Fluorine in PDB 7kcb: Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol

The structure of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol (pdb code 7kcb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol, PDB code: 7kcb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:39.2 occ:1.00 F1 A:ETF404 0.0 39.2 1.0 C1 A:ETF404 1.3 39.2 1.0 F2 A:ETF404 2.1 39.2 1.0 F3 A:ETF404 2.1 39.2 1.0 C2 A:ETF404 2.3 39.2 1.0 CE1 A:TYR294 2.9 32.3 1.0 CD1 A:TYR294 3.5 32.3 1.0 O A:ETF404 3.5 39.2 1.0 CE A:MET270 3.6 37.6 1.0 C7N A:NAD403 3.6 37.1 1.0 C3N A:NAD403 3.7 37.1 1.0 O7N A:NAD403 3.7 37.1 1.0 NE1 A:TRP92 3.8 38.5 1.0 CG1 A:VAL295 3.9 33.2 1.0 C4N A:NAD403 4.0 37.1 1.0 CZ A:TYR294 4.0 32.3 1.0 CD1 A:TRP92 4.0 38.5 1.0 CE2 A:TRP92 4.1 38.5 1.0 N7N A:NAD403 4.1 37.1 1.0 C2N A:NAD403 4.2 37.1 1.0 OH A:TYR294 4.2 32.3 1.0 OG1 A:THR45 4.3 42.0 1.0 CG A:TRP92 4.4 38.5 1.0 CD2 A:TRP92 4.5 38.5 1.0 CH2 A:TRP54 4.5 42.6 1.0 CZ2 A:TRP92 4.7 38.5 1.0 C5N A:NAD403 4.7 37.1 1.0 CG A:TYR294 4.8 32.3 1.0 N1N A:NAD403 4.9 37.1 1.0 CZ3 A:TRP54 4.9 42.6 1.0 N A:VAL295 5.0 33.2 1.0 SD A:MET270 5.0 37.6 1.0

Fluorine binding site 2 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:39.2 occ:1.00 F2 A:ETF404 0.0 39.2 1.0 C1 A:ETF404 1.3 39.2 1.0 F3 A:ETF404 2.1 39.2 1.0 F1 A:ETF404 2.1 39.2 1.0 C2 A:ETF404 2.3 39.2 1.0 O A:ETF404 2.9 39.2 1.0 OG1 A:THR45 3.1 42.0 1.0 CH2 A:TRP54 3.1 42.6 1.0 CG2 A:THR45 3.2 42.0 1.0 CE2 A:TRP92 3.2 38.5 1.0 CZ2 A:TRP92 3.4 38.5 1.0 CZ3 A:TRP54 3.4 42.6 1.0 CD2 A:TRP92 3.5 38.5 1.0 CB A:THR45 3.7 42.0 1.0 NE1 A:TRP92 3.7 38.5 1.0 CH2 A:TRP92 3.7 38.5 1.0 CE3 A:TRP92 3.9 38.5 1.0 CZ3 A:TRP92 4.0 38.5 1.0 CG A:TRP92 4.1 38.5 1.0 CE A:MET270 4.1 37.6 1.0 CD1 A:TRP92 4.2 38.5 1.0 CZ2 A:TRP54 4.3 42.6 1.0 CE1 A:TYR294 4.4 32.3 1.0 CE3 A:TRP54 4.7 42.6 1.0 OH A:TYR294 4.7 32.3 1.0 CA A:THR45 5.0 42.0 1.0 C3N A:NAD403 5.0 37.1 1.0

Fluorine binding site 3 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:39.2 occ:1.00 F3 A:ETF404 0.0 39.2 1.0 C1 A:ETF404 1.3 39.2 1.0 F2 A:ETF404 2.1 39.2 1.0 F1 A:ETF404 2.1 39.2 1.0 C2 A:ETF404 2.3 39.2 1.0 OG1 A:THR45 2.5 42.0 1.0 O A:ETF404 2.7 39.2 1.0 C2N A:NAD403 3.1 37.1 1.0 C3N A:NAD403 3.1 37.1 1.0 CE A:MET270 3.3 37.6 1.0 N1N A:NAD403 3.3 37.1 1.0 C4N A:NAD403 3.3 37.1 1.0 C6N A:NAD403 3.5 37.1 1.0 C5N A:NAD403 3.5 37.1 1.0 CH2 A:TRP54 3.5 42.6 1.0 O2D A:NAD403 3.7 37.1 1.0 CB A:THR45 3.7 42.0 1.0 C7N A:NAD403 3.9 37.1 1.0 CG2 A:THR45 4.0 42.0 1.0 C1D A:NAD403 4.1 37.1 1.0 CZ2 A:TRP54 4.1 42.6 1.0 C2D A:NAD403 4.3 37.1 1.0 N7N A:NAD403 4.4 37.1 1.0 CZ3 A:TRP54 4.4 42.6 1.0 O7N A:NAD403 4.4 37.1 1.0 ZN A:ZN401 4.5 61.1 1.0 CA A:THR45 4.8 42.0 1.0 CE1 A:TYR294 5.0 32.3 1.0

