Calcium in PDB 5o0z: Structure of Laspartomycin C in Complex with Geranyl-Phosphate

The structure of Structure of Laspartomycin C in Complex with Geranyl-Phosphate, PDB code: 5o0z was solved by H.C.Vlieg, L.H.J.Kleijn, 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)	40.26 / 1.28
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	56.933, 56.933, 56.933, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.5

The structure of Structure of Laspartomycin C in Complex with Geranyl-Phosphate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Structure of Laspartomycin C in Complex with Geranyl-Phosphate (pdb code 5o0z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Laspartomycin C in Complex with Geranyl-Phosphate, PDB code: 5o0z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Laspartomycin C 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 Laspartomycin C in Complex with Geranyl-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:14.8 occ:1.00 O A:GLY8 2.3 16.6 1.0 O1A A:9GB101 2.3 14.7 1.0 O A:DNP2 2.3 15.1 1.0 OD1 A:ASP5 2.3 16.8 1.0 O A:ILE10 2.3 16.5 1.0 O A:GLY6 2.3 16.0 1.0 CG A:ASP5 3.4 20.0 1.0 C A:ILE10 3.5 16.1 1.0 C A:GLY8 3.5 15.6 1.0 C A:DNP2 3.5 14.2 1.0 C A:GLY6 3.6 15.8 1.0 PA A:9GB101 3.7 13.8 1.0 N A:ILE10 3.9 17.4 1.0 N A:DNP2 3.9 14.9 1.0 OD2 A:ASP5 3.9 20.1 1.0 N A:GLY8 4.0 14.3 1.0 C A:ASP7 4.1 16.3 1.0 N A:GLY6 4.2 17.1 1.0 O3A A:9GB101 4.3 15.3 1.0 CA A:ILE10 4.3 17.8 1.0 CA A:GLY8 4.3 14.3 1.0 C A:ASP5 4.3 18.6 1.0 C A:2TL9 4.3 16.6 1.0 CA A:DNP2 4.3 14.4 1.0 C A:PRO11 4.4 16.4 1.0 N A:PRO11 4.4 16.2 1.0 NG A:DNP2 4.4 15.3 1.0 N A:CPI3 4.5 16.5 1.0 O2A A:9GB101 4.5 16.2 1.0 N A:2TL9 4.5 18.4 1.0 N A:ASP7 4.5 17.4 1.0 CA A:PRO11 4.5 15.1 1.0 CA A:CPI3 4.5 17.3 1.0 CA A:GLY6 4.5 18.4 1.0 CA A:ASP7 4.5 16.9 1.0 O A:ASP5 4.6 20.6 1.0 N A:ASP5 4.6 18.5 1.0 O A:ASP7 4.6 18.9 1.0 CA A:2TL9 4.6 18.5 1.0 O1 A:9GB101 4.7 15.1 1.0 CB A:ASP5 4.7 20.9 1.0 O A:HOH207 4.7 36.1 1.0 CA A:ASP5 4.7 20.6 1.0 CB A:ILE10 4.8 20.1 1.0 O A:2TL9 4.8 18.8 1.0 O A:HOH204 5.0 15.0 1.0 CB A:DNP2 5.0 15.4 1.0 CB A:ASP1 5.0 16.3 1.0

Calcium binding site 2 out of 4 in the Structure of Laspartomycin C 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 Laspartomycin C in Complex with Geranyl-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:15.6 occ:1.00 O2A A:9GB101 2.2 16.2 1.0 OD1 A:ASP7 2.3 16.6 1.0 OD1 A:ASP1 2.3 16.5 1.0 O A:9GE0 2.4 16.1 1.0 O B:HOH205 2.4 15.9 1.0 O B:HOH206 2.4 20.8 1.0 C A:9GE0 3.4 15.4 1.0 CG A:ASP7 3.4 17.8 1.0 CG A:ASP1 3.5 16.0 1.0 CH3 A:ACY106 3.7 47.5 1.0 PA A:9GB101 3.7 13.8 1.0 CA A:ASP1 3.8 14.3 1.0 O B:2TL9 3.9 17.4 1.0 N A:ASP1 3.9 15.1 1.0 CA A:ASP7 4.0 16.9 1.0 CB A:ASP7 4.1 17.3 1.0 CB A:ASP1 4.2 16.3 1.0 C1 A:9GB101 4.2 17.4 1.0 O1 A:9GB101 4.2 15.1 1.0 O1A B:9GB101 4.3 15.5 1.0 N A:GLY8 4.4 14.3 1.0 OD2 A:ASP7 4.5 17.5 1.0 CA A:9GE0 4.5 18.5 1.0 OD2 A:ASP1 4.5 19.6 1.0 O3A A:9GB101 4.5 15.3 1.0 O1A A:9GB101 4.7 14.7 1.0 CG B:PRO11 4.7 22.2 1.0 CA B:GLY8 4.8 16.8 1.0 C A:ASP7 4.8 16.3 1.0 C04 A:9GE0 4.8 25.9 1.0 N B:2TL9 4.9 16.7 1.0 C B:GLY8 5.0 15.5 1.0 C B:2TL9 5.0 16.1 1.0

