Magnesium in PDB 5z9p: Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment

All present enzymatic activity of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment:
5.99.1.3;

The structure of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment, PDB code: 5z9p was solved by X.Huang, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.40 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.103, 55.660, 51.055, 90.00, 100.27, 90.00
R / Rfree (%)	19.3 / 21

The binding sites of Magnesium atom in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment (pdb code 5z9p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment, PDB code: 5z9p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:14.2 occ:1.00 OD1 A:ASN54 2.0 10.9 1.0 O A:HOH499 2.1 12.0 1.0 O A:HOH541 2.1 15.0 1.0 O A:HOH406 2.1 15.2 1.0 O A:HOH495 2.1 19.3 1.0 CG A:ASN54 3.1 10.1 1.0 ND2 A:ASN54 3.5 11.1 1.0 O A:HOH426 4.2 22.4 1.0 OD2 A:ASP57 4.2 13.2 1.0 O A:HOH450 4.2 23.0 1.0 O A:GLU50 4.3 9.2 1.0 O A:HOH430 4.3 18.7 1.0 O A:HOH417 4.4 14.9 1.0 O A:HOH567 4.4 19.6 1.0 CB A:ASN54 4.4 9.5 1.0 N A:ASN54 4.6 8.8 1.0 CA A:ASN54 4.6 9.0 1.0 CB A:ASP53 4.9 10.3 1.0 OE1 A:GLU50 4.9 14.6 1.0

Magnesium binding site 2 out of 2 in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:29.7 occ:1.00 O B:HOH556 2.0 28.5 1.0 O B:HOH468 2.0 19.0 1.0 O B:HOH409 2.1 26.9 1.0 OD1 B:ASN54 2.3 16.5 1.0 O B:HOH536 2.3 25.8 1.0 CG B:ASN54 3.4 13.5 1.0 O B:HOH447 3.8 28.9 1.0 ND2 B:ASN54 3.9 15.7 1.0 O B:HOH457 4.1 33.5 1.0 O B:HOH520 4.3 27.3 1.0 OD2 B:ASP57 4.3 13.2 1.0 O B:GLU50 4.4 10.3 1.0 N B:ASN54 4.5 9.9 1.0 CB B:ASP53 4.5 11.5 1.0 CB B:ASN54 4.6 11.8 1.0 CA B:ASN54 4.6 10.4 1.0 OE1 B:GLU50 4.7 19.0 1.0 O B:HOH557 4.7 22.9 1.0 C B:ASP53 4.8 9.8 1.0

X.Huang, J.Guo, Q.Liu, Q.Gu, J.Xu, H.Zhou. Identification of An Auxiliary Druggable Pocket in the Dna Gyrase Atpase Domain Using Fragment Probes Medchemcomm V. 9 1619 2018.
ISSN: ESSN 2040-2511
PubMed: 30429968
DOI: 10.1039/C8MD00148K