Magnesium in PDB 9dls: Vibrio Cholerae Dnab

All present enzymatic activity of Vibrio Cholerae Dnab:
5.6.2.3;

The binding sites of Magnesium atom in the Vibrio Cholerae Dnab (pdb code 9dls). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Vibrio Cholerae Dnab, PDB code: 9dls:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:67.0 occ:1.00 O2B A:AGS501 2.1 56.1 1.0 OG1 A:THR235 2.5 49.7 1.0 O3G A:AGS501 2.6 59.9 1.0 OE1 A:GLU259 3.6 69.3 1.0 PB A:AGS501 3.6 55.1 1.0 CB A:THR235 3.8 45.1 1.0 PG A:AGS501 3.8 64.1 1.0 OD2 A:ASP340 3.8 53.5 1.0 OD1 A:ASP340 3.9 54.5 1.0 O3B A:AGS501 4.2 60.4 1.0 CG A:ASP340 4.3 52.7 1.0 O3A A:AGS501 4.3 52.5 1.0 S1G A:AGS501 4.4 72.1 1.0 O1B A:AGS501 4.5 49.8 1.0 CD A:GLU259 4.6 72.0 1.0 N A:THR235 4.6 42.7 1.0 CG2 A:THR235 4.6 46.4 1.0 CA A:THR235 4.8 43.8 1.0 O1A A:AGS501 5.0 51.4 1.0

Magnesium binding site 2 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:94.3 occ:1.00 OG1 B:THR235 2.0 82.2 1.0 OD2 B:ASP340 2.0 89.0 1.0 CG2 B:THR235 2.5 74.4 1.0 CB B:THR235 2.5 78.7 1.0 CG B:ASP340 2.6 82.5 1.0 OD1 B:ASP340 3.0 81.1 1.0 CA B:THR235 3.0 75.5 1.0 CD1 B:LEU379 3.2 65.4 1.0 O3G B:AGS501 3.4 88.6 1.0 N B:THR235 3.7 74.2 1.0 CB B:ASP340 3.8 74.7 1.0 C B:THR235 4.3 74.4 1.0 O B:THR235 4.6 75.8 1.0 PG B:AGS501 4.6 103.0 1.0 CG B:LEU379 4.6 56.8 1.0 C B:LYS234 4.6 72.5 1.0 O2G B:AGS501 4.8 98.0 1.0 O B:LYS234 5.0 76.3 1.0

Magnesium binding site 3 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.6 occ:1.00 OE2 C:GLU259 2.0 54.3 1.0 OG1 C:THR235 2.1 45.6 1.0 O2G C:AGS501 2.3 53.3 1.0 O2B C:AGS501 2.4 43.8 1.0 CD C:GLU259 3.2 56.1 1.0 OD2 C:ASP340 3.3 60.9 1.0 CB C:THR235 3.3 38.4 1.0 PG C:AGS501 3.7 52.7 1.0 PB C:AGS501 3.8 38.4 1.0 OD1 C:ASP340 3.8 52.8 1.0 OE1 C:GLU259 3.9 53.6 1.0 CG C:ASP340 4.0 54.9 1.0 CG2 C:THR235 4.0 37.6 1.0 O2A C:AGS501 4.0 46.7 1.0 CG C:GLU259 4.2 52.7 1.0 O3G C:AGS501 4.2 50.3 1.0 O3B C:AGS501 4.3 43.1 1.0 O1B C:AGS501 4.3 40.4 1.0 SD C:MET260 4.3 46.2 1.0 CA C:THR235 4.4 34.4 1.0 N C:THR235 4.5 36.1 1.0 O3A C:AGS501 4.9 42.4 1.0 PA C:AGS501 4.9 40.0 1.0

