Magnesium in PDB 8dgc: AVS3 Bound to Phage Phiv-1 Terminase

The binding sites of Magnesium atom in the AVS3 Bound to Phage Phiv-1 Terminase (pdb code 8dgc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the AVS3 Bound to Phage Phiv-1 Terminase, PDB code: 8dgc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2102 b:49.5 occ:1.00 O1G A:ATP2101 2.3 63.9 1.0 OG A:SER294 2.6 51.5 1.0 O2B A:ATP2101 3.2 71.0 1.0 PG A:ATP2101 3.6 50.0 1.0 O3B A:ATP2101 3.8 60.7 1.0 CB A:SER294 3.9 51.8 1.0 PB A:ATP2101 4.2 59.5 1.0 O1A A:ATP2101 4.5 63.7 1.0 O3G A:ATP2101 4.5 58.3 1.0 O2G A:ATP2101 4.6 61.7 1.0 OD2 A:ASP391 4.9 59.5 1.0 O3A A:ATP2101 4.9 62.9 1.0 N A:SER294 5.0 56.6 1.0 CA A:SER294 5.0 49.8 1.0

Magnesium binding site 2 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2102 b:39.6 occ:1.00 O2B B:ATP2101 2.1 71.9 1.0 OG B:SER294 2.3 46.5 1.0 O1G B:ATP2101 2.8 64.3 1.0 PB B:ATP2101 3.4 63.2 1.0 O3B B:ATP2101 3.6 63.2 1.0 CB B:SER294 3.7 49.2 1.0 PG B:ATP2101 3.8 55.0 1.0 O1A B:ATP2101 4.2 63.0 1.0 O3A B:ATP2101 4.3 65.8 1.0 OD2 B:ASP391 4.3 59.8 1.0 N B:SER294 4.3 48.1 1.0 O1B B:ATP2101 4.4 67.0 1.0 OD1 B:ASP391 4.5 55.9 1.0 O2A B:ATP2101 4.5 65.4 1.0 CA B:SER294 4.5 44.4 1.0 PA B:ATP2101 4.5 58.7 1.0 O3G B:ATP2101 4.6 67.8 1.0 CG B:ASP391 4.8 52.0 1.0 O2G B:ATP2101 4.9 63.4 1.0

Magnesium binding site 3 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2102 b:50.5 occ:1.00 O1G C:ATP2101 2.3 63.1 1.0 OG C:SER294 2.6 52.4 1.0 O2B C:ATP2101 3.2 69.8 1.0 PG C:ATP2101 3.6 47.9 1.0 O3B C:ATP2101 3.8 60.5 1.0 CB C:SER294 3.9 52.8 1.0 PB C:ATP2101 4.2 58.8 1.0 O1A C:ATP2101 4.5 63.2 1.0 O3G C:ATP2101 4.5 57.5 1.0 O2G C:ATP2101 4.6 61.6 1.0 OD2 C:ASP391 4.9 59.7 1.0 O3A C:ATP2101 4.9 62.5 1.0 N C:SER294 4.9 58.0 1.0 CA C:SER294 5.0 51.2 1.0

Magnesium binding site 4 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2102 b:37.5 occ:1.00 O2B D:ATP2101 2.1 72.1 1.0 OG D:SER294 2.3 45.1 1.0 O1G D:ATP2101 2.8 63.7 1.0 PB D:ATP2101 3.4 62.2 1.0 O3B D:ATP2101 3.6 62.7 1.0 CB D:SER294 3.7 49.1 1.0 PG D:ATP2101 3.8 54.7 1.0 O1A D:ATP2101 4.2 62.8 1.0 O3A D:ATP2101 4.3 65.0 1.0 OD2 D:ASP391 4.3 60.3 1.0 N D:SER294 4.3 48.6 1.0 O1B D:ATP2101 4.4 66.9 1.0 OD1 D:ASP391 4.5 56.3 1.0 O2A D:ATP2101 4.5 65.4 1.0 CA D:SER294 4.5 44.9 1.0 PA D:ATP2101 4.5 58.1 1.0 O3G D:ATP2101 4.6 67.7 1.0 CG D:ASP391 4.8 52.7 1.0 O2G D:ATP2101 4.9 63.3 1.0

