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Fluorine in PDB 5env: Yeast Alcohol Dehydrogenase with Bound Coenzyme

Enzymatic activity of Yeast Alcohol Dehydrogenase with Bound Coenzyme

All present enzymatic activity of Yeast Alcohol Dehydrogenase with Bound Coenzyme:
1.1.1.1;

Protein crystallography data

The structure of Yeast Alcohol Dehydrogenase with Bound Coenzyme, PDB code: 5env was solved by B.V.Plapp, H.A.Charlier Jr., S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.00
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.256, 146.256, 65.980, 90.00, 90.00, 120.00
R / Rfree (%) 13.2 / 19.7

Other elements in 5env:

The structure of Yeast Alcohol Dehydrogenase with Bound Coenzyme also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Yeast Alcohol Dehydrogenase with Bound Coenzyme (pdb code 5env). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Yeast Alcohol Dehydrogenase with Bound Coenzyme, PDB code: 5env:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5env

Go back to Fluorine Binding Sites List in 5env
Fluorine binding site 1 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:52.1
occ:1.00
 F1 A:ETF404 0.0 52.1 1.0
C1 A:ETF404 1.3 54.1 1.0
F3 A:ETF404 2.1 55.0 1.0
F2 A:ETF404 2.2 56.4 1.0
C2 A:ETF404 2.3 52.9 1.0
CE1 A:TYR294 3.2 41.8 1.0
O7N A:NAD403 3.4 40.3 1.0
C7N A:NAD403 3.6 40.0 1.0
O A:ETF404 3.6 53.2 1.0
CD1 A:TYR294 3.6 40.4 1.0
CE A:MET270 3.6 44.2 1.0
C3N A:NAD403 3.6 40.5 1.0
NE1 A:TRP92 3.8 46.1 1.0
C4N A:NAD403 3.8 40.7 1.0
CG1 A:VAL295 3.9 37.1 1.0
CD1 A:TRP92 3.9 44.6 1.0
CZ A:TYR294 4.2 42.0 1.0
CE2 A:TRP92 4.2 47.3 1.0
C2N A:NAD403 4.3 41.1 1.0
N7N A:NAD403 4.4 39.7 1.0
CG A:TRP92 4.4 45.0 1.0
OH A:TYR294 4.5 44.0 1.0
OG1 A:THR45 4.5 48.1 1.0
CD2 A:TRP92 4.5 46.7 1.0
C5N A:NAD403 4.6 42.1 1.0
CZ2 A:TRP92 4.8 49.1 1.0
CG A:TYR294 4.9 39.5 1.0
CH2 A:TRP54 5.0 52.3 1.0
N1N A:NAD403 5.0 42.4 1.0

Fluorine binding site 2 out of 6 in 5env

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Fluorine binding site 2 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:56.4
occ:1.00
 F2 A:ETF404 0.0 56.4 1.0
C1 A:ETF404 1.3 54.1 1.0
F1 A:ETF404 2.2 52.1 1.0
F3 A:ETF404 2.2 55.0 1.0
C2 A:ETF404 2.3 52.9 1.0
O A:ETF404 3.0 53.2 1.0
CE2 A:TRP92 3.0 47.3 1.0
CZ2 A:TRP92 3.2 49.1 1.0
OG1 A:THR45 3.4 48.1 1.0
NE1 A:TRP92 3.4 46.1 1.0
CD2 A:TRP92 3.4 46.7 1.0
CG2 A:THR45 3.5 50.2 1.0
CH2 A:TRP54 3.6 52.3 1.0
CZ3 A:TRP54 3.6 53.1 1.0
CH2 A:TRP92 3.7 50.8 1.0
CE3 A:TRP92 3.9 48.2 1.0
CD1 A:TRP92 3.9 44.6 1.0
CE A:MET270 3.9 44.2 1.0
CG A:TRP92 4.0 45.0 1.0
CZ3 A:TRP92 4.0 50.4 1.0
CB A:THR45 4.0 50.0 1.0
CE1 A:TYR294 4.4 41.8 1.0
OH A:TYR294 4.7 44.0 1.0
CZ2 A:TRP54 4.9 53.5 1.0
CE3 A:TRP54 5.0 54.8 1.0

Fluorine binding site 3 out of 6 in 5env

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Fluorine binding site 3 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:55.0
occ:1.00
 F3 A:ETF404 0.0 55.0 1.0
C1 A:ETF404 1.3 54.1 1.0
F1 A:ETF404 2.1 52.1 1.0
F2 A:ETF404 2.2 56.4 1.0
C2 A:ETF404 2.3 52.9 1.0
OG1 A:THR45 2.6 48.1 1.0
O A:ETF404 2.7 53.2 1.0
CE A:MET270 3.1 44.2 1.0
C3N A:NAD403 3.2 40.5 1.0
C2N A:NAD403 3.2 41.1 1.0
C4N A:NAD403 3.3 40.7 1.0
N1N A:NAD403 3.4 42.4 1.0
C5N A:NAD403 3.5 42.1 1.0
C6N A:NAD403 3.6 43.2 1.0
CH2 A:TRP54 3.7 52.3 1.0
CB A:THR45 3.9 50.0 1.0
C7N A:NAD403 3.9 40.0 1.0
O2D A:NAD403 4.0 47.2 1.0
CG2 A:THR45 4.2 50.2 1.0
C1D A:NAD403 4.3 43.1 1.0
O7N A:NAD403 4.3 40.3 1.0
ZN A:ZN401 4.4 51.0 1.0
CZ3 A:TRP54 4.5 53.1 1.0
CZ2 A:TRP54 4.6 53.5 1.0
C2D A:NAD403 4.6 45.6 1.0
N7N A:NAD403 4.7 39.7 1.0
SD A:MET270 4.9 43.9 1.0
CA A:THR45 5.0 52.5 1.0

