Fluorine in PDB 6a9k: Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog

The structure of Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog, PDB code: 6a9k was solved by Y.Tsuchiya, I.Fujii, T.Tada, A.Yamaguchi, T.Tsumuraya, A.Kumon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.986, 36.553, 111.986, 90.00, 91.50, 90.00
R / Rfree (%)	19.4 / 24.9

The structure of Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog (pdb code 6a9k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog, PDB code: 6a9k:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


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 Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F301 b:23.9 occ:1.00 F1 H:9T0301 0.0 23.9 1.0 C1 H:9T0301 1.3 22.6 1.0 F3 H:9T0301 2.1 21.7 1.0 F2 H:9T0301 2.2 24.2 1.0 C2 H:9T0301 2.3 21.3 1.0 O1 H:9T0301 3.0 20.5 1.0 N3 H:9T0301 3.1 22.2 1.0 CG L:PRO96 3.3 23.3 1.0 CB L:PRO96 3.4 24.3 1.0 CZ L:PHE89 3.4 18.0 1.0 NE1 H:TRP47 3.5 19.5 1.0 CD1 H:TRP47 3.5 18.6 1.0 CZ H:PHE100a 3.7 18.7 1.0 CE2 H:TRP47 3.9 20.3 1.0 CG H:TRP47 3.9 18.8 1.0 OG1 L:THR91 4.1 26.7 1.0 CE2 L:PHE89 4.1 20.7 1.0 CD2 H:TRP47 4.2 18.9 1.0 OG1 H:THR50 4.2 20.4 1.0 CE1 H:PHE100a 4.3 20.4 1.0 C3 H:9T0301 4.4 21.4 1.0 CE1 L:PHE89 4.4 20.1 1.0 CB L:THR91 4.5 24.1 1.0 CE2 H:PHE100a 4.5 19.9 1.0 O7 H:9T0301 4.6 27.4 1.0 CD L:PRO96 4.7 23.9 1.0 CZ2 H:TRP47 4.7 21.7 1.0 CB H:TRP47 4.7 19.5 1.0 NH1 H:ARG95 4.8 20.4 1.0 CA L:PRO96 4.9 23.6 1.0 C6 H:9T0301 4.9 23.6 1.0 CD H:ARG95 5.0 23.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


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 Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F301 b:24.2 occ:1.00 F2 H:9T0301 0.0 24.2 1.0 C1 H:9T0301 1.3 22.6 1.0 F1 H:9T0301 2.2 23.9 1.0 F3 H:9T0301 2.2 21.7 1.0 C2 H:9T0301 2.4 21.3 1.0 N3 H:9T0301 2.6 22.2 1.0 OG1 L:THR91 3.0 26.7 1.0 CZ H:ARG95 3.4 21.5 1.0 CB L:THR91 3.4 24.1 1.0 NE H:ARG95 3.4 21.2 1.0 O1 H:9T0301 3.5 20.5 1.0 O7 H:9T0301 3.6 27.4 1.0 NH1 H:ARG95 3.6 20.4 1.0 CG2 L:THR91 3.7 22.2 1.0 NH2 H:ARG95 3.8 23.1 1.0 CD H:ARG95 3.8 23.5 1.0 N2 H:9T0301 3.9 25.5 1.0 C3 H:9T0301 4.0 21.4 1.0 CE2 L:PHE89 4.0 20.7 1.0 CZ L:PHE89 4.1 18.0 1.0 O8 H:9T0301 4.1 24.8 1.0 CZ H:PHE100a 4.4 18.7 1.0 CG L:PRO96 4.5 23.3 1.0 CG H:ARG95 4.6 22.0 1.0 C4 H:9T0301 4.7 20.2 1.0 CB L:PRO96 4.7 24.3 1.0 CE1 H:PHE100a 4.8 20.4 1.0 C18 H:9T0301 4.8 23.1 1.0 CA L:THR91 4.9 22.8 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


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 Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ H:F301 b:21.7 occ:1.00 F3 H:9T0301 0.0 21.7 1.0 C1 H:9T0301 1.3 22.6 1.0 F1 H:9T0301 2.1 23.9 1.0 F2 H:9T0301 2.2 24.2 1.0 C2 H:9T0301 2.4 21.3 1.0 O1 H:9T0301 2.8 20.5 1.0 O7 H:9T0301 3.0 27.4 1.0 OG1 H:THR50 3.2 20.4 1.0 CD H:ARG95 3.2 23.5 1.0 OG H:SER35 3.5 15.7 1.0 CE1 H:PHE100a 3.5 20.4 1.0 N3 H:9T0301 3.5 22.2 1.0 CZ H:PHE100a 3.6 18.7 1.0 NE H:ARG95 3.7 21.2 1.0 CG H:ARG95 3.8 22.0 1.0 NE1 H:TRP47 3.9 19.5 1.0 N2 H:9T0301 4.0 25.5 1.0 CZ H:ARG95 4.2 21.5 1.0 NH1 H:ARG95 4.2 20.4 1.0 CD1 H:TRP47 4.2 18.6 1.0 CB H:THR50 4.4 20.7 1.0 CB H:SER35 4.5 18.9 1.0 O8 H:9T0301 4.5 24.8 1.0 CG2 H:THR50 4.5 20.7 1.0 CD1 H:PHE100a 4.6 19.5 1.0 CB H:ARG95 4.7 24.5 1.0 CE2 H:PHE100a 4.7 19.9 1.0 C3 H:9T0301 4.7 21.4 1.0 CE2 H:TRP47 4.8 20.3 1.0 CZ L:PHE89 5.0 18.0 1.0 OG1 L:THR91 5.0 26.7 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


