Calcium in PDB 7ag5: Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate

The structure of Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate, PDB code: 7ag5 was solved by M.R.Zeronian, N.M.Pearce, T.M.Wood, N.I.Martin, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.01 / 1.04
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.428, 40.428, 31.033, 90, 90, 120
R / Rfree (%)	12 / 14.3

The binding sites of Calcium atom in the Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate (pdb code 7ag5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate, PDB code: 7ag5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:7.2 occ:1.00 O3 A:RDZ103 2.3 7.5 0.7 O3 A:RDZ103 2.3 11.2 0.3 O A:ILE10 2.3 7.5 1.0 O A:GLY8 2.3 8.1 1.0 OD1 A:ASP5 2.3 8.8 1.0 O A:DNP2 2.3 7.5 1.0 O A:GLY6 2.4 8.0 1.0 H A:DNP2 3.1 8.5 1.0 CG A:ASP5 3.4 8.7 1.0 C A:ILE10 3.5 7.9 1.0 C A:GLY8 3.5 7.9 1.0 C A:DNP2 3.5 7.4 1.0 C A:GLY6 3.5 7.9 1.0 P1 A:RDZ103 3.7 7.0 0.7 P1 A:RDZ103 3.7 10.8 0.3 HA A:CPI3 3.7 8.8 1.0 H A:ASP5 3.8 8.2 1.0 HA A:PRO11 3.9 8.0 1.0 OD2 A:ASP5 3.9 10.1 1.0 N A:DNP2 3.9 8.3 1.0 N A:ILE10 4.0 8.2 1.0 N A:GLY8 4.0 7.9 1.0 H A:ILE10 4.0 8.0 1.0 HB3 A:ASP1 4.0 9.2 1.0 O4 A:RDZ103 4.1 11.7 0.3 C A:ASP7 4.2 8.1 1.0 H A:GLY8 4.2 7.8 1.0 HG1 A:DNP2 4.2 8.3 1.0 N A:GLY6 4.2 8.7 1.0 C A:2RA9 4.2 7.7 1.0 NG A:DNP2 4.3 8.2 1.0 HB A:ILE10 4.3 9.8 1.0 CA A:GLY8 4.3 8.3 1.0 CA A:DNP2 4.3 8.0 1.0 C A:ASP5 4.3 8.9 1.0 CA A:ILE10 4.3 7.8 1.0 HA A:ASP7 4.3 8.4 1.0 C A:PRO11 4.3 8.2 1.0 O2 A:RDZ103 4.3 7.8 0.7 O4 A:RDZ103 4.3 7.6 0.7 CA A:PRO11 4.4 8.0 1.0 N A:PRO11 4.4 8.1 1.0 H A:GLY6 4.4 8.7 1.0 HA A:2RA9 4.4 8.3 1.0 CA A:GLY6 4.5 9.2 1.0 N A:ASP7 4.5 9.2 1.0 N A:2RA9 4.5 8.1 1.0 N A:CPI3 4.5 8.3 1.0 CA A:CPI3 4.5 8.7 1.0 O2 A:RDZ103 4.5 9.4 0.3 CA A:ASP7 4.6 8.2 1.0 HA2 A:GLY8 4.6 8.3 1.0 O A:ASP7 4.6 10.3 1.0 N A:ASP5 4.6 8.1 1.0 O1 A:RDZ103 4.6 8.7 0.7 CA A:2RA9 4.6 8.1 1.0 O A:ASP5 4.6 10.6 1.0 CB A:ASP5 4.6 8.9 1.0 O1 A:RDZ103 4.7 11.0 0.3 CA A:ASP5 4.8 8.7 1.0 HA A:ASP1 4.8 9.3 1.0 O A:2RA9 4.8 7.9 1.0 CB A:ILE10 4.9 9.6 1.0 O A:PRO11 4.9 9.3 1.0 CB A:DNP2 4.9 8.7 1.0 CB A:ASP1 4.9 9.2 1.0

Calcium binding site 2 out of 2 in the Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Laspartomycin C Double Mutant G4D D-Allo-THR9D-Dap in Complex with Geranyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:8.2 occ:1.00 O2 A:RDZ103 2.2 9.4 0.3 O2 A:RDZ103 2.3 7.8 0.7 OD1 A:ASP7 2.3 8.8 1.0 OD1 A:ASP1 2.3 9.1 1.0 O A:9GE104 2.3 9.8 1.0 O A:HOH212 2.4 8.5 1.0 HA A:ASP1 3.1 9.3 1.0 HA A:ASP7 3.2 8.4 1.0 C A:9GE104 3.3 9.8 1.0 H A:GLY8 3.4 7.8 1.0 CG A:ASP7 3.4 8.4 1.0 H10 A:RDZ103 3.5 9.6 0.3 CG A:ASP1 3.5 10.0 1.0 H10 A:RDZ103 3.6 12.1 0.7 P1 A:RDZ103 3.7 7.0 0.7 P1 A:RDZ103 3.7 10.8 0.3 CA A:ASP1 3.8 9.1 1.0 N A:ASP1 3.9 9.3 1.0 H2 A:9GE104 4.0 11.4 0.6 CA A:ASP7 4.0 8.2 1.0 CB A:ASP7 4.1 9.2 1.0 H11 A:RDZ103 4.1 12.1 0.7 C8 A:RDZ103 4.2 12.3 0.7 O1 A:RDZ103 4.2 8.7 0.7 CB A:ASP1 4.2 9.2 1.0 HB2 A:ASP7 4.2 8.8 1.0 CA A:9GE104 4.2 12.5 0.4 C8 A:RDZ103 4.2 9.4 0.3 N A:GLY8 4.3 7.9 1.0 O1 A:RDZ103 4.4 11.0 0.3 H11 A:RDZ103 4.4 9.9 0.3 OD2 A:ASP7 4.4 13.7 1.0 CA A:9GE104 4.5 9.6 0.6 HB3 A:ASP1 4.5 9.2 1.0 O4 A:RDZ103 4.5 7.6 0.7 O4 A:RDZ103 4.5 11.7 0.3 O3 A:RDZ103 4.6 11.2 0.3 OD2 A:ASP1 4.6 13.1 1.0 C04 A:9GE104 4.6 12.0 0.6 O3 A:RDZ103 4.6 7.5 0.7 H1 A:9GE104 4.6 12.5 0.4 H12 A:RDZ103 4.7 9.2 0.3 H2 A:9GE104 4.7 15.7 0.4 H1 A:ASP1 4.7 9.2 1.0 C A:ASP7 4.7 8.1 1.0 C04 A:9GE104 4.8 16.1 0.4 H A:DNP2 4.9 8.5 1.0

T.M.Wood, M.R.Zeronian, N.Buijs, K.Bertheussen, H.K.Abedian, A.V.Johnson, N.M.Pearce, M.Lutz, J.Kemmink, T.Seirsma, L.W.Hamoen, B.J.C.Janssen, N.I.Martin. Mechanistic Insights Into the C55-P Targeting Lipopeptide Antibiotics Revealed By Structure-Activity Studies and High-Resolution Crystal Structures Chem Sci V. 13 2985 2022.
ISSN: ESSN 2041-6539
DOI: 10.1039/D1SC07190D