Magnesium binding site 5 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:51.5 occ:1.00 O2G E:ATP601 2.0 87.5 1.0 O2B E:ATP601 2.0 91.6 1.0 O3B E:ATP601 2.8 90.8 1.0 PB E:ATP601 3.0 93.0 1.0 PG E:ATP601 3.0 86.0 1.0 OG E:SER66 3.2 80.7 1.0 OH A:TYR1714 3.7 52.3 1.0 O3A E:ATP601 4.0 88.4 1.0 O2A E:ATP601 4.0 95.7 1.0 O1G E:ATP601 4.0 97.3 1.0 O3G E:ATP601 4.0 87.6 1.0 O1B E:ATP601 4.1 99.4 1.0 NZ E:LYS65 4.1 88.5 1.0 PA E:ATP601 4.4 92.1 1.0 CB E:SER66 4.5 83.1 1.0 O1A E:ATP601 4.6 97.1 1.0 OD2 E:ASP162 4.7 103.6 1.0 NE2 A:HIS1770 4.7 54.7 1.0 N E:SER66 5.0 82.7 1.0

Magnesium binding site 6 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:52.0 occ:1.00 O2G F:ATP601 2.0 81.7 1.0 O2B F:ATP601 2.0 86.9 1.0 O3B F:ATP601 2.8 86.3 1.0 PB F:ATP601 3.0 85.3 1.0 PG F:ATP601 3.0 85.5 1.0 OG F:SER66 3.2 83.3 1.0 OH B:TYR1714 3.7 59.7 1.0 O1G F:ATP601 4.0 91.9 1.0 O3A F:ATP601 4.0 81.3 1.0 O3G F:ATP601 4.0 83.5 1.0 O1B F:ATP601 4.0 92.4 1.0 O2A F:ATP601 4.1 89.0 1.0 NZ F:LYS65 4.1 88.0 1.0 PA F:ATP601 4.4 82.3 1.0 CB F:SER66 4.5 85.6 1.0 O1A F:ATP601 4.6 87.6 1.0 NE2 B:HIS1770 4.7 55.9 1.0 N F:SER66 5.0 84.3 1.0 CD2 B:HIS1770 5.0 58.9 1.0

Magnesium binding site 7 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg602 b:50.9 occ:1.00 O2G G:ATP601 2.0 85.2 1.0 O2B G:ATP601 2.0 89.6 1.0 O3B G:ATP601 2.8 89.3 1.0 PB G:ATP601 3.0 91.7 1.0 PG G:ATP601 3.0 84.8 1.0 OG G:SER66 3.2 80.1 1.0 OH C:TYR1714 3.7 51.2 1.0 O1G G:ATP601 4.0 96.2 1.0 O3A G:ATP601 4.0 87.1 1.0 O3G G:ATP601 4.0 85.7 1.0 O1B G:ATP601 4.0 98.0 1.0 NZ G:LYS65 4.1 86.8 1.0 O2A G:ATP601 4.1 93.5 1.0 PA G:ATP601 4.4 89.3 1.0 CB G:SER66 4.5 82.3 1.0 O1A G:ATP601 4.6 94.5 1.0 OD2 G:ASP162 4.7 101.4 1.0 NE2 C:HIS1770 4.7 53.3 1.0 N G:SER66 5.0 81.9 1.0

Magnesium binding site 8 out of 8 in the AVS3 Bound to Phage Phiv-1 Terminase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of AVS3 Bound to Phage Phiv-1 Terminase within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg602 b:51.4 occ:1.00 O2G H:ATP601 2.0 85.0 1.0 O2B H:ATP601 2.0 91.3 1.0 O3B H:ATP601 2.8 89.8 1.0 PB H:ATP601 3.0 89.2 1.0 PG H:ATP601 3.0 88.1 1.0 OG H:SER66 3.2 86.8 1.0 OH D:TYR1714 3.7 59.0 1.0 O3A H:ATP601 3.9 84.8 1.0 O2A H:ATP601 4.0 92.1 1.0 O1G H:ATP601 4.0 95.6 1.0 O3G H:ATP601 4.0 87.5 1.0 O1B H:ATP601 4.1 96.4 1.0 NZ H:LYS65 4.1 91.0 1.0 PA H:ATP601 4.4 84.8 1.0 CB H:SER66 4.5 89.0 1.0 O1A H:ATP601 4.6 92.1 1.0 NE2 D:HIS1770 4.7 56.2 1.0 N H:SER66 5.0 87.6 1.0 CD2 D:HIS1770 5.0 59.0 1.0

L.A.Gao, M.E.Wilkinson, J.Strecker, K.S.Makarova, R.K.Macrae, E.V.Koonin, F.Zhang. Prokaryotic Innate Immunity Through Pattern Recognition of Conserved Viral Proteins. Science V. 377 M4096 2022.
ISSN: ESSN 1095-9203
PubMed: 35951700
DOI: 10.1126/SCIENCE.ABM4096