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Fluorine in PDB 4w6z: Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme

Enzymatic activity of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme

All present enzymatic activity of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme:
1.1.1.1;

Protein crystallography data

The structure of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme, PDB code: 4w6z was solved by B.V.Plapp, B.R.Savarimuthu, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.09 / 2.40
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.338, 144.338, 128.204, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.2

Other elements in 4w6z:

The structure of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme also contains other interesting chemical elements:

Iodine (I) 2 atoms
Zinc (Zn) 8 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme (pdb code 4w6z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme, PDB code: 4w6z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4w6z

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Fluorine binding site 1 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:27.5
occ:1.00
 F1 A:ETF404 0.0 27.5 1.0
C1 A:ETF404 1.3 31.3 1.0
F2 A:ETF404 2.1 34.8 1.0
F3 A:ETF404 2.1 31.5 1.0
C2 A:ETF404 2.3 31.8 1.0
NE1 A:TRP92 3.0 32.2 1.0
CD1 A:TRP92 3.2 31.8 1.0
CE1 A:TYR294 3.3 30.3 1.0
CE2 A:TRP92 3.3 35.3 1.0
O A:ETF404 3.5 27.0 1.0
CG A:TRP92 3.7 31.9 1.0
CD2 A:TRP92 3.7 34.1 1.0
CD1 A:TYR294 3.9 30.9 1.0
CG1 A:VAL295 4.0 28.5 1.0
CZ2 A:TRP92 4.0 35.2 1.0
O7N A:8ID403 4.2 36.4 1.0
C7N A:8ID403 4.2 35.1 1.0
CZ A:TYR294 4.2 31.7 1.0
C3N A:8ID403 4.2 34.6 1.0
OH A:TYR294 4.4 32.0 1.0
C4N A:8ID403 4.4 35.0 1.0
CE A:MET270 4.5 38.7 1.0
OG1 A:THR45 4.5 27.5 1.0
CB A:TRP92 4.6 31.1 1.0
CE3 A:TRP92 4.7 35.6 1.0
N7N A:8ID403 4.7 38.7 1.0
C2N A:8ID403 4.8 36.0 1.0
CH2 A:TRP54 4.9 30.4 1.0
CZ3 A:TRP54 4.9 30.3 1.0
CH2 A:TRP92 4.9 36.1 1.0
CG2 A:THR45 4.9 28.6 1.0

Fluorine binding site 2 out of 12 in 4w6z

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Fluorine binding site 2 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:34.8
occ:1.00
 F2 A:ETF404 0.0 34.8 1.0
C1 A:ETF404 1.3 31.3 1.0
F1 A:ETF404 2.1 27.5 1.0
F3 A:ETF404 2.1 31.5 1.0
C2 A:ETF404 2.3 31.8 1.0
OG1 A:THR45 2.8 27.5 1.0
O A:ETF404 3.0 27.0 1.0
CG2 A:THR45 3.0 28.6 1.0
CH2 A:TRP54 3.1 30.4 1.0
CZ3 A:TRP54 3.2 30.3 1.0
CB A:THR45 3.5 28.1 1.0
CE2 A:TRP92 3.7 35.3 1.0
CZ2 A:TRP92 3.8 35.2 1.0
CD2 A:TRP92 4.0 34.1 1.0
CH2 A:TRP92 4.1 36.1 1.0
NE1 A:TRP92 4.1 32.2 1.0
CE3 A:TRP92 4.3 35.6 1.0
CZ2 A:TRP54 4.3 31.2 1.0
CE A:MET270 4.3 38.7 1.0
CZ3 A:TRP92 4.4 35.9 1.0
O2' A:8ID403 4.4 26.8 1.0
CG A:TRP92 4.6 31.9 1.0
CD1 A:TRP92 4.6 31.8 1.0
CE3 A:TRP54 4.6 31.9 1.0
CA A:THR45 4.7 29.7 1.0
ZN A:ZN401 4.7 33.1 1.0
C2N A:8ID403 4.7 36.0 1.0
C3N A:8ID403 4.8 34.6 1.0
N1N A:8ID403 4.9 33.4 1.0
C4N A:8ID403 4.9 35.0 1.0
CE1 A:TYR294 5.0 30.3 1.0