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 Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:33.9 occ:1.00 F1 B:9T0301 0.0 33.9 1.0 C1 B:9T0301 1.2 30.7 1.0 F3 B:9T0301 1.9 29.4 1.0 F2 B:9T0301 2.1 27.4 1.0 C2 B:9T0301 2.3 33.7 1.0 N3 B:9T0301 3.1 32.4 1.0 O1 B:9T0301 3.1 35.0 1.0 CD1 B:TRP47 3.4 25.8 1.0 NE1 B:TRP47 3.4 26.9 1.0 CG A:PRO96 3.4 30.5 1.0 CZ B:PHE100a 3.6 23.6 1.0 CZ A:PHE89 3.6 20.9 1.0 CB A:PRO96 3.7 29.4 1.0 CG B:TRP47 3.8 25.2 1.0 CE2 B:TRP47 3.8 26.5 1.0 CD2 B:TRP47 4.1 26.5 1.0 OG1 A:THR91 4.1 29.6 1.0 OG1 B:THR50 4.2 27.5 1.0 CE1 B:PHE100a 4.2 21.4 1.0 C3 B:9T0301 4.3 37.0 1.0 CE2 A:PHE89 4.5 23.7 1.0 CE1 A:PHE89 4.5 23.1 1.0 CE2 B:PHE100a 4.6 24.6 1.0 CD A:PRO96 4.6 28.9 1.0 CB A:THR91 4.6 26.7 1.0 CB B:TRP47 4.6 25.1 1.0 CZ2 B:TRP47 4.6 27.7 1.0 O7 B:9T0301 4.7 41.4 1.0 NH1 B:ARG95 4.8 24.4 1.0 C6 B:9T0301 4.9 36.9 1.0 CZ B:ARG95 4.9 24.0 1.0 NE B:ARG95 5.0 25.0 1.0 CD B:ARG95 5.0 23.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:27.4 occ:1.00 F2 B:9T0301 0.0 27.4 1.0 C1 B:9T0301 1.4 30.7 1.0 F1 B:9T0301 2.1 33.9 1.0 F3 B:9T0301 2.2 29.4 1.0 C2 B:9T0301 2.4 33.7 1.0 N3 B:9T0301 2.6 32.4 1.0 OG1 A:THR91 3.1 29.6 1.0 CZ B:ARG95 3.3 24.0 1.0 NE B:ARG95 3.4 25.0 1.0 CB A:THR91 3.4 26.7 1.0 O1 B:9T0301 3.5 35.0 1.0 NH2 B:ARG95 3.6 25.5 1.0 NH1 B:ARG95 3.7 24.4 1.0 O7 B:9T0301 3.7 41.4 1.0 CG2 A:THR91 3.7 26.2 1.0 CZ A:PHE89 3.9 20.9 1.0 C3 B:9T0301 4.0 37.0 1.0 CD B:ARG95 4.0 23.5 1.0 CE2 A:PHE89 4.1 23.7 1.0 N2 B:9T0301 4.1 40.8 1.0 O8 B:9T0301 4.1 41.7 1.0 CG A:PRO96 4.3 30.5 1.0 CZ B:PHE100a 4.3 23.6 1.0 CE1 B:PHE100a 4.7 21.4 1.0 C4 B:9T0301 4.7 33.4 1.0 CB A:PRO96 4.7 29.4 1.0 CG B:ARG95 4.8 25.8 1.0 C18 B:9T0301 4.9 41.4 1.0 CA A:THR91 4.9 27.5 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:29.4 occ:1.00 F3 B:9T0301 0.0 29.4 1.0 C1 B:9T0301 1.2 30.7 1.0 F1 B:9T0301 1.9 33.9 1.0 F2 B:9T0301 2.2 27.4 1.0 C2 B:9T0301 2.2 33.7 1.0 O1 B:9T0301 2.5 35.0 1.0 OG1 B:THR50 3.1 27.5 1.0 O7 B:9T0301 3.2 41.4 1.0 N3 B:9T0301 3.4 32.4 1.0 CD B:ARG95 3.5 23.5 1.0 CE1 B:PHE100a 3.6 21.4 1.0 OG B:SER35 3.6 22.8 1.0 CZ B:PHE100a 3.6 23.6 1.0 NE B:ARG95 3.7 25.0 1.0 NE1 B:TRP47 3.8 26.9 1.0 CG B:ARG95 3.9 25.8 1.0 CD1 B:TRP47 4.1 25.8 1.0 CZ B:ARG95 4.1 24.0 1.0 N2 B:9T0301 4.2 40.8 1.0 CB B:THR50 4.3 26.1 1.0 NH1 B:ARG95 4.4 24.4 1.0 CG2 B:THR50 4.5 28.0 1.0 C3 B:9T0301 4.6 37.0 1.0 CE2 B:TRP47 4.6 26.5 1.0 O8 B:9T0301 4.6 41.7 1.0 CB B:SER35 4.6 23.7 1.0 CD1 B:PHE100a 4.7 22.1 1.0 CE2 B:PHE100a 4.8 24.6 1.0 CB B:ARG95 4.9 24.0 1.0 NH2 B:ARG95 5.0 25.5 1.0 CZ A:PHE89 5.0 20.9 1.0 CG B:TRP47 5.0 25.2 1.0 OG1 A:THR91 5.0 29.6 1.0

Y.Tsuchiya, I.Fujii, T.Tada, A.Yamaguchi, T.Tsumuraya, A.Kumon. Crystal Structure of the Complex of the Hydrolytic Antibody Fab 9C10 with A Transition-State Analog To Be Published.