Fluorine binding site 4 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:39.2 occ:1.00 F1 B:ETF404 0.0 39.2 1.0 C1 B:ETF404 1.3 39.2 1.0 F2 B:ETF404 2.1 39.2 1.0 F3 B:ETF404 2.1 39.2 1.0 C2 B:ETF404 2.3 39.2 1.0 CE1 B:TYR294 2.9 32.5 1.0 CD1 B:TYR294 3.5 32.5 1.0 O B:ETF404 3.5 39.2 1.0 CE B:MET270 3.6 37.6 1.0 C7N B:NAD403 3.6 37.2 1.0 C3N B:NAD403 3.7 37.2 1.0 O7N B:NAD403 3.7 37.2 1.0 NE1 B:TRP92 3.8 38.5 1.0 CG1 B:VAL295 3.9 33.2 1.0 C4N B:NAD403 4.0 37.2 1.0 CZ B:TYR294 4.0 32.5 1.0 CD1 B:TRP92 4.0 38.5 1.0 CE2 B:TRP92 4.1 38.5 1.0 N7N B:NAD403 4.1 37.2 1.0 C2N B:NAD403 4.2 37.2 1.0 OH B:TYR294 4.2 32.5 1.0 OG1 B:THR45 4.3 42.1 1.0 CG B:TRP92 4.4 38.5 1.0 CD2 B:TRP92 4.5 38.5 1.0 CH2 B:TRP54 4.5 42.9 1.0 CZ2 B:TRP92 4.7 38.5 1.0 C5N B:NAD403 4.7 37.2 1.0 CG B:TYR294 4.8 32.5 1.0 N1N B:NAD403 4.9 37.2 1.0 CZ3 B:TRP54 4.9 42.9 1.0 N B:VAL295 5.0 33.2 1.0 SD B:MET270 5.0 37.6 1.0

Fluorine binding site 5 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:39.2 occ:1.00 F2 B:ETF404 0.0 39.2 1.0 C1 B:ETF404 1.3 39.2 1.0 F3 B:ETF404 2.1 39.2 1.0 F1 B:ETF404 2.1 39.2 1.0 C2 B:ETF404 2.3 39.2 1.0 O B:ETF404 2.9 39.2 1.0 OG1 B:THR45 3.1 42.1 1.0 CH2 B:TRP54 3.1 42.9 1.0 CG2 B:THR45 3.2 42.1 1.0 CE2 B:TRP92 3.2 38.5 1.0 CZ2 B:TRP92 3.4 38.5 1.0 CZ3 B:TRP54 3.4 42.9 1.0 CD2 B:TRP92 3.5 38.5 1.0 CB B:THR45 3.7 42.1 1.0 NE1 B:TRP92 3.7 38.5 1.0 CH2 B:TRP92 3.7 38.5 1.0 CE3 B:TRP92 3.9 38.5 1.0 CZ3 B:TRP92 4.0 38.5 1.0 CG B:TRP92 4.1 38.5 1.0 CE B:MET270 4.1 37.6 1.0 CD1 B:TRP92 4.2 38.5 1.0 CZ2 B:TRP54 4.3 42.9 1.0 CE1 B:TYR294 4.4 32.5 1.0 CE3 B:TRP54 4.7 42.9 1.0 OH B:TYR294 4.7 32.5 1.0 CA B:THR45 5.0 42.1 1.0 C3N B:NAD403 5.0 37.2 1.0

