Magnesium in PDB 7z9c: E.Coli Gyrase Holocomplex with 217 Bp Dna and Albicidin

All present enzymatic activity of E.Coli Gyrase Holocomplex with 217 Bp Dna and Albicidin:
5.6.2.2;

The binding sites of Magnesium atom in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albicidin (pdb code 7z9c). 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 217 Bp Dna and Albicidin, PDB code: 7z9c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albicidin


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 217 Bp Dna and Albicidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:56.2 occ:1.00 O B:HOH1002 1.9 46.4 1.0 O C:HOH1001 1.9 40.7 1.0 O B:HOH1003 1.9 44.0 1.0 O B:HOH1001 2.0 51.3 1.0 O B:HOH1004 2.0 49.9 1.0 OD2 B:ASP500 2.1 39.6 1.0 CG B:ASP500 3.3 39.6 1.0 OD2 B:ASP498 3.8 45.6 1.0 OD1 B:ASP500 3.9 39.6 1.0 H5' E:DT14 4.0 45.2 1.0 CB B:ASP500 4.4 39.6 1.0 OP1 E:DT14 4.4 45.2 1.0 HB2 B:ASP502 4.4 38.7 1.0 HB3 B:ASP500 4.4 39.6 1.0 CG B:ASP498 4.5 45.6 1.0 HB2 B:ASP500 4.5 39.6 1.0 OD2 B:ASP502 4.6 38.7 1.0 HB3 B:ASP498 4.6 45.6 1.0 O B:LYS740 4.9 51.6 1.0 C5' E:DT14 5.0 45.2 1.0

Magnesium binding site 2 out of 2 in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albicidin


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 217 Bp Dna and Albicidin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:56.7 occ:1.00 O D:HOH1002 1.9 45.0 1.0 O F:HOH101 1.9 42.6 1.0 O D:HOH1001 1.9 44.0 1.0 O F:HOH102 1.9 44.3 1.0 O D:HOH1003 2.0 39.1 1.0 OD2 D:ASP500 2.1 35.0 1.0 CG D:ASP500 3.2 35.0 1.0 H5' F:DA14 3.5 45.2 1.0 OD1 D:ASP500 3.8 35.0 1.0 OD2 D:ASP498 4.0 33.5 1.0 OP1 F:DA14 4.1 45.2 1.0 HB2 D:ASP502 4.3 33.8 1.0 CB D:ASP500 4.4 35.0 1.0 HB3 D:ASP500 4.5 35.0 1.0 C5' F:DA14 4.5 45.2 1.0 HB2 D:ASP500 4.6 35.0 1.0 CG D:ASP498 4.6 33.5 1.0 HB3 D:ASP498 4.6 33.5 1.0 O D:LYS740 4.7 31.8 1.0 OD2 D:ASP502 4.8 33.8 1.0 H5'' F:DA14 4.8 45.2 1.0 H3' F:DA14 4.9 45.2 1.0

E.Michalczyk, K.Hommernick, I.Behroz, M.Kulike, Z.Pakosz-Stepien, L.Mazurek, M.Seidel, M.Kunert, K.Santos, H.Von Moeller, B.Loll, J.B.Weston, A.Mainz, J.G.Heddle, R.D.Sussmuth, D.Ghilarov. Molecular Mechanism of Topoisomerase Poisoning By the Peptide Antibiotic Albicidin. Nat Catal V. 6 52 2023.
ISSN: ESSN 2520-1158
PubMed: 36741192
DOI: 10.1038/S41929-022-00904-1