Magnesium binding site 4 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:43.6 occ:1.00 OE2 D:GLU259 2.0 53.7 1.0 OG1 D:THR235 2.2 35.2 1.0 O2B D:AGS501 2.3 30.4 1.0 S1G D:AGS501 2.5 66.9 1.0 O3G D:AGS501 2.9 44.3 1.0 CD D:GLU259 3.0 55.5 1.0 PG D:AGS501 3.1 49.2 1.0 OE1 D:GLU259 3.4 54.0 1.0 PB D:AGS501 3.5 27.3 1.0 CB D:THR235 3.6 27.4 1.0 OD1 D:ASP340 3.7 51.8 1.0 O3B D:AGS501 3.8 34.5 1.0 OD2 D:ASP340 3.8 54.7 1.0 O1B D:AGS501 4.1 30.1 1.0 CG D:ASP340 4.2 51.4 1.0 CG D:GLU259 4.3 50.6 1.0 N D:THR235 4.4 26.2 1.0 CG2 D:THR235 4.4 30.8 1.0 CA D:THR235 4.5 23.6 1.0 O2G D:AGS501 4.5 34.0 1.0 O1A D:AGS501 4.8 27.6 1.0 O3A D:AGS501 4.8 26.6 1.0

Magnesium binding site 5 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:48.9 occ:1.00 OG1 E:THR235 2.1 44.3 1.0 O3G E:AGS501 2.5 62.4 1.0 OE1 E:GLU259 2.6 72.4 1.0 O2B E:AGS501 2.7 47.3 1.0 OD1 E:ASP340 3.3 62.9 1.0 CB E:THR235 3.5 35.6 1.0 CD E:GLU259 3.6 79.3 1.0 OD2 E:ASP340 3.6 59.7 1.0 PB E:AGS501 3.9 43.7 1.0 CG E:ASP340 3.9 56.5 1.0 PG E:AGS501 3.9 63.5 1.0 OE2 E:GLU259 3.9 84.3 1.0 O1B E:AGS501 4.1 50.3 1.0 CG2 E:THR235 4.2 37.2 1.0 O3B E:AGS501 4.4 49.5 1.0 CA E:THR235 4.5 34.3 1.0 N E:THR235 4.5 39.2 1.0 S1G E:AGS501 4.7 75.5 1.0 O1A E:AGS501 4.7 40.4 1.0 SD E:MET260 4.8 55.3 1.0 CG E:GLU259 4.8 67.0 1.0

Magnesium binding site 6 out of 6 in the Vibrio Cholerae Dnab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Vibrio Cholerae Dnab within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:45.4 occ:1.00 OE1 F:GLU259 2.1 75.7 1.0 OG1 F:THR235 2.3 50.8 1.0 O3G F:AGS501 2.4 64.1 1.0 O1B F:AGS501 2.6 63.3 1.0 CD F:GLU259 2.8 80.7 1.0 OE2 F:GLU259 2.8 90.0 1.0 CB F:THR235 3.6 41.7 1.0 OD2 F:ASP340 3.7 70.7 1.0 PB F:AGS501 3.8 59.0 1.0 OD1 F:ASP340 3.8 70.8 1.0 PG F:AGS501 3.9 67.5 1.0 O3A F:AGS501 4.1 49.3 1.0 CG F:ASP340 4.2 66.0 1.0 CG F:GLU259 4.2 70.4 1.0 CG2 F:THR235 4.3 45.1 1.0 NH1 E:ARG439 4.3 52.1 1.0 O3B F:AGS501 4.3 54.1 1.0 O2G F:AGS501 4.6 66.4 1.0 CA F:THR235 4.7 41.9 1.0 N F:THR235 4.7 46.7 1.0 CB F:GLU259 4.8 61.3 1.0

N.Gao, D.Mazzoletti, A.Peng, P.D.B.Olinares, C.Morrone, A.Garavaglia, N.Gouda, S.Tsoy, A.Mendoza, A.Chowdhury, A.Cerullo, H.Bhavsar, F.Rossi, M.Rizzi, B.T.Chait, R.Miggiano, D.Jeruzalmi. Dnab and Dcia: Mechanisms of Helicase Loading and Translocation on Ssdna. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40598899
DOI: 10.1093/NAR/GKAF521