Fluorine binding site 6 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:39.2 occ:1.00 F3 B:ETF404 0.0 39.2 1.0 C1 B:ETF404 1.3 39.2 1.0 F2 B:ETF404 2.1 39.2 1.0 F1 B:ETF404 2.1 39.2 1.0 C2 B:ETF404 2.3 39.2 1.0 OG1 B:THR45 2.5 42.1 1.0 O B:ETF404 2.7 39.2 1.0 C2N B:NAD403 3.1 37.2 1.0 C3N B:NAD403 3.1 37.2 1.0 CE B:MET270 3.3 37.6 1.0 N1N B:NAD403 3.3 37.2 1.0 C4N B:NAD403 3.3 37.2 1.0 C6N B:NAD403 3.5 37.2 1.0 C5N B:NAD403 3.5 37.2 1.0 CH2 B:TRP54 3.5 42.9 1.0 O2D B:NAD403 3.7 37.2 1.0 CB B:THR45 3.7 42.1 1.0 C7N B:NAD403 3.9 37.2 1.0 CG2 B:THR45 4.0 42.1 1.0 C1D B:NAD403 4.1 37.2 1.0 CZ2 B:TRP54 4.1 42.9 1.0 C2D B:NAD403 4.3 37.2 1.0 N7N B:NAD403 4.4 37.2 1.0 CZ3 B:TRP54 4.4 42.9 1.0 O7N B:NAD403 4.4 37.2 1.0 ZN B:ZN401 4.5 61.2 1.0 CA B:THR45 4.8 42.1 1.0 CE1 B:TYR294 5.0 32.5 1.0

Fluorine binding site 7 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ C:F404 b:39.4 occ:1.00 F1 C:ETF404 0.0 39.4 1.0 C1 C:ETF404 1.3 39.4 1.0 F2 C:ETF404 2.1 39.4 1.0 F3 C:ETF404 2.1 39.4 1.0 C2 C:ETF404 2.3 39.4 1.0 CE1 C:TYR294 2.9 32.4 1.0 CD1 C:TYR294 3.5 32.4 1.0 O C:ETF404 3.5 39.4 1.0 CE C:MET270 3.6 37.7 1.0 C7N C:NAD403 3.6 37.4 1.0 C3N C:NAD403 3.7 37.4 1.0 O7N C:NAD403 3.7 37.4 1.0 NE1 C:TRP92 3.8 38.6 1.0 CG1 C:VAL295 3.9 33.3 1.0 C4N C:NAD403 4.0 37.4 1.0 CZ C:TYR294 4.0 32.4 1.0 CD1 C:TRP92 4.0 38.6 1.0 CE2 C:TRP92 4.1 38.6 1.0 N7N C:NAD403 4.1 37.4 1.0 C2N C:NAD403 4.2 37.4 1.0 OH C:TYR294 4.2 32.4 1.0 OG1 C:THR45 4.3 42.2 1.0 CG C:TRP92 4.4 38.6 1.0 CD2 C:TRP92 4.5 38.6 1.0 CH2 C:TRP54 4.5 43.0 1.0 CZ2 C:TRP92 4.7 38.6 1.0 C5N C:NAD403 4.7 37.4 1.0 CG C:TYR294 4.8 32.4 1.0 N1N C:NAD403 4.9 37.4 1.0 CZ3 C:TRP54 4.9 43.0 1.0 N C:VAL295 5.0 33.3 1.0 SD C:MET270 5.0 37.7 1.0

Fluorine binding site 8 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ C:F404 b:39.4 occ:1.00 F2 C:ETF404 0.0 39.4 1.0 C1 C:ETF404 1.3 39.4 1.0 F3 C:ETF404 2.1 39.4 1.0 F1 C:ETF404 2.1 39.4 1.0 C2 C:ETF404 2.3 39.4 1.0 O C:ETF404 2.9 39.4 1.0 OG1 C:THR45 3.1 42.2 1.0 CH2 C:TRP54 3.1 43.0 1.0 CG2 C:THR45 3.2 42.2 1.0 CE2 C:TRP92 3.2 38.6 1.0 CZ2 C:TRP92 3.4 38.6 1.0 CZ3 C:TRP54 3.4 43.0 1.0 CD2 C:TRP92 3.5 38.6 1.0 CB C:THR45 3.7 42.2 1.0 NE1 C:TRP92 3.7 38.6 1.0 CH2 C:TRP92 3.7 38.6 1.0 CE3 C:TRP92 3.9 38.6 1.0 CZ3 C:TRP92 4.0 38.6 1.0 CG C:TRP92 4.1 38.6 1.0 CE C:MET270 4.1 37.7 1.0 CD1 C:TRP92 4.2 38.6 1.0 CZ2 C:TRP54 4.3 43.0 1.0 CE1 C:TYR294 4.4 32.4 1.0 CE3 C:TRP54 4.7 43.0 1.0 OH C:TYR294 4.7 32.4 1.0 CA C:THR45 5.0 42.2 1.0 C3N C:NAD403 5.0 37.4 1.0

