Chlorine in PDB 6ko9: Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy

The structure of Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy, PDB code: 6ko9 was solved by T.Matsumoto, R.Nakashima, A.Yamano, K.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.44 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.513, 54.792, 92.224, 74.64, 81.94, 89.98
R / Rfree (%)	22 / 29.9

The structure of Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy (pdb code 6ko9). 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 the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy, PDB code: 6ko9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy


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 the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:76.3 occ:1.00 CL1 A:XZ1201 0.0 76.3 1.0 C12 A:XZ1201 1.8 65.7 1.0 C13 A:XZ1201 2.6 62.7 1.0 C11 A:XZ1201 2.8 76.1 1.0 F1 A:XZ1201 2.8 73.6 1.0 O A:HOH400 3.2 83.0 1.0 OH A:TYR59 3.3 51.1 1.0 CB A:ALA110 3.5 55.8 1.0 C14 A:XZ1201 3.9 77.0 1.0 NZ A:LYS63 4.0 58.1 1.0 CE1 A:TYR59 4.0 44.7 1.0 C10 A:XZ1201 4.1 76.6 1.0 CZ A:TYR59 4.1 42.3 1.0 CD A:LYS63 4.3 49.1 1.0 O A:HOH343 4.3 50.1 1.0 CD2 A:LEU156 4.4 44.0 1.0 CG1 A:ILE106 4.4 59.7 1.0 CD1 A:LEU156 4.4 42.0 1.0 C15 A:XZ1201 4.5 80.8 1.0 CD1 A:ILE106 4.5 63.8 1.0 O A:ILE106 4.6 39.2 1.0 O A:HOH330 4.6 0.2 1.0 CA A:ALA110 4.7 53.0 1.0 CE A:LYS63 4.8 52.6 1.0 CG2 A:ILE106 4.8 51.2 1.0 CG A:LEU156 5.0 44.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy


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 the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:84.5 occ:1.00 CL1 B:XZ1201 0.0 84.5 1.0 C12 B:XZ1201 1.8 64.5 1.0 C13 B:XZ1201 2.6 58.2 1.0 F1 B:XZ1201 2.7 52.1 1.0 C11 B:XZ1201 2.8 55.8 1.0 CD2 B:LEU66 3.2 56.5 1.0 CE1 B:TYR92 3.3 47.8 1.0 CZ B:TYR92 3.7 47.5 1.0 CD2 B:LEU156 3.8 51.3 1.0 CD1 B:ILE106 3.8 56.9 1.0 OH B:TYR92 3.9 58.5 1.0 C14 B:XZ1201 3.9 58.4 1.0 CD1 B:TYR92 3.9 47.0 1.0 C10 B:XZ1201 4.0 52.9 1.0 CG2 B:ILE106 4.1 55.1 1.0 CE2 B:TYR92 4.5 42.0 1.0 C15 B:XZ1201 4.5 57.5 1.0 O B:HOH303 4.5 50.2 1.0 NZ B:LYS63 4.7 51.0 1.0 CG B:TYR92 4.7 45.3 1.0 CG B:LEU66 4.7 54.2 1.0 O B:HOH347 4.8 56.4 1.0 CG1 B:ILE106 4.9 60.3 1.0 CD2 B:TYR92 4.9 46.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy


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 the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:85.7 occ:1.00 CL1 C:XZ1201 0.0 85.7 1.0 C12 C:XZ1201 1.8 65.3 1.0 O C:HOH438 1.9 85.0 1.0 C13 C:XZ1201 2.7 59.3 1.0 C11 C:XZ1201 2.7 59.9 1.0 O C:HOH355 2.8 63.6 1.0 F1 C:XZ1201 2.9 73.7 1.0 CD2 C:LEU66 3.3 54.4 1.0 CE1 C:TYR92 3.4 60.5 1.0 CZ C:TYR92 3.7 51.7 1.0 OH C:TYR92 3.7 38.0 1.0 CD2 C:LEU156 3.8 39.4 1.0 O C:HOH312 3.8 0.7 1.0 CD1 C:ILE106 3.9 58.3 1.0 C14 C:XZ1201 4.0 70.8 1.0 C10 C:XZ1201 4.0 68.8 1.0 CD1 C:TYR92 4.1 53.3 1.0 CG2 C:ILE106 4.4 46.8 1.0 O C:HOH351 4.4 93.7 1.0 C15 C:XZ1201 4.5 79.7 1.0 CE2 C:TYR92 4.6 47.3 1.0 O C:HOH393 4.7 0.5 1.0 CG C:LEU66 4.7 53.7 1.0 CG1 C:ILE106 4.8 47.5 1.0 CG C:TYR92 5.0 44.5 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy


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 the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:72.6 occ:1.00 CL1 D:XZ1201 0.0 72.6 1.0 C12 D:XZ1201 1.8 71.4 1.0 C13 D:XZ1201 2.5 59.2 1.0 F1 D:XZ1201 2.6 71.6 1.0 C11 D:XZ1201 2.8 73.5 1.0 CB D:ALA110 3.4 44.9 1.0 CG1 D:ILE106 3.7 44.0 1.0 C14 D:XZ1201 3.8 68.4 1.0 O D:HOH373 3.9 0.1 1.0 CE1 D:TYR59 3.9 48.5 1.0 O D:ILE106 4.1 44.2 1.0 C10 D:XZ1201 4.1 67.2 1.0 CD1 D:ILE106 4.1 45.1 1.0 OH D:TYR59 4.2 51.6 1.0 CD D:LYS63 4.2 56.9 1.0 CE D:LYS63 4.3 61.4 1.0 CD1 D:LEU156 4.3 39.1 1.0 CG2 D:ILE106 4.4 46.6 1.0 C15 D:XZ1201 4.4 74.0 1.0 CA D:ALA110 4.5 44.4 1.0 CD2 D:LEU156 4.5 35.9 1.0 CZ D:TYR59 4.6 49.9 1.0 CB D:ILE106 4.6 42.9 1.0 C D:ILE106 4.7 43.9 1.0 CD1 D:TYR59 5.0 41.0 1.0 O D:HOH381 5.0 0.1 1.0

T.Matsumoto, R.Nakashima, A.Yamano, K.Nishino. Development of A Structure Determination Method Using A Multidrug-Resistance Regulator Protein As A Framework. Biochem.Biophys.Res.Commun. V. 518 402 2019.
ISSN: ESSN 1090-2104
PubMed: 31431261
DOI: 10.1016/J.BBRC.2019.08.070