Magnesium in PDB 8qbm: Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments)

The binding sites of Magnesium atom in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments) (pdb code 8qbm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments), PDB code: 8qbm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:107.7 occ:1.00 OP1 B:DG85 2.6 127.0 1.0 OD2 A:ASP119 3.3 81.3 1.0 OD1 A:ASP119 3.5 81.7 1.0 OD2 A:ASP198 3.6 89.2 1.0 CG A:ASP119 3.8 80.9 1.0 P B:DG85 3.8 127.4 1.0 CB A:ASP198 3.8 88.0 1.0 O5' B:DG85 3.9 128.1 1.0 C5' B:DG85 4.0 127.5 1.0 CG A:ASP198 4.1 88.9 1.0 NZ A:LYS231 4.2 110.7 1.0 CE A:LYS231 4.2 110.1 1.0 O3' B:DG85 4.4 127.8 1.0 OD1 A:ASN117 4.5 65.4 1.0 OP2 B:DG85 4.7 128.6 1.0 C4' B:DG85 4.9 126.6 1.0 C3' B:DG85 5.0 126.8 1.0 O3' B:DA84 5.0 126.2 1.0

Magnesium binding site 2 out of 3 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments) within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg401 b:119.4 occ:1.00 OP1 L:DG85 2.4 124.8 1.0 OD2 K:ASP198 3.3 145.6 1.0 P L:DG85 3.9 126.1 1.0 OD2 K:ASP119 4.3 137.9 1.0 CG K:ASP198 4.3 145.5 1.0 OP1 M:G69 4.4 229.3 1.0 OP2 L:DG85 4.6 125.3 1.0 OD1 K:ASP119 4.7 137.8 1.0 O5' L:DG85 4.7 124.8 1.0 O3' L:DA84 4.8 119.4 1.0 CG K:ASP119 5.0 138.1 1.0 OP2 M:G69 5.0 229.1 1.0 C5' L:DG85 5.0 124.3 1.0

Magnesium binding site 3 out of 3 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Full Map with 2 Segments) within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg401 b:109.9 occ:1.00 OP1 V:DG85 2.2 127.7 1.0 OD2 U:ASP198 3.1 105.5 1.0 OD2 U:ASP119 3.2 85.0 1.0 P V:DG85 3.5 127.6 1.0 NZ U:LYS231 3.6 146.1 1.0 O5' V:DG85 4.0 127.7 1.0 CG U:ASP119 4.1 83.4 1.0 OD1 U:ASP119 4.2 83.0 1.0 C5' V:DG85 4.2 127.6 1.0 CG U:ASP198 4.3 104.9 1.0 OP2 V:DG85 4.3 128.4 1.0 CE U:LYS231 4.4 145.9 1.0 O3' V:DA84 4.7 126.7 1.0 OP1 W:G69 4.8 156.4 1.0 CB U:ASP198 4.8 104.1 1.0 OD1 U:ASN117 4.9 65.8 1.0

A.Carabias, S.Camara-Wilpert, M.R.Mestre, B.Lopez-Mendez, I.A.Hendriks, R.Zhao, T.Pape, A.Fuglsang, S.H.Luk, M.L.Nielsen, R.Pinilla-Redondo, G.Montoya. Retron-ECO1 Assembles Nad + -Hydrolyzing Filaments That Provide Immunity Against Bacteriophages. Mol.Cell 2024.
ISSN: ISSN 1097-2765
PubMed: 38788717
DOI: 10.1016/J.MOLCEL.2024.05.001