Calcium binding site 3 out of 4 in the Structure of Laspartomycin C 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 3 of Structure of Laspartomycin C in Complex with Geranyl-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:14.6 occ:1.00 O3A B:9GB101 2.3 14.0 1.0 O B:GLY8 2.3 15.5 1.0 O B:DNP2 2.3 14.8 1.0 OD1 B:ASP5 2.3 17.4 1.0 O B:ILE10 2.3 15.8 1.0 O B:GLY6 2.4 15.8 1.0 CG B:ASP5 3.5 19.2 1.0 C B:DNP2 3.5 15.2 1.0 C B:ILE10 3.5 15.5 1.0 C B:GLY8 3.5 15.5 1.0 C B:GLY6 3.6 15.9 1.0 PA B:9GB101 3.7 13.6 1.0 N B:ILE10 4.0 18.3 1.0 N B:DNP2 4.0 13.7 1.0 OD2 B:ASP5 4.0 20.6 1.0 N B:GLY8 4.0 16.7 1.0 N B:GLY6 4.2 18.4 1.0 C B:ASP7 4.2 16.5 1.0 C B:2TL9 4.2 16.1 1.0 C B:ASP5 4.3 17.9 1.0 O1A B:9GB101 4.3 15.5 1.0 CA B:ILE10 4.3 17.7 1.0 CA B:DNP2 4.3 14.7 1.0 CA B:GLY8 4.3 16.8 1.0 NG B:DNP2 4.4 15.1 1.0 N B:CPI3 4.4 16.9 1.0 N B:PRO11 4.4 16.9 1.0 CA B:CPI3 4.4 16.8 1.0 O2A B:9GB101 4.4 15.0 1.0 N B:2TL9 4.4 16.7 1.0 CA B:PRO11 4.5 16.6 1.0 C B:PRO11 4.5 16.2 1.0 CA B:GLY6 4.5 17.7 1.0 N B:ASP7 4.5 16.8 1.0 CA B:2TL9 4.5 17.7 1.0 O B:HOH204 4.6 32.5 1.0 N B:ASP5 4.6 16.4 1.0 CA B:ASP7 4.6 16.8 1.0 O B:ASP7 4.6 19.1 1.0 O B:ASP5 4.6 21.4 1.0 O1 B:9GB101 4.6 15.9 1.0 CB B:ASP5 4.7 20.2 1.0 CA B:ASP5 4.7 17.4 1.0 O B:2TL9 4.8 17.4 1.0 O B:HOH205 4.9 15.9 1.0 CB B:DNP2 4.9 16.9 1.0 CB B:ILE10 4.9 20.6 1.0 CB B:ASP1 5.0 15.2 1.0

Calcium binding site 4 out of 4 in the Structure of Laspartomycin C 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 4 of Structure of Laspartomycin C in Complex with Geranyl-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:16.1 occ:1.00 O2A B:9GB101 2.3 15.0 1.0 OD1 B:ASP7 2.3 17.6 1.0 OD1 B:ASP1 2.3 18.1 1.0 O A:HOH206 2.3 21.2 1.0 O A:HOH204 2.4 15.0 1.0 O B:9GE0 2.4 17.3 1.0 C B:9GE0 3.4 17.0 1.0 CG B:ASP7 3.4 19.0 1.0 CG B:ASP1 3.5 17.3 1.0 PA B:9GB101 3.7 13.6 1.0 CA B:ASP1 3.8 15.9 1.0 O A:2TL9 3.9 18.8 1.0 N B:ASP1 4.0 15.9 1.0 CA B:ASP7 4.0 16.8 1.0 CB B:ASP7 4.1 17.9 1.0 C1 B:9GB101 4.2 16.9 1.0 CB B:ASP1 4.2 15.2 1.0 O1 B:9GB101 4.3 15.9 1.0 O3A A:9GB101 4.3 15.3 1.0 OD2 B:ASP7 4.4 20.6 1.0 N B:GLY8 4.5 16.7 1.0 O1A B:9GB101 4.5 15.5 1.0 CA B:9GE0 4.5 18.2 1.0 O B:ACY104 4.5 62.2 1.0 C B:ACY104 4.5 76.6 1.0 OD2 B:ASP1 4.5 19.4 1.0 CH3 B:ACY104 4.6 64.0 1.0 O3A B:9GB101 4.7 14.0 1.0 N A:2TL9 4.8 18.4 1.0 CA A:GLY8 4.8 14.3 1.0 C B:ASP7 4.8 16.5 1.0 CG A:PRO11 4.8 19.5 1.0 C04 B:9GE0 4.9 22.7 1.0 C A:GLY8 5.0 15.6 1.0 C A:2TL9 5.0 16.6 1.0

L.H.J.Kleijn, H.C.Vlieg, T.M.Wood, J.Sastre Torano, B.J.C.Janssen, N.I.Martin. A High-Resolution Crystal Structure That Reveals Molecular Details of Target Recognition By the Calcium-Dependent Lipopeptide Antibiotic Laspartomycin C. Angew. Chem. Int. Ed. Engl. V. 56 16546 2017.
ISSN: ESSN 1521-3773
PubMed: 29108098
DOI: 10.1002/ANIE.201709240