Chlorine 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:

Calcium

(Ca)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine, PDB code: 8r1m:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl902 b:49.0 occ:1.00 H A:LYS363 2.5 23.5 1.0 O A:HOH1351 2.6 33.1 1.0 H A:ASN364 2.7 20.1 1.0 HB3 A:ASN364 2.7 22.0 1.0 O A:HOH1217 2.9 36.4 1.0 HA3 A:GLY362 3.2 20.4 1.0 N A:LYS363 3.3 23.5 1.0 N A:ASN364 3.4 20.1 1.0 CG A:ASN364 3.4 24.4 1.0 CB A:ASN364 3.4 22.0 1.0 OD1 A:ASN364 3.6 23.9 1.0 HD21 A:ASN367 3.6 22.1 1.0 CA A:GLY362 3.8 20.4 1.0 ND2 A:ASN364 3.8 23.9 1.0 HA2 A:GLY362 3.8 20.4 1.0 C A:GLY362 3.9 22.3 1.0 CA A:ASN364 4.0 19.7 1.0 HD22 A:ASN364 4.0 23.9 1.0 O A:HOH1332 4.2 35.4 1.0 HD21 A:ASN364 4.2 23.9 1.0 C A:LYS363 4.2 21.0 1.0 HB2 A:ASN364 4.2 22.0 1.0 HB2 A:LYS363 4.3 22.7 1.0 CA A:LYS363 4.3 22.2 1.0 ND2 A:ASN367 4.5 22.1 1.0 HA A:ASN364 4.5 19.7 1.0 CB A:LYS363 4.8 22.7 1.0 OD1 A:ASN367 4.9 23.1 1.0

Chlorine binding site 2 out of 3 in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl903 b:19.6 occ:1.00 H A:ASP401 2.4 17.1 1.0 H B:ASP401 2.4 16.7 1.0 O A:HOH1349 3.0 20.0 1.0 HA A:PRO400 3.1 16.3 1.0 HA B:PRO400 3.1 16.2 1.0 O B:HOH1354 3.2 20.4 1.0 HB2 A:ASP401 3.3 18.3 1.0 N A:ASP401 3.3 17.1 1.0 N B:ASP401 3.3 16.7 1.0 HB2 B:ASP401 3.4 17.1 1.0 HB3 B:PRO400 3.7 16.9 1.0 CA A:PRO400 3.8 16.3 1.0 CA B:PRO400 3.8 16.2 1.0 HB2 B:PRO400 3.8 16.9 1.0 HB3 A:PRO400 3.9 16.2 1.0 HB2 A:PRO400 3.9 16.2 1.0 CB A:ASP401 3.9 18.3 1.0 CB B:PRO400 4.0 16.9 1.0 CG A:ASP401 4.0 19.5 1.0 O A:HOH1388 4.0 34.1 1.0 CB B:ASP401 4.0 17.1 1.0 CG B:ASP401 4.0 18.5 1.0 C A:PRO400 4.1 16.4 1.0 CB A:PRO400 4.1 16.2 1.0 C B:PRO400 4.1 15.9 1.0 CA A:ASP401 4.2 17.2 1.0 CA B:ASP401 4.3 16.8 1.0 OD2 A:ASP401 4.3 22.8 1.0 O B:HOH1375 4.3 13.2 0.5 OD1 A:ASP401 4.3 20.4 1.0 OD1 B:ASP401 4.3 18.4 1.0 OD2 B:ASP401 4.3 21.0 1.0 H B:TRP402 4.4 15.6 1.0 H A:TRP402 4.4 16.0 1.0 O B:HOH1020 4.8 27.5 1.0 HB3 A:ASP401 4.8 18.3 1.0 HA A:ASP401 4.8 17.2 1.0 O A:HOH1110 4.9 23.7 1.0 HA B:ASP401 4.9 16.8 1.0 HB3 B:ASP401 4.9 17.1 1.0 HD1 A:TRP402 5.0 17.6 1.0

Chlorine binding site 3 out of 3 in the Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of TXGH116 with Covalently Bound N-Azido-Octyl Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl902 b:68.5 occ:1.00 HG2 B:PRO717 2.8 33.2 1.0 H B:ASP718 2.9 30.5 1.0 HB3 B:ASP718 2.9 34.0 1.0 HB3 B:ARG716 3.0 31.8 0.5 HB3 B:ARG716 3.0 31.9 0.5 HD2 B:PRO717 3.1 34.8 1.0 CG B:ASP718 3.4 38.2 1.0 HE B:ARG716 3.4 33.9 0.5 HH11 B:ARG716 3.4 35.4 0.5 N B:ASP718 3.5 30.5 1.0 CB B:ASP718 3.5 34.0 1.0 CG B:PRO717 3.6 33.2 1.0 OD2 B:ASP718 3.6 39.3 1.0 CD B:PRO717 3.6 34.8 1.0 OD1 B:ASP718 3.7 37.7 1.0 HD3 B:ARG716 3.9 35.4 0.5 CB B:ARG716 3.9 31.8 0.5 CB B:ARG716 3.9 31.9 0.5 N B:PRO717 4.0 34.1 1.0 NH1 B:ARG716 4.0 35.4 0.5 HG2 B:ARG716 4.1 32.6 0.5 HB2 B:ARG716 4.1 31.9 0.5 CA B:ASP718 4.1 34.1 1.0 NE B:ARG716 4.2 33.9 0.5 HG3 B:PRO717 4.2 33.2 1.0 HH12 B:ARG716 4.2 35.4 0.5 C B:PRO717 4.3 30.6 1.0 HB2 B:ASP718 4.4 34.0 1.0 HB2 B:ARG716 4.4 31.8 0.5 CG B:ARG716 4.5 32.6 0.5 CA B:PRO717 4.5 32.4 1.0 HH11 B:ARG716 4.5 32.4 0.5 CB B:PRO717 4.5 34.8 1.0 C B:ARG716 4.5 32.8 1.0 HD3 B:PRO717 4.5 34.8 1.0 HB2 B:PRO717 4.6 34.8 1.0 HA B:ASP718 4.6 34.1 1.0 CD B:ARG716 4.7 35.4 0.5 CA B:ARG716 4.7 31.9 0.5 CA B:ARG716 4.8 31.9 0.5 CG B:ARG716 4.8 32.8 0.5 OD2 B:ASP662 4.8 48.2 1.0 CD B:ARG716 4.8 36.1 0.5 HA B:ARG716 4.9 31.9 0.5 HA B:ARG716 4.9 31.9 0.5 CZ B:ARG716 5.0 33.6 0.5

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