Fluorine binding site 3 out of 12 in 4w6z

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Fluorine binding site 3 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:31.5
occ:1.00
 F3 A:ETF404 0.0 31.5 1.0
C1 A:ETF404 1.3 31.3 1.0
F1 A:ETF404 2.1 27.5 1.0
F2 A:ETF404 2.1 34.8 1.0
C2 A:ETF404 2.4 31.8 1.0
C3N A:8ID403 2.6 34.6 1.0
O A:ETF404 2.8 27.0 1.0
C2N A:8ID403 2.8 36.0 1.0
C4N A:8ID403 3.0 35.0 1.0
C7N A:8ID403 3.1 35.1 1.0
OG1 A:THR45 3.2 27.5 1.0
N1N A:8ID403 3.3 33.4 1.0
C5N A:8ID403 3.5 39.2 1.0
C6N A:8ID403 3.6 34.9 1.0
CE A:MET270 3.7 38.7 1.0
O7N A:8ID403 3.7 36.4 1.0
N7N A:8ID403 3.7 38.7 1.0
O2' A:8ID403 4.2 26.8 1.0
C1' A:8ID403 4.2 29.6 1.0
CH2 A:TRP54 4.3 30.4 1.0
CB A:THR45 4.4 28.1 1.0
ZN A:ZN401 4.4 33.1 1.0
CG2 A:THR45 4.6 28.6 1.0
CG1 A:VAL295 4.7 28.5 1.0
C2' A:8ID403 4.7 27.2 1.0
CE1 A:TYR294 4.8 30.3 1.0
CZ3 A:TRP54 4.9 30.3 1.0

Fluorine binding site 4 out of 12 in 4w6z

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Fluorine binding site 4 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:71.5
occ:1.00
 F1 B:ETF404 0.0 71.5 1.0
C1 B:ETF404 1.3 74.4 1.0
F3 B:ETF404 2.2 71.6 1.0
F2 B:ETF404 2.2 78.0 1.0
C2 B:ETF404 2.3 71.3 1.0
O B:ETF404 2.6 61.3 1.0
OG1 B:THR45 2.8 47.6 1.0
SD B:MET270 3.3 64.9 1.0
CG2 B:THR45 3.6 47.3 1.0
CB B:THR45 3.6 48.1 1.0
CD2 B:TRP92 3.9 43.2 1.0
CE2 B:TRP92 4.0 43.4 1.0
CG B:TRP92 4.1 42.2 1.0
CG B:MET270 4.2 63.4 1.0
CE3 B:TRP92 4.3 44.0 1.0
NE1 B:TRP92 4.3 41.8 1.0
CD1 B:TRP92 4.4 42.5 1.0
CZ2 B:TRP92 4.5 46.9 1.0
NE2 B:HIS66 4.6 43.8 1.0
CZ3 B:TRP92 4.7 44.7 1.0
CB B:TRP92 4.7 38.5 1.0
CH2 B:TRP92 4.8 46.4 1.0
CE B:MET270 4.8 64.6 1.0
CD2 B:HIS66 4.9 40.4 1.0
CG1 B:VAL295 4.9 32.9 1.0
CH2 B:TRP54 5.0 72.5 1.0

Fluorine binding site 5 out of 12 in 4w6z

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Fluorine binding site 5 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:78.0
occ:1.00
 F2 B:ETF404 0.0 78.0 1.0
C1 B:ETF404 1.3 74.4 1.0
F3 B:ETF404 2.1 71.6 1.0
F1 B:ETF404 2.2 71.5 1.0
C2 B:ETF404 2.4 71.3 1.0
O B:ETF404 2.9 61.3 1.0
OG1 B:THR45 3.3 47.6 1.0
SD B:MET270 4.2 64.9 1.0
CG B:MET270 4.2 63.4 1.0
SG B:CYS153 4.3 41.9 1.0
CB B:THR45 4.4 48.1 1.0
CB B:MET270 4.8 64.7 1.0

