Magnesium in PDB 8qbk: Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)

The binding sites of Magnesium atom in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) (pdb code 8qbk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment), PDB code: 8qbk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


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 (Local Map with 1 Segment) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:89.2 occ:1.00 OP1 B:DG85 2.4 98.0 1.0 OD2 A:ASP119 3.2 119.4 1.0 P B:DG85 3.7 110.2 1.0 C5' B:DG85 4.0 94.4 1.0 O5' B:DG85 4.0 101.8 1.0 CG A:ASP119 4.1 116.5 1.0 OD1 A:ASP119 4.1 121.0 1.0 CB A:ASP198 4.3 93.8 1.0 OD1 A:ASN117 4.4 106.0 1.0 CE A:LYS231 4.4 162.5 1.0 OP2 B:DG85 4.6 94.8 1.0 OD2 A:ASP198 4.7 118.5 1.0 NZ A:LYS231 4.8 169.6 1.0 CG A:ASP198 4.8 111.1 1.0 O3' B:DA84 4.8 91.8 1.0 OP1 C:G69 4.9 201.7 1.0 O3' B:DG85 4.9 94.1 1.0

Magnesium binding site 2 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


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 (Local Map with 1 Segment) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg101 b:119.8 occ:1.00 OP1 L:DG85 2.4 126.0 1.0 P L:DG85 3.8 140.7 1.0 ND2 K:ASN117 4.3 127.3 1.0 OD2 K:ASP119 4.5 135.6 1.0 O3' L:DA84 4.6 113.8 1.0 OP2 L:DG85 4.6 127.1 1.0 OD1 K:ASP119 4.7 142.0 1.0 O5' L:DG85 4.7 122.5 1.0 C5' L:DG85 4.9 117.0 1.0

Magnesium binding site 3 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


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 (Local Map with 1 Segment) within 5.0Å range: probe atom residue distance (Å) B Occ Q:Mg101 b:108.8 occ:1.00 OP1 Q:DG85 2.4 111.2 1.0 P Q:DG85 3.8 126.4 1.0 OD1 P:ASP119 4.1 135.5 1.0 O5' Q:DG85 4.4 116.9 1.0 C5' Q:DG85 4.5 106.4 1.0 OP1 R:G69 4.5 222.5 1.0 OD1 P:ASN117 4.5 115.7 1.0 OP2 Q:DG85 4.5 111.2 1.0 OP2 R:G69 4.6 223.6 1.0 CD P:LYS231 4.8 167.1 1.0 O3' Q:DA84 4.8 107.7 1.0 CB P:ASP198 4.9 105.0 1.0

Magnesium binding site 4 out of 4 in the Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Retron-ECO1 Filament with Adp-Ribosylated Effector (Local Map with 1 Segment) within 5.0Å range: probe atom residue distance (Å) B Occ U:Mg401 b:114.4 occ:1.00 OP1 V:DG85 2.6 110.3 1.0 OD2 U:ASP198 3.1 123.8 1.0 P V:DG85 4.1 128.4 1.0 OD1 U:ASN117 4.1 103.0 1.0 CE U:LYS231 4.3 152.8 1.0 CG U:ASP198 4.3 130.3 1.0 N U:THR244 4.3 105.4 1.0 CA U:THR244 4.6 105.8 1.0 O3' V:DA84 4.7 96.1 1.0 ND2 U:ASN117 4.7 105.4 1.0 CG U:ASN117 4.7 104.5 1.0 OD2 U:ASP119 4.8 137.7 1.0 NZ U:LYS231 4.9 152.2 1.0 O5' V:DG85 4.9 112.0 1.0 C5' V:DG85 5.0 101.2 1.0 OP2 V:DG85 5.0 108.3 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