Fluorine binding site 4 out of 6 in 5env

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Fluorine binding site 4 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:59.6
occ:0.51
 F1 B:ETF404 0.0 59.6 0.5
C1 B:ETF404 1.3 61.1 0.5
F2 B:ETF404 2.1 61.1 0.5
F3 B:ETF404 2.2 64.3 0.5
C2 B:ETF404 2.3 59.2 0.5
C4N B:NAD403 3.0 72.6 1.0
O B:ETF404 3.3 61.4 0.5
O7N B:NAD403 3.4 67.8 1.0
CE1 B:TYR294 3.5 54.8 1.0
C3N B:NAD403 3.6 71.0 1.0
C5N B:NAD403 3.7 76.1 1.0
CG1 B:VAL295 3.7 47.0 1.0
C7N B:NAD403 3.9 67.8 1.0
CD1 B:TYR294 4.1 53.0 1.0
CZ B:TYR294 4.2 54.4 1.0
OH B:TYR294 4.3 56.5 1.0
CE B:MET270 4.4 55.5 1.0
CD1 B:TRP92 4.6 55.0 1.0
C2N B:NAD403 4.7 71.5 1.0
C6N B:NAD403 4.7 76.8 1.0
NE1 B:TRP92 4.7 57.5 1.0
CG B:TRP92 4.8 55.3 1.0
CE2 B:TRP92 5.0 59.7 1.0
OG1 B:THR45 5.0 80.5 1.0

Fluorine binding site 5 out of 6 in 5env

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Fluorine binding site 5 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:61.1
occ:0.51
 F2 B:ETF404 0.0 61.1 0.5
C1 B:ETF404 1.3 61.1 0.5
F1 B:ETF404 2.1 59.6 0.5
F3 B:ETF404 2.2 64.3 0.5
C2 B:ETF404 2.3 59.2 0.5
CE2 B:TRP92 3.1 59.7 1.0
CD2 B:TRP92 3.1 58.6 1.0
O B:ETF404 3.3 61.4 0.5
NE1 B:TRP92 3.3 57.5 1.0
CG B:TRP92 3.4 55.3 1.0
CD1 B:TRP92 3.5 55.0 1.0
CZ2 B:TRP92 3.7 63.1 1.0
CE3 B:TRP92 3.7 60.8 1.0
OH B:TYR294 3.8 56.5 1.0
CG2 B:THR45 3.9 81.2 1.0
CH2 B:TRP54 4.1 93.1 1.0
CH2 B:TRP92 4.1 65.4 1.0
CZ3 B:TRP92 4.2 64.3 1.0
CB B:TRP92 4.3 52.9 1.0
CE1 B:TYR294 4.3 54.8 1.0
CZ B:TYR294 4.4 54.4 1.0
CG1 B:VAL295 4.6 47.0 1.0
OG1 B:THR45 4.6 80.5 1.0
CB B:THR45 4.8 81.7 1.0
CZ2 B:TRP54 4.8 97.0 1.0
C4N B:NAD403 4.9 72.6 1.0
CZ3 B:TRP54 4.9 93.3 1.0

Fluorine binding site 6 out of 6 in 5env

Go back to Fluorine Binding Sites List in 5env
Fluorine binding site 6 out of 6 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:64.3
occ:0.51
 F3 B:ETF404 0.0 64.3 0.5
C1 B:ETF404 1.3 61.1 0.5
F1 B:ETF404 2.2 59.6 0.5
F2 B:ETF404 2.2 61.1 0.5
C2 B:ETF404 2.4 59.2 0.5
O B:ETF404 2.5 61.4 0.5
OG1 B:THR45 3.1 80.5 1.0
CG2 B:THR45 3.2 81.2 1.0
C5N B:NAD403 3.5 76.1 1.0
C4N B:NAD403 3.6 72.6 1.0
CB B:THR45 3.7 81.7 1.0
C6N B:NAD403 4.2 76.8 1.0
CH2 B:TRP54 4.3 93.1 1.0
CE B:MET270 4.3 55.5 1.0
C3N B:NAD403 4.3 71.0 1.0
CZ2 B:TRP54 4.4 97.0 1.0
N1N B:NAD403 4.8 74.2 1.0
C2N B:NAD403 4.9 71.5 1.0
CA B:THR45 5.0 86.4 1.0
CE1 B:TYR294 5.0 54.8 1.0

Reference:

B.V.Plapp, H.A.Charlier, S.Ramaswamy. Mechanistic Implications From Structures of Yeast Alcohol Dehydrogenase Complexed with Coenzyme and An Alcohol. Arch.Biochem.Biophys. V. 591 35 2015.
ISSN: ESSN 1096-0384
PubMed: 26743849
DOI: 10.1016/J.ABB.2015.12.009
Page generated: Sun Dec 13 12:21:44 2020

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