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Magnesium in PDB 7z9k: E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg)

Enzymatic activity of E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg)

All present enzymatic activity of E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg):
5.6.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg) (pdb code 7z9k). 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 Albi-1 (Site Tg), PDB code: 7z9k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7z9k

Go back to Magnesium Binding Sites List in 7z9k
Magnesium binding site 1 out of 2 in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg)


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 Albi-1 (Site Tg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:35.8
occ:1.00
OD2 B:ASP500 2.0 36.6 1.0
CG B:ASP500 3.2 36.6 1.0
OD2 B:ASP498 3.6 35.4 1.0
OD1 B:ASP500 3.8 36.6 1.0
H5' E:DT14 3.9 49.0 1.0
N4 A:IL1901 4.2 38.5 1.0
HB2 B:ASP502 4.3 37.4 1.0
OP1 E:DT14 4.3 49.0 1.0
CG B:ASP498 4.3 35.4 1.0
CB B:ASP500 4.3 36.6 1.0
HB3 B:ASP500 4.4 36.6 1.0
OD2 B:ASP502 4.5 37.4 1.0
HB2 B:ASP500 4.5 36.6 1.0
HB3 B:ASP498 4.6 35.4 1.0
O B:LYS740 4.8 39.5 1.0
N3 A:IL1901 4.8 38.5 1.0
C5' E:DT14 4.8 49.0 1.0
CB B:ASP498 5.0 35.4 1.0
OD1 B:ASP498 5.0 35.4 1.0

Magnesium binding site 2 out of 2 in 7z9k

Go back to Magnesium Binding Sites List in 7z9k
Magnesium binding site 2 out of 2 in the E.Coli Gyrase Holocomplex with 217 Bp Dna and Albi-1 (Site Tg)


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 Albi-1 (Site Tg) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:38.1
occ:1.00
OD2 D:ASP500 2.9 36.2 1.0
H5' F:DA14 3.5 49.0 1.0
OD2 D:ASP498 3.7 31.1 1.0
OP1 F:DA14 3.9 49.0 1.0
CG D:ASP500 4.1 36.2 1.0
C5' F:DA14 4.4 49.0 1.0
OD1 D:ASP500 4.7 36.2 1.0
CG D:ASP498 4.7 31.1 1.0
O D:LYS740 4.7 35.8 1.0
H5'' F:DA14 4.8 49.0 1.0
HG2 D:LYS740 4.8 35.8 1.0
H3' F:DA14 4.8 49.0 1.0
HB2 D:ASP502 4.9 37.3 1.0
O5' F:DA14 5.0 49.0 1.0

Reference:

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
Page generated: Thu Oct 3 16:19:43 2024

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