG A:ASP216 3.0 89.4 1.0 HB2 A:ASP216 3.3 89.4 1.0 OD2 A:ASP215 3.4 82.3 1.0 HH22 B:ARG277 3.4 79.7 1.0 CB A:ASP216 3.7 89.4 1.0 HD21 A:ASN256 3.8 98.5 1.0 NZ A:LYS180 3.9 95.6 1.0 O3A A:ADP400 3.9 98.3 1.0 HH21 B:ARG277 4.0 79.7 1.0 OD1 A:ASP216 4.0 89.4 1.0 NH2 B:ARG277 4.0 79.7 1.0 HZ3 A:LYS180 4.1 95.6 1.0 HG A:SER181 4.2 86.2 1.0 HA A:ASP216 4.2 89.4 1.0 HB3 A:SER181 4.3 86.2 1.0 HZ1 A:LYS180 4.3 95.6 1.0 HB3 A:ASP216 4.4 89.4 1.0 CA A:ASP216 4.5 89.4 1.0 HD2 A:LYS180 4.5 95.6 1.0 CG A:ASP215 4.6 82.3 1.0 OD2 B:ASP231 4.6 76.1 1.0 OG A:SER181 4.6 86.2 1.0 ND2 A:ASN256 4.7 98.5 1.0 H A:ASP216 4.7 89.4 1.0 HH21 B:ARG228 4.7 69.4 1.0 HE3 A:LYS180 4.8 95.6 1.0 CE A:LYS180 4.9 95.6 1.0 N A:ASP216 4.9 89.4 1.0 CB A:SER181 4.9 86.2 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:61.2 occ:1.00 HB3 B:SER181 1.9 71.7 1.0 CB B:SER181 2.5 71.7 1.0 HG B:SER181 2.5 71.7 1.0 OG B:SER181 2.6 71.7 1.0 OD2 B:ASP215 2.6 63.5 1.0 HB2 B:SER181 2.8 71.7 1.0 OD1 B:ASP215 2.9 63.5 1.0 O3B B:ADP400 2.9 86.8 1.0 CG B:ASP215 3.1 63.5 1.0 OD2 C:ASP231 3.8 67.1 1.0 HD2 C:TYR233 3.8 64.4 1.0 CA B:SER181 3.8 71.7 1.0 OD2 B:ASP216 3.9 68.0 1.0 H B:SER181 3.9 71.7 1.0 HA B:SER181 4.1 71.7 1.0 HG21 B:THR254 4.1 68.7 1.0 HE2 C:TYR233 4.1 64.4 1.0 O1A B:ADP400 4.2 86.8 1.0 N B:SER181 4.3 71.7 1.0 PB B:ADP400 4.4 86.8 1.0 HB2 B:ASP216 4.4 68.0 1.0 HZ3 B:TRP195 4.4 57.4 1.0 H B:ASP216 4.5 68.0 1.0 HG22 B:THR254 4.5 68.7 1.0 CD2 C:TYR233 4.6 64.4 1.0 CB B:ASP215 4.6 63.5 1.0 CG C:ASP231 4.7 67.1 1.0 HB2 B:LYS180 4.7 73.6 1.0 HE2 B:LYS180 4.7 73.6 1.0 CG B:ASP216 4.7 68.0 1.0 CE2 C:TYR233 4.8 64.4 1.0 CG2 B:THR254 4.8 68.7 1.0 HZ3 B:LYS180 4.8 73.6 1.0 O1B B:ADP400 4.9 86.8 1.0 HB3 B:ASP215 4.9 63.5 1.0 N B:ASP216 5.0 68.0 1.0 HB B:THR254 5.0 68.7 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:56.3 occ:1.00 OG C:SER181 2.1 66.0 1.0 OD1 C:ASP215 2.4 56.0 1.0 OD2 C:ASP216 2.5 59.2 1.0 O1B C:ADP400 3.2 85.0 1.0 CG C:ASP215 3.3 56.0 1.0 CB C:SER181 3.5 66.0 1.0 OD2 C:ASP215 3.6 56.0 1.0 CG C:ASP216 3.7 59.2 1.0 HB3 C:SER181 3.7 66.0 1.0 HZ3 C:LYS180 3.7 69.4 1.0 HB2 C:ASP216 3.9 59.2 1.0 HB2 C:SER181 3.9 66.0 1.0 HZ1 C:LYS180 4.1 69.4 1.0 H C:SER181 4.1 66.0 1.0 HG21 C:THR254 4.1 59.3 1.0 HG22 C:THR254 4.2 59.3 1.0 H C:ASP216 4.2 59.2 1.0 CB C:ASP216 4.3 59.2 1.0 PB C:ADP400 4.3 85.0 1.0 NZ C:LYS180 4.3 69.4 1.0 CA C:SER181 4.4 66.0 1.0 HA C:SER181 4.4 66.0 1.0 N C:SER181 4.5 66.0 1.0 OD2 D:ASP231 4.6 63.0 1.0 HA C:ASP216 4.6 59.2 1.0 N C:ASP216 4.6 59.2 1.0 HB2 C:LYS180 4.6 69.4 1.0 CG2 C:THR254 4.7 59.3 1.0 OD1 C:ASP216 4.7 59.2 1.0 CB C:ASP215 4.7 56.0 1.0 HZ2 C:LYS180 4.7 69.4 1.0 CA C:ASP216 4.8 59.2 1.0 O3B C:ADP400 4.8 85.0 1.0 HB3 C:ASP215 4.8 56.0 1.0 O2B C:ADP400 4.8 85.0 1.0 HZ3 C:TRP195 4.9 49.4 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:64.8 occ:1.00 HG D:SER181 2.2 62.4 1.0 OG D:SER181 2.6 62.4 1.0 O1B D:ADP400 3.2 79.8 1.0 OD1 D:ASP215 3.3 59.3 1.0 OD2 E:ASP231 3.5 77.9 1.0 HB2 D:ASP216 3.5 64.1 1.0 HZ3 D:LYS180 3.5 65.2 1.0 HZ2 D:LYS180 3.5 65.2 1.0 CB D:SER181 3.8 62.4 1.0 HB2 D:SER181 3.9 62.4 1.0 NZ D:LYS180 3.9 65.2 1.0 OD2 D:ASP216 4.1 64.1 1.0 CG D:ASP215 4.2 59.3 1.0 H D:SER181 4.3 62.4 1.0 HB3 D:SER181 4.3 62.4 1.0 CB D:ASP216 4.4 64.1 1.0 HG21 D:THR254 4.5 59.4 1.0 HZ1 D:LYS180 4.5 65.2 1.0 OD2 D:ASP215 4.5 59.3 1.0 HG22 D:THR254 4.5 59.4 1.0 PB D:ADP400 4.6 79.8 1.0 HE2 D:LYS180 4.6 65.2 1.0 CG E:ASP231 4.6 77.9 1.0 HH11 E:ARG228 4.7 68.9 1.0 HB3 D:LYS180 4.7 65.2 1.0 CG D:ASP216 4.8 64.1 1.0 N D:SER181 4.8 62.4 1.0 HB3 D:ASP216 4.9 64.1 1.0 HB2 D:LYS180 4.9 65.2 1.0 CA D:SER181 4.9 62.4 1.0 CE D:LYS180 4.9 65.2 1.0 H D:ASP216 5.0 64.1 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