Calcium in PDB 8bn6: Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021

All present enzymatic activity of Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021:
5.6.2.2;

The structure of Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021, PDB code: 8bn6 was solved by M.Durcik, A.Zega, N.Zidar, J.Ilas, T.Tomasic, L.P.Masic, J.E.A.Mundy, C.E.M.Stevenson, N.Burton, D.M.Lawson, A.Maxwell, D.Kikelj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.63 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.2, 115.65, 38.63, 90, 90, 90
R / Rfree (%)	18.1 / 22.3

The structure of Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021 (pdb code 8bn6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021, PDB code: 8bn6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:36.5 occ:1.00 O A:HOH534 2.3 33.5 1.0 OG A:SER165 2.3 27.4 1.0 O A:HOH490 2.4 37.0 1.0 O A:ASN76 2.4 21.8 1.0 O A:HOH521 2.4 30.8 1.0 O A:GLY77 2.6 25.2 1.0 O A:HOH499 2.7 42.6 1.0 O A:SER165 2.7 26.3 1.0 C A:ASN76 3.3 20.3 1.0 C A:SER165 3.4 25.3 1.0 C A:GLY77 3.5 24.4 1.0 CB A:SER165 3.5 28.0 1.0 CA A:SER165 3.8 26.2 1.0 N A:SER165 3.9 26.3 1.0 N A:GLY77 4.0 21.5 1.0 CA A:GLY77 4.0 23.1 1.0 CA A:ASN76 4.2 21.9 1.0 O A:TYR57 4.3 30.0 1.0 O A:HOH546 4.3 41.6 1.0 CB A:ASN76 4.3 21.8 1.0 N A:GLY166 4.4 23.2 1.0 N A:ARG78 4.5 23.8 1.0 O A:HOH560 4.6 51.1 1.0 O A:HOH567 4.7 47.2 1.0 CA A:ARG78 4.7 23.9 1.0 CG A:ASN76 4.8 23.1 1.0 CA A:GLY166 4.9 22.3 1.0

Calcium binding site 2 out of 2 in the Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Aeruginosa Dna Gyrase B 24KDA Atpase Subdomain Complexed with EBL3021 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:51.8 occ:1.00 O A:HOH417 2.4 34.9 1.0 O A:HOH602 2.4 54.0 1.0 O A:HOH593 2.5 46.2 1.0 O A:HOH411 2.5 43.4 1.0 O A:HOH587 2.6 38.5 1.0 O A:HOH511 2.7 34.3 1.0 O A:HOH588 2.8 46.2 1.0 CA A:GLY119 4.1 33.7 1.0 OD2 A:ASP51 4.3 34.5 1.0 CB A:ASP47 4.4 23.0 1.0 O A:HOH405 4.5 46.9 1.0 OD1 A:ASP51 4.6 30.4 1.0 OD2 A:ASP47 4.8 26.9 1.0 CG A:ASP51 4.9 31.5 1.0 O A:HOH523 4.9 26.1 1.0 OE1 A:GLU44 5.0 40.6 1.0 C A:GLY119 5.0 35.6 1.0

M.Durcik, A.E.Cotman, Z.Toplak, S.Mozina, Z.Skok, P.E.Szili, M.Czikkely, E.Maharramov, T.H.Vu, M.V.Piras, N.Zidar, J.Ilas, A.Zega, J.Trontelj, L.A.Pardo, D.Hughes, D.Huseby, T.Berruga-Fernandez, S.Cao, I.Simoff, R.Svensson, S.V.Korol, Z.Jin, F.Vicente, M.C.Ramos, J.E.A.Mundy, A.Maxwell, C.E.M.Stevenson, D.M.Lawson, B.Glinghammar, E.Sjostrom, M.Bohlin, J.Oreskar, S.Alver, G.V.Janssen, G.J.Sterk, D.Kikelj, C.Pal, T.Tomasic, L.Peterlin Masic. New Dual Inhibitors of Bacterial Topoisomerases with Broad-Spectrum Antibacterial Activity and in Vivo Efficacy Against Vancomycin-Intermediate Staphylococcus Aureus. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 36877255
DOI: 10.1021/ACS.JMEDCHEM.2C01905