Calcium in PDB 8r1m: Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine

The structure of Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine, PDB code: 8r1m was solved by W.A.Offen, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.10 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.975, 165.149, 178.921, 90, 90, 90
R / Rfree (%)	17.7 / 22.7

The structure of Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine (pdb code 8r1m). 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 TXGH116 with Covalently Bound N-Azido-Octyl Aziridine, PDB code: 8r1m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:29.9 occ:1.00 OD1 A:ASP583 2.0 36.2 1.0 OD1 A:ASP579 2.0 25.9 1.0 O A:ILE581 2.2 30.3 1.0 OD1 A:ASP575 2.3 36.1 1.0 OD1 A:ASP577 2.3 38.9 1.0 O A:HOH1115 2.4 37.2 1.0 CG A:ASP579 3.0 31.1 1.0 CG A:ASP583 3.2 40.8 1.0 H A:ILE581 3.2 27.0 1.0 HA A:ASP575 3.2 35.5 1.0 H A:ASP579 3.3 38.7 1.0 CG A:ASP577 3.4 45.6 1.0 C A:ILE581 3.4 30.8 1.0 CG A:ASP575 3.4 37.9 1.0 HB A:ILE581 3.4 29.4 1.0 H A:ASP577 3.4 47.2 1.0 OD2 A:ASP579 3.5 30.2 1.0 OD2 A:ASP583 3.8 53.1 1.0 OD2 A:ASP577 3.8 50.3 1.0 N A:ILE581 3.9 27.0 1.0 CA A:ASP575 3.9 35.5 1.0 CB A:ASP575 4.0 35.9 1.0 HG1 A:THR600 4.0 28.3 0.0 CA A:ILE581 4.0 29.8 1.0 HB2 A:ASP575 4.0 35.9 1.0 HA A:ASP583 4.1 32.5 1.0 C A:PRO582 4.1 31.1 1.0 N A:ASP583 4.1 32.5 1.0 N A:ASP579 4.1 38.7 1.0 CB A:ILE581 4.2 29.4 1.0 H A:ASN578 4.2 40.5 1.0 CB A:ASP579 4.2 33.0 1.0 N A:ASP577 4.2 47.2 1.0 O A:PRO582 4.2 33.2 1.0 CB A:ASP583 4.3 35.4 1.0 H A:LYS576 4.3 38.9 1.0 H A:GLY580 4.4 29.4 1.0 C A:ASP575 4.4 36.0 1.0 H A:ASP583 4.4 32.5 1.0 CA A:ASP583 4.4 32.5 1.0 OD2 A:ASP575 4.4 38.6 1.0 OG1 A:THR600 4.4 28.3 1.0 N A:PRO582 4.4 29.8 1.0 HB3 A:ASP579 4.5 33.0 1.0 N A:LYS576 4.5 38.9 1.0 N A:ASN578 4.5 40.5 1.0 HA A:PRO582 4.6 30.1 1.0 CA A:ASP579 4.6 31.4 1.0 CB A:ASP577 4.6 44.5 1.0 CA A:PRO582 4.7 30.1 1.0 N A:GLY580 4.7 29.4 1.0 CA A:ASP577 4.7 42.8 1.0 C A:ASP577 4.7 43.0 1.0 HG23 A:ILE581 4.7 29.1 1.0 C A:ASP579 4.8 33.0 1.0 HB3 A:ASP583 4.8 35.4 1.0 HB3 A:ASP575 4.9 35.9 1.0 HB2 A:ASP583 4.9 35.4 1.0 HG13 A:ILE581 5.0 28.1 1.0 HA A:ILE581 5.0 29.8 1.0 O A:ASP575 5.0 40.2 1.0 HB2 A:ASP579 5.0 33.0 1.0

Calcium binding site 2 out of 2 in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:31.6 occ:1.00 OD1 B:ASP583 2.0 31.1 1.0 O B:ILE581 2.1 30.3 1.0 O B:HOH1036 2.2 16.3 0.5 OD1 B:ASP575 2.3 35.7 1.0 OD1 B:ASP579 2.3 32.8 1.0 OD1 B:ASP577 2.4 44.8 1.0 CG B:ASP579 3.1 35.9 1.0 CG B:ASP583 3.1 34.7 1.0 CG B:ASP577 3.2 48.0 1.0 H B:ASP579 3.3 45.7 1.0 H B:ILE581 3.3 30.7 1.0 CG B:ASP575 3.3 34.6 1.0 C B:ILE581 3.3 29.8 1.0 HA B:ASP575 3.4 36.8 1.0 HB B:ILE581 3.4 32.7 1.0 OD2 B:ASP579 3.5 34.9 1.0 H B:ASP577 3.5 47.9 1.0 OD2 B:ASP577 3.5 53.4 1.0 OD2 B:ASP583 3.8 38.6 0.5 HB2 B:ASP575 3.9 34.8 1.0 CB B:ASP575 4.0 34.8 1.0 HG1 B:THR600 4.0 30.4 0.0 N B:ILE581 4.0 30.7 1.0 HA B:ASP583 4.0 30.9 1.0 CA B:ILE581 4.0 32.8 1.0 CA B:ASP575 4.1 36.8 1.0 H B:LYS576 4.1 43.6 1.0 N B:ASP583 4.1 30.3 1.0 N B:ASP579 4.1 45.7 1.0 C B:PRO582 4.2 29.6 1.0 CB B:ILE581 4.2 32.7 1.0 CB B:ASP583 4.2 32.6 1.0 OD2 B:ASP575 4.3 34.0 1.0 H B:ASN578 4.3 40.9 1.0 CB B:ASP579 4.3 37.7 1.0 H B:ASP583 4.3 30.3 1.0 CA B:ASP583 4.3 30.9 1.0 N B:ASP577 4.3 47.9 1.0 OG1 B:THR600 4.4 30.4 1.0 N B:PRO582 4.4 27.6 1.0 HA B:PRO582 4.4 29.5 1.0 HB3 B:ASP579 4.4 37.7 1.0 H B:GLY580 4.5 31.6 1.0 HG23 B:ILE581 4.5 33.1 1.0 N B:LYS576 4.5 43.6 1.0 O B:PRO582 4.5 33.0 1.0 CB B:ASP577 4.5 45.6 1.0 C B:ASP575 4.5 38.5 1.0 HB3 B:ASP583 4.6 32.6 1.0 CA B:PRO582 4.6 29.5 1.0 N B:ASN578 4.6 40.9 1.0 CA B:ASP579 4.6 38.3 1.0 N B:GLY580 4.8 31.6 1.0 CA B:ASP577 4.8 46.4 1.0 C B:ASP577 4.8 44.8 1.0 C B:ASP579 4.8 35.3 1.0 HB3 B:ASP575 4.9 34.8 1.0 CG2 B:ILE581 4.9 33.1 1.0 HB2 B:ASP583 5.0 32.6 1.0 HB3 B:ASP577 5.0 45.6 1.0 HA B:ILE581 5.0 32.8 1.0

Q.Su, M.Louwerse, R.F.Lammers, E.Maurits, M.Janssen, R.G.Boot, V.Borlandelli, W.A.Offen, D.Linzel, S.P.Schroder, G.J.Davies, H.S.Overkleeft, M.Artola, J.M.F.G.Aerts. Selective Labelling of GBA2 in Cells with Fluorescent Beta-D-Arabinofuranosyl Cyclitol Aziridines. Chem Sci 2024.
ISSN: ISSN 2041-6520
PubMed: 39246358
DOI: 10.1039/D3SC06146A