Fluorine binding site 6 out of 12 in 4w6z

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Fluorine binding site 6 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:71.6
occ:1.00
 F3 B:ETF404 0.0 71.6 1.0
C1 B:ETF404 1.3 74.4 1.0
F2 B:ETF404 2.1 78.0 1.0
F1 B:ETF404 2.2 71.5 1.0
C2 B:ETF404 2.4 71.3 1.0
CG1 B:VAL295 3.4 32.9 1.0
O B:ETF404 3.6 61.3 1.0
SD B:MET270 3.8 64.9 1.0
CE1 B:TYR294 4.0 37.7 1.0
CG B:MET270 4.0 63.4 1.0
CD1 B:TYR294 4.3 36.5 1.0
CD1 B:TRP92 4.4 42.5 1.0
OG1 B:THR45 4.6 47.6 1.0
NE1 B:TRP92 4.7 41.8 1.0
CG B:TRP92 4.7 42.2 1.0
CB B:VAL295 4.8 32.6 1.0
OG1 B:THR157 4.9 30.2 1.0
CZ B:TYR294 4.9 37.0 1.0

Fluorine binding site 7 out of 12 in 4w6z

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Fluorine binding site 7 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:24.9
occ:1.00
 F1 C:ETF404 0.0 24.9 1.0
C1 C:ETF404 1.4 23.9 1.0
F2 C:ETF404 2.2 19.6 1.0
F3 C:ETF404 2.3 25.8 1.0
C2 C:ETF404 2.4 22.9 1.0
C3N C:8ID403 2.8 24.0 1.0
C2N C:8ID403 2.8 23.9 1.0
O C:ETF404 3.1 18.2 1.0
CE C:MET270 3.1 23.5 1.0
C7N C:8ID403 3.3 24.9 1.0
OG1 C:THR45 3.3 22.1 1.0
N1N C:8ID403 3.3 22.2 1.0
C4N C:8ID403 3.3 23.8 1.0
O7N C:8ID403 3.7 30.1 1.0
C5N C:8ID403 3.7 24.2 1.0
C6N C:8ID403 3.7 23.6 1.0
N7N C:8ID403 4.0 24.8 1.0
CH2 C:TRP54 4.1 29.1 1.0
C1' C:8ID403 4.2 21.8 1.0
O2' C:8ID403 4.2 20.3 1.0
CB C:THR45 4.5 23.4 1.0
CE1 C:TYR294 4.6 27.4 1.0
CG2 C:THR45 4.7 23.8 1.0
ZN C:ZN401 4.7 25.9 1.0
C2' C:8ID403 4.7 20.2 1.0
CZ3 C:TRP54 4.8 28.7 1.0
CG1 C:VAL295 4.8 24.6 1.0
SD C:MET270 4.8 24.5 1.0
CZ2 C:TRP54 4.9 29.5 1.0
CD1 C:TYR294 4.9 27.3 1.0
O C:VAL268 5.0 25.4 1.0

Fluorine binding site 8 out of 12 in 4w6z

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Fluorine binding site 8 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:19.6
occ:1.00
 F2 C:ETF404 0.0 19.6 1.0
C1 C:ETF404 1.3 23.9 1.0
F3 C:ETF404 2.1 25.8 1.0
F1 C:ETF404 2.2 24.9 1.0
C2 C:ETF404 2.2 22.9 1.0
NE1 C:TRP92 3.0 28.6 1.0
CE2 C:TRP92 3.2 28.7 1.0
CE1 C:TYR294 3.2 27.4 1.0
CD1 C:TRP92 3.3 28.6 1.0
O C:ETF404 3.5 18.2 1.0
CD2 C:TRP92 3.6 28.3 1.0
CG C:TRP92 3.7 28.1 1.0
CZ2 C:TRP92 3.8 28.4 1.0
CG1 C:VAL295 3.8 24.6 1.0
CD1 C:TYR294 3.9 27.3 1.0
O7N C:8ID403 4.0 30.1 1.0
CZ C:TYR294 4.1 29.3 1.0
OH C:TYR294 4.3 32.0 1.0
C7N C:8ID403 4.3 24.9 1.0
C3N C:8ID403 4.3 24.0 1.0
CE C:MET270 4.4 23.5 1.0
CE3 C:TRP92 4.4 28.3 1.0
C4N C:8ID403 4.5 23.8 1.0
OG1 C:THR45 4.5 22.1 1.0
CH2 C:TRP92 4.5 27.9 1.0
CB C:TRP92 4.7 27.0 1.0
C2N C:8ID403 4.8 23.9 1.0
CZ3 C:TRP92 4.8 28.2 1.0
CH2 C:TRP54 4.9 29.1 1.0
CG2 C:THR45 4.9 23.8 1.0

