Chlorine in PDB 5jjq: Crystal Structure of IDNL1

The structure of Crystal Structure of IDNL1, PDB code: 5jjq was solved by J.Cieslak, A.Miyanaga, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.51 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.750, 104.450, 120.000, 81.78, 83.01, 81.98
R / Rfree (%)	23.4 / 26.5

The binding sites of Chlorine atom in the Crystal Structure of IDNL1 (pdb code 5jjq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of IDNL1, PDB code: 5jjq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of IDNL1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of IDNL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:34.3 occ:1.00 NH1 A:ARG412 3.2 31.4 1.0 N A:ALA343 3.3 24.1 1.0 NH2 A:ARG412 3.5 30.6 1.0 N A:MET349 3.5 27.5 1.0 CB A:HIS342 3.6 29.1 1.0 CA A:HIS342 3.7 27.7 1.0 CZ A:ARG412 3.8 30.0 1.0 O A:MET349 3.9 30.0 1.0 CD1 A:LEU418 3.9 25.8 1.0 C A:HIS342 4.0 28.3 1.0 CB A:ALA343 4.1 23.0 1.0 CB A:MET349 4.1 28.6 1.0 NH1 B:ARG158 4.1 50.4 1.0 CD B:ARG158 4.2 47.0 1.0 CA A:MET349 4.3 28.5 1.0 CA A:ALA343 4.3 22.9 1.0 CA A:GLU348 4.4 29.1 1.0 C A:GLU348 4.5 27.1 1.0 C A:MET349 4.5 27.5 1.0 CG A:GLU348 4.6 34.2 1.0 CE A:MET349 4.8 27.3 1.0 CG B:ARG158 4.8 45.5 1.0 CZ B:ARG158 4.9 49.2 1.0 CG A:LEU418 4.9 25.9 1.0 NE B:ARG158 5.0 49.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of IDNL1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of IDNL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl602 b:30.2 occ:1.00 N B:ALA343 2.9 27.7 1.0 CA B:HIS342 3.4 28.9 1.0 NH1 B:ARG412 3.4 38.1 1.0 N B:MET349 3.5 28.6 1.0 CB B:HIS342 3.5 29.6 1.0 C B:HIS342 3.6 29.4 1.0 CD1 B:LEU418 3.7 38.8 1.0 NH2 B:ARG412 3.8 37.4 1.0 CB B:ALA343 3.8 27.4 1.0 CB B:MET349 3.9 27.1 1.0 CA B:ALA343 4.0 27.7 1.0 O B:MET349 4.0 24.5 1.0 CZ B:ARG412 4.1 37.1 1.0 CA B:MET349 4.2 27.8 1.0 CE B:MET349 4.3 24.6 1.0 CA B:GLU348 4.4 25.1 1.0 C B:GLU348 4.5 27.8 1.0 C B:MET349 4.5 27.2 1.0 CD A:ARG158 4.6 41.3 1.0 NH1 A:ARG158 4.6 44.6 1.0 CG B:MET349 4.7 24.3 1.0 N B:HIS342 4.7 30.5 1.0 CG B:LEU418 4.8 37.1 1.0 O B:GLY341 4.9 30.6 1.0 O B:HIS342 4.9 28.1 1.0 CG B:HIS342 4.9 33.5 1.0 CG B:GLU348 4.9 24.3 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of IDNL1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of IDNL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl602 b:24.2 occ:1.00 NH1 C:ARG412 3.3 36.9 1.0 N C:ALA343 3.3 25.3 1.0 N C:MET349 3.3 25.2 1.0 NH2 C:ARG412 3.4 33.4 1.0 O C:MET349 3.6 20.8 1.0 CD1 C:LEU418 3.8 30.3 1.0 CA C:HIS342 3.8 33.3 1.0 CB C:MET349 3.8 25.9 1.0 CZ C:ARG412 3.8 36.1 1.0 CB C:HIS342 3.8 37.8 1.0 CA C:MET349 4.0 25.9 1.0 CB C:ALA343 4.0 21.1 1.0 C C:HIS342 4.1 31.4 1.0 C C:MET349 4.2 23.6 1.0 CA C:ALA343 4.3 22.4 1.0 C C:GLU348 4.3 23.6 1.0 CA C:GLU348 4.4 23.1 1.0 CD D:ARG158 4.4 49.2 1.0 NH1 D:ARG158 4.5 59.3 1.0 CE C:MET349 4.6 26.8 1.0 CG C:GLU348 4.7 30.0 1.0 CG C:MET349 4.7 27.0 1.0 CG C:LEU418 4.9 27.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of IDNL1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of IDNL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl602 b:33.3 occ:1.00 N D:ALA343 2.8 28.2 1.0 NH2 D:ARG412 3.1 42.3 1.0 CA D:HIS342 3.4 30.6 1.0 CB D:HIS342 3.5 31.0 1.0 N D:MET349 3.5 30.4 1.0 C D:HIS342 3.6 30.8 1.0 CB D:ALA343 3.7 28.3 1.0 CD1 D:LEU418 3.8 33.7 1.0 CA D:ALA343 3.8 28.1 1.0 CB D:MET349 4.0 28.0 1.0 O D:MET349 4.1 26.7 1.0 CA D:MET349 4.2 28.8 1.0 CZ D:ARG412 4.3 38.3 1.0 CE D:MET349 4.4 25.7 1.0 CA D:GLU348 4.4 27.1 1.0 C D:GLU348 4.5 30.8 1.0 NE C:ARG158 4.6 47.8 1.0 C D:MET349 4.6 27.5 1.0 N D:HIS342 4.7 29.4 1.0 CG D:MET349 4.8 24.6 1.0 O D:HIS342 4.8 30.4 1.0 NE D:ARG412 4.8 40.6 1.0 CG D:HIS342 4.8 34.4 1.0 O D:GLY341 4.9 30.8 1.0 CG D:GLU348 4.9 26.0 1.0 CG D:LEU418 4.9 30.7 1.0

J.Cieslak, A.Miyanaga, R.Takaku, M.Takaishi, K.Amagai, F.Kudo, T.Eguchi. Biochemical Characterization and Structural Insight Into Aliphatic Beta-Amino Acid Adenylation Enzymes IDNL1 and CMIS6 Proteins V. 85 1238 2017.
ISSN: ESSN 1097-0134
PubMed: 28316096
DOI: 10.1002/PROT.25284