Chlorine in PDB 9km6: The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin

The structure of The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin, PDB code: 9km6 was solved by L.Wu, G.L.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.98 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.02, 147.02, 128.87, 90, 90, 90
R / Rfree (%)	20.1 / 23.6

The binding sites of Chlorine atom in the The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin (pdb code 9km6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin, PDB code: 9km6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:74.1 occ:1.00 NH2 A:ARG60 3.4 63.5 1.0 N B:ARG60 3.8 40.4 1.0 NH1 A:ARG60 3.9 64.2 1.0 CZ A:ARG60 4.1 73.3 1.0 CG B:ARG60 4.1 58.9 1.0 CB B:THR59 4.1 39.1 1.0 CB B:ARG60 4.3 48.9 1.0 CD B:ARG60 4.4 57.7 1.0 CA B:THR59 4.4 40.4 1.0 C B:THR59 4.6 49.3 1.0 CG2 B:THR59 4.6 53.1 1.0 CA B:ARG60 4.7 46.0 1.0 O B:HOH414 4.9 51.0 1.0

Chlorine binding site 2 out of 3 in the The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:71.5 occ:1.00 NH1 B:ARG139 3.1 34.0 1.0 O B:HOH484 3.3 48.6 1.0 CG B:GLU136 3.3 54.7 1.0 CB B:GLU136 3.6 31.7 1.0 OE2 B:GLU136 3.6 80.7 1.0 CA B:GLU136 3.7 31.9 1.0 CD B:ARG139 3.9 38.1 1.0 CD B:GLU136 4.0 76.6 1.0 CZ B:ARG139 4.2 36.1 1.0 O B:HOH492 4.3 45.0 1.0 NE B:ARG139 4.5 34.4 1.0 N B:GLU136 4.5 33.1 1.0 O B:GLU136 4.7 30.3 1.0 C B:GLU136 4.8 43.4 1.0 CB B:ARG139 4.9 33.3 1.0 CG B:ARG139 4.9 37.3 1.0

Chlorine binding site 3 out of 3 in the The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of XHNM1 and Its Inhibitor Sinefugin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl303 b:78.8 occ:1.00 O A:ASP70 3.8 28.7 1.0 O A:HOH501 3.8 43.8 1.0 N B:GLY34 4.2 37.3 1.0 O B:GLY34 4.3 39.3 1.0 CB A:ASP70 4.5 36.5 1.0 CA B:ALA33 4.6 37.8 1.0 CH2 A:TRP219 4.6 35.7 1.0 C B:ALA33 4.8 39.4 1.0 C B:GLY34 4.8 36.0 1.0 C A:ASP70 4.8 30.1 1.0 O B:ALA32 4.9 51.2 1.0 CZ2 A:TRP219 5.0 42.1 1.0

Q.Y.Nie, S.Q.Fang, L.Wu, R.Q.Gao, Y.Hu, D.Ding, H.X.Pan, Z.F.Pei, J.B.He, Q.Zhou, Z.H.Chen, X.F.Hou, X.Q.Zhao, G.L.Tang. Targeted Discovery and Characterization of Type-II Pks-Nrps Hybrid Dna-Alkylating Antibiotics. Angew.Chem.Int.Ed.Engl. 12820 2025.
ISSN: ESSN 1521-3773
PubMed: 40761108
DOI: 10.1002/ANIE.202512820