Fluorine binding site 9 out of 12 in 4w6z

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Fluorine binding site 9 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F404

b:25.8
occ:1.00
 F3 C:ETF404 0.0 25.8 1.0
C1 C:ETF404 1.3 23.9 1.0
F2 C:ETF404 2.1 19.6 1.0
F1 C:ETF404 2.3 24.9 1.0
C2 C:ETF404 2.4 22.9 1.0
O C:ETF404 2.8 18.2 1.0
OG1 C:THR45 2.9 22.1 1.0
CG2 C:THR45 2.9 23.8 1.0
CH2 C:TRP54 3.2 29.1 1.0
CZ3 C:TRP54 3.4 28.7 1.0
CZ2 C:TRP92 3.5 28.4 1.0
CE2 C:TRP92 3.5 28.7 1.0
CB C:THR45 3.5 23.4 1.0
CH2 C:TRP92 3.6 27.9 1.0
CD2 C:TRP92 3.8 28.3 1.0
CZ3 C:TRP92 3.8 28.2 1.0
CE3 C:TRP92 3.9 28.3 1.0
NE1 C:TRP92 4.1 28.6 1.0
CE C:MET270 4.1 23.5 1.0
CZ2 C:TRP54 4.5 29.5 1.0
CG C:TRP92 4.5 28.1 1.0
CD1 C:TRP92 4.6 28.6 1.0
ZN C:ZN401 4.6 25.9 1.0
CE3 C:TRP54 4.7 29.1 1.0
CA C:THR45 4.7 26.7 1.0
O2' C:8ID403 4.8 20.3 1.0
CE1 C:TYR294 4.9 27.4 1.0
C2N C:8ID403 5.0 23.9 1.0

Fluorine binding site 10 out of 12 in 4w6z

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Fluorine binding site 10 out of 12 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F404

b:61.1
occ:1.00
 F1 D:ETF404 0.0 61.1 1.0
C1 D:ETF404 1.3 52.3 1.0
F3 D:ETF404 2.0 54.5 1.0
F2 D:ETF404 2.1 47.8 1.0
C2 D:ETF404 2.4 56.4 1.0
CG1 D:VAL295 3.2 35.9 1.0
O D:ETF404 3.6 52.8 1.0
CE1 D:TYR294 3.9 39.4 1.0
O D:HOH526 4.0 43.1 1.0
CD1 D:TYR294 4.2 38.7 1.0
OG1 D:THR157 4.4 29.7 1.0
CE D:MET270 4.5 82.0 1.0
CZ D:TYR294 4.6 39.0 1.0
CD1 D:TRP92 4.7 36.5 1.0
CB D:VAL295 4.7 34.5 1.0
CG D:TRP92 4.8 35.5 1.0
OH D:TYR294 4.8 41.5 1.0
OG1 D:THR45 5.0 59.9 1.0

Reference:

S.B.Raj, S.Ramaswamy, B.V.Plapp. Yeast Alcohol Dehydrogenase Structure and Catalysis. Biochemistry V. 53 5791 2014.
ISSN: ISSN 0006-2960
PubMed: 25157460
DOI: 10.1021/BI5006442
Page generated: Thu Aug 1 06:19:36 2024

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