Fluorine binding site 9 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ C:F404 b:39.4 occ:1.00 F3 C:ETF404 0.0 39.4 1.0 C1 C:ETF404 1.3 39.4 1.0 F2 C:ETF404 2.1 39.4 1.0 F1 C:ETF404 2.1 39.4 1.0 C2 C:ETF404 2.3 39.4 1.0 OG1 C:THR45 2.5 42.2 1.0 O C:ETF404 2.7 39.4 1.0 C2N C:NAD403 3.1 37.4 1.0 C3N C:NAD403 3.1 37.4 1.0 CE C:MET270 3.3 37.7 1.0 N1N C:NAD403 3.3 37.4 1.0 C4N C:NAD403 3.3 37.4 1.0 C6N C:NAD403 3.5 37.4 1.0 C5N C:NAD403 3.5 37.4 1.0 CH2 C:TRP54 3.5 43.0 1.0 O2D C:NAD403 3.7 37.4 1.0 CB C:THR45 3.7 42.2 1.0 C7N C:NAD403 3.9 37.4 1.0 CG2 C:THR45 4.0 42.2 1.0 C1D C:NAD403 4.1 37.4 1.0 CZ2 C:TRP54 4.1 43.0 1.0 C2D C:NAD403 4.3 37.4 1.0 N7N C:NAD403 4.4 37.4 1.0 CZ3 C:TRP54 4.4 43.0 1.0 O7N C:NAD403 4.4 37.4 1.0 ZN C:ZN401 4.5 61.6 1.0 CA C:THR45 4.8 42.2 1.0 CE1 C:TYR294 5.0 32.4 1.0

Fluorine binding site 10 out of 12 in the Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Symmetry in Yeast Alcohol Dehydrogenase 1 -Closed Form with Nad+ and Trifluoroethanol within 5.0Å range: probe atom residue distance (Å) B Occ D:F404 b:39.0 occ:1.00 F1 D:ETF404 0.0 39.0 1.0 C1 D:ETF404 1.3 39.0 1.0 F2 D:ETF404 2.1 39.0 1.0 F3 D:ETF404 2.1 39.0 1.0 C2 D:ETF404 2.3 39.0 1.0 CE1 D:TYR294 2.9 32.2 1.0 CD1 D:TYR294 3.5 32.2 1.0 O D:ETF404 3.5 39.0 1.0 CE D:MET270 3.6 37.3 1.0 C7N D:NAD403 3.6 36.8 1.0 C3N D:NAD403 3.7 36.8 1.0 O7N D:NAD403 3.7 36.8 1.0 NE1 D:TRP92 3.8 38.5 1.0 CG1 D:VAL295 3.9 32.9 1.0 C4N D:NAD403 4.0 36.8 1.0 CZ D:TYR294 4.0 32.2 1.0 CD1 D:TRP92 4.0 38.5 1.0 CE2 D:TRP92 4.1 38.5 1.0 N7N D:NAD403 4.1 36.8 1.0 C2N D:NAD403 4.2 36.8 1.0 OH D:TYR294 4.2 32.2 1.0 OG1 D:THR45 4.3 41.8 1.0 CG D:TRP92 4.4 38.5 1.0 CD2 D:TRP92 4.5 38.5 1.0 CH2 D:TRP54 4.5 42.6 1.0 CZ2 D:TRP92 4.7 38.5 1.0 C5N D:NAD403 4.7 36.8 1.0 CG D:TYR294 4.8 32.2 1.0 N1N D:NAD403 4.9 36.8 1.0 CZ3 D:TRP54 4.9 42.6 1.0 N D:VAL295 5.0 32.9 1.0 SD D:MET270 5.0 37.3 1.0

S.R.Guntupalli, Z.Li, L.Chang, B.V.Plapp, R.Subramanian. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry V. 60 663 2021.
ISSN: ISSN 0006-2960
PubMed: 33620215
DOI: 10.1021/ACS.BIOCHEM.0C00921