Fluorine 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:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Gefitinib Intermediate 1 Bound Ramr Determined with Xtalab Synergy, PDB code: 6ko9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine 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 Fluorine with other atoms in the F 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:F201 b:73.6 occ:1.00 F1 A:XZ1201 0.0 73.6 1.0 C13 A:XZ1201 1.3 62.7 1.0 C12 A:XZ1201 2.3 65.7 1.0 C14 A:XZ1201 2.4 77.0 1.0 CL1 A:XZ1201 2.8 76.3 1.0 CD2 A:LEU66 3.4 48.7 1.0 CD1 A:ILE106 3.5 63.8 1.0 CG2 A:ILE106 3.5 51.2 1.0 OH A:TYR92 3.5 41.3 1.0 C15 A:XZ1201 3.6 80.8 1.0 C11 A:XZ1201 3.6 76.1 1.0 CE1 A:TYR92 3.8 51.4 1.0 CZ A:TYR92 3.9 53.0 1.0 CD2 A:LEU156 3.9 44.0 1.0 O A:HOH400 3.9 83.0 1.0 CG1 A:ILE106 4.0 59.7 1.0 C10 A:XZ1201 4.1 76.6 1.0 CB A:ILE106 4.4 47.6 1.0 CD1 A:TYR92 4.7 46.6 1.0 CG A:LEU66 4.9 46.2 1.0 CE2 A:TYR92 4.9 44.0 1.0 CD2 A:HIS103 5.0 52.3 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F201 b:52.1 occ:1.00 F1 B:XZ1201 0.0 52.1 1.0 C13 B:XZ1201 1.3 58.2 1.0 C12 B:XZ1201 2.3 64.5 1.0 C14 B:XZ1201 2.4 58.4 1.0 CL1 B:XZ1201 2.7 84.5 1.0 O B:HOH331 3.2 90.9 1.0 CD1 B:ILE106 3.3 56.9 1.0 CB B:ALA110 3.6 67.6 1.0 C15 B:XZ1201 3.6 57.5 1.0 C11 B:XZ1201 3.6 55.8 1.0 CE1 B:TYR59 3.9 42.1 1.0 CG1 B:ILE106 4.0 60.3 1.0 OH B:TYR59 4.0 50.7 1.0 C10 B:XZ1201 4.1 52.9 1.0 CD B:LYS63 4.3 45.5 1.0 CZ B:TYR59 4.4 46.5 1.0 CG2 B:ILE106 4.4 55.1 1.0 NZ B:LYS63 4.5 51.0 1.0 O B:ILE106 4.5 41.3 1.0 CD2 B:LEU156 4.5 51.3 1.0 CB B:ILE106 4.8 54.0 1.0 CD1 B:LEU156 4.8 43.6 1.0 CA B:ALA110 4.8 66.9 1.0 CD2 B:LEU66 4.9 56.5 1.0 O B:HOH303 4.9 50.2 1.0 C B:ILE106 5.0 53.3 1.0 CD1 B:TYR59 5.0 45.7 1.0 CE B:LYS63 5.0 53.4 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F201 b:73.7 occ:1.00 F1 C:XZ1201 0.0 73.7 1.0 C13 C:XZ1201 1.3 59.3 1.0 O C:HOH312 2.3 0.7 1.0 C14 C:XZ1201 2.3 70.8 1.0 C12 C:XZ1201 2.3 65.3 1.0 O C:HOH438 2.4 85.0 1.0 O C:HOH393 2.8 0.5 1.0 CL1 C:XZ1201 2.9 85.7 1.0 OH C:TYR59 3.4 42.0 1.0 C15 C:XZ1201 3.6 79.7 1.0 C11 C:XZ1201 3.6 59.9 1.0 CD1 C:ILE106 3.8 58.3 1.0 NZ C:LYS63 3.8 66.1 1.0 CD C:LYS63 3.9 52.3 1.0 CE1 C:TYR59 3.9 49.2 1.0 CB C:ALA110 3.9 52.6 1.0 C10 C:XZ1201 4.1 68.8 1.0 CZ C:TYR59 4.1 41.0 1.0 CG1 C:ILE106 4.1 47.5 1.0 CE C:LYS63 4.5 62.3 1.0 CD2 C:LEU156 4.6 39.4 1.0 O C:ILE106 4.6 35.7 1.0 CG2 C:ILE106 4.9 46.8 1.0 CD1 C:LEU156 5.0 44.9 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F201 b:71.6 occ:1.00 F1 D:XZ1201 0.0 71.6 1.0 C13 D:XZ1201 1.3 59.2 1.0 C12 D:XZ1201 2.3 71.4 1.0 C14 D:XZ1201 2.4 68.4 1.0 CL1 D:XZ1201 2.6 72.6 1.0 CD2 D:LEU66 3.2 41.5 1.0 CE1 D:TYR92 3.3 43.5 1.0 CG2 D:ILE106 3.4 46.6 1.0 CD1 D:ILE106 3.6 45.1 1.0 C15 D:XZ1201 3.6 74.0 1.0 C11 D:XZ1201 3.6 73.5 1.0 CZ D:TYR92 3.6 44.0 1.0 OH D:TYR92 3.7 44.6 1.0 CG1 D:ILE106 3.8 44.0 1.0 CD1 D:TYR92 4.0 39.5 1.0 CD2 D:LEU156 4.1 35.9 1.0 C10 D:XZ1201 4.1 67.2 1.0 CB D:ILE106 4.3 42.9 1.0 CE2 D:TYR92 4.6 39.3 1.0 CG D:LEU66 4.7 41.7 1.0 CD D:LYS63 4.8 56.9 1.0 CG D:TYR92 4.9 37.3 1.0 O D:HOH373 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