Magnesium in PDB 9gbv: E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment

All present enzymatic activity of E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment:
5.6.2.2;

The binding sites of Magnesium atom in the E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment (pdb code 9gbv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment, PDB code: 9gbv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:78.4 occ:1.00 OD2 D:ASP498 3.1 78.9 1.0 O D:LYS740 3.5 80.0 1.0 OD2 D:ASP500 3.5 73.2 1.0 OP1 E:DA19 3.5 37.3 1.0 NZ D:LYS740 3.6 83.3 1.0 O3' E:DA18 3.9 37.8 1.0 P E:DA19 4.2 34.4 1.0 CG D:ASP498 4.2 77.8 1.0 CG D:ASP500 4.2 73.6 1.0 OD1 D:ASP500 4.3 74.6 1.0 CG D:LYS740 4.4 82.3 1.0 C D:LYS740 4.4 80.7 1.0 CB D:ASP498 4.6 76.0 1.0 OP2 E:DA19 4.7 37.0 1.0 C5' E:DA18 4.7 36.9 1.0 OE1 D:GLU424 4.8 77.3 1.0 CE D:LYS740 4.8 83.4 1.0 OP1 E:DA18 4.8 36.2 1.0 C4' E:DA18 4.9 37.2 1.0 C3' E:DA18 4.9 37.4 1.0 CA D:GLY741 5.0 79.4 1.0

Magnesium binding site 2 out of 2 in the E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Gyrase Holocomplex with Chirally Wrapped 217 Bp Dna Fragment within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:65.8 occ:1.00 OD2 B:ASP498 2.4 69.2 1.0 OP1 F:DG21 2.7 224.6 1.0 O3' F:DT20 3.1 221.5 1.0 P F:DG21 3.5 224.6 1.0 OE1 B:GLU424 3.6 67.3 1.0 CG B:ASP498 3.6 68.0 1.0 O B:LYS740 4.0 69.8 1.0 CB B:ASP498 4.2 66.7 1.0 OD2 B:ASP500 4.2 67.8 1.0 OP2 F:DG21 4.3 224.6 1.0 C3' F:DT20 4.4 221.5 1.0 NZ B:LYS740 4.4 71.7 1.0 CD B:GLU424 4.6 66.3 1.0 C4' F:DT20 4.6 221.5 1.0 OD1 B:ASP500 4.6 68.0 1.0 OD1 B:ASP498 4.6 66.3 1.0 C5' F:DT20 4.7 221.5 1.0 O5' F:DG21 4.8 224.6 1.0 OE2 B:GLU424 4.8 65.8 1.0 CG B:ASP500 4.8 67.3 1.0 C5' F:DG21 4.9 224.6 1.0 C B:LYS740 4.9 69.9 1.0

E.Michalczyk, Z.Pakosz-Stepien, J.Liston, O.Gittins, M.Pabis, J.G.Heddle, D.Ghilarov. Structure of Escherichia Coli Dna Gyrase with Chirally Wrapped Dna Supports Ratchet-and-Pawl Mechanism For An Atp-Powered Supercoiling Motor Proceedings of the National 2024ACADEMY of Sciences Usa.