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Fluorine in PDB 1yl1: Effect of Alcohols on Protein Hydration

Enzymatic activity of Effect of Alcohols on Protein Hydration

All present enzymatic activity of Effect of Alcohols on Protein Hydration:
3.2.1.17;

Protein crystallography data

The structure of Effect of Alcohols on Protein Hydration, PDB code: 1yl1 was solved by A.A.Deshpande, S.Nimsadkar, S.C.Mande, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.23 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.288, 79.288, 37.957, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Other elements in 1yl1:

The structure of Effect of Alcohols on Protein Hydration also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Effect of Alcohols on Protein Hydration (pdb code 1yl1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Effect of Alcohols on Protein Hydration, PDB code: 1yl1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 1 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1940

b:40.8
occ:1.00
 F1 X:ETF1940 0.0 40.8 1.0
C1 X:ETF1940 1.3 40.6 1.0
F3 X:ETF1940 2.1 40.1 1.0
F2 X:ETF1940 2.1 40.3 1.0
C2 X:ETF1940 2.4 40.4 1.0
O X:HOH1986 3.0 36.5 1.0
O X:ETF1940 3.0 40.6 1.0
NE1 X:TRP63 3.7 22.7 1.0
CB X:ASN59 3.8 19.0 1.0
CD1 X:TRP63 4.0 20.9 1.0
N X:ASN59 4.1 15.8 1.0
O X:ALA107 4.2 18.9 1.0
CA X:ASN59 4.6 18.2 1.0
O X:HOH1985 4.7 80.9 1.0
CE2 X:TRP63 4.9 21.2 1.0
O X:HOH1968 4.9 31.7 1.0
CG X:ASN59 4.9 21.4 1.0
O X:GLN57 5.0 15.5 1.0

Fluorine binding site 2 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 2 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1940

b:40.3
occ:1.00
 F2 X:ETF1940 0.0 40.3 1.0
C1 X:ETF1940 1.3 40.6 1.0
F1 X:ETF1940 2.1 40.8 1.0
F3 X:ETF1940 2.2 40.1 1.0
C2 X:ETF1940 2.4 40.4 1.0
O X:ETF1940 2.8 40.6 1.0
N X:ASN59 3.1 15.8 1.0
CA X:ILE58 3.2 13.8 1.0
C X:ILE58 3.7 15.8 1.0
O X:GLN57 3.7 15.5 1.0
CD1 X:TRP63 3.7 20.9 1.0
CD1 X:ILE98 3.8 12.8 1.0
CG2 X:ILE58 3.8 11.7 1.0
CB X:ILE58 3.9 14.4 1.0
NE1 X:TRP63 4.0 22.7 1.0
CB X:ASN59 4.1 19.0 1.0
CG1 X:ILE58 4.1 11.3 1.0
CA X:ASN59 4.2 18.2 1.0
N X:ILE58 4.2 14.2 1.0
C X:GLN57 4.3 13.4 1.0
NE1 X:TRP108 4.5 16.9 1.0
O X:HOH1985 4.6 80.9 1.0
CG X:TRP63 4.7 19.1 1.0
O X:ILE58 4.9 13.6 1.0
O X:HOH1986 4.9 36.5 1.0
CE2 X:TRP108 4.9 17.2 1.0
O X:LEU56 4.9 14.4 1.0
CG1 X:ILE98 5.0 14.9 1.0
CE2 X:TRP63 5.0 21.2 1.0
CG2 X:ILE98 5.0 13.2 1.0

Fluorine binding site 3 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 3 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1940

b:40.1
occ:1.00
 F3 X:ETF1940 0.0 40.1 1.0
C1 X:ETF1940 1.3 40.6 1.0
F1 X:ETF1940 2.1 40.8 1.0
F2 X:ETF1940 2.2 40.3 1.0
C2 X:ETF1940 2.3 40.4 1.0
O X:HOH1985 2.9 80.9 1.0
O X:GLN57 3.0 15.5 1.0
N X:ASN59 3.3 15.8 1.0
CB X:ASN59 3.4 19.0 1.0
O X:ETF1940 3.6 40.6 1.0
CA X:ASN59 3.9 18.2 1.0
CA X:ILE58 4.0 13.8 1.0
OD1 X:ASP52 4.0 16.4 1.0
C X:ILE58 4.0 15.8 1.0
C X:GLN57 4.1 13.4 1.0
O X:HOH1968 4.2 31.7 1.0
O X:HOH1986 4.3 36.5 1.0
N X:ILE58 4.5 14.2 1.0
CG X:ASN59 4.6 21.4 1.0
CG X:ASP52 4.6 17.0 1.0
O X:ALA107 4.8 18.9 1.0
ND2 X:ASN59 5.0 23.3 1.0

Fluorine binding site 4 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 4 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1941

b:40.4
occ:1.00
 F1 X:ETF1941 0.0 40.4 1.0
C1 X:ETF1941 1.3 40.9 1.0
F3 X:ETF1941 2.1 40.8 1.0
F2 X:ETF1941 2.3 40.6 1.0
C2 X:ETF1941 2.3 40.5 1.0
O X:ETF1941 2.9 40.0 1.0
CB X:CYS6 4.1 21.4 1.0
N X:GLU7 4.4 16.1 1.0
N X:CYS6 4.6 16.8 1.0
CA X:CYS6 4.7 18.0 1.0
C X:CYS6 4.9 17.6 1.0
CB X:GLU7 5.0 19.6 1.0
SG X:CYS6 5.0 23.1 1.0

Fluorine binding site 5 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 5 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1941

b:40.6
occ:1.00
 F2 X:ETF1941 0.0 40.6 1.0
C1 X:ETF1941 1.7 40.9 1.0
F1 X:ETF1941 2.3 40.4 1.0
F3 X:ETF1941 2.4 40.8 1.0
C2 X:ETF1941 2.8 40.5 1.0
CA X:GLY4 3.3 18.4 1.0
CB X:GLU7 3.5 19.6 1.0
C X:GLY4 3.9 19.6 1.0
N X:GLU7 3.9 16.1 1.0
O X:ETF1941 4.0 40.0 1.0
N X:GLY4 4.0 21.4 1.0
OE1 X:GLU7 4.1 24.8 1.0
CA X:GLU7 4.3 16.7 1.0
O X:GLY4 4.4 18.9 1.0
N X:ARG5 4.5 19.9 1.0
CD X:GLU7 4.6 24.6 1.0
CG X:GLU7 4.7 21.4 1.0
N X:CYS6 4.8 16.8 1.0
C X:CYS6 5.0 17.6 1.0

Fluorine binding site 6 out of 6 in 1yl1

Go back to Fluorine Binding Sites List in 1yl1
Fluorine binding site 6 out of 6 in the Effect of Alcohols on Protein Hydration


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Effect of Alcohols on Protein Hydration within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1941

b:40.8
occ:1.00
 F3 X:ETF1941 0.0 40.8 1.0
C1 X:ETF1941 1.3 40.9 1.0
F1 X:ETF1941 2.1 40.4 1.0
C2 X:ETF1941 2.3 40.5 1.0
N X:GLU7 2.3 16.1 1.0
F2 X:ETF1941 2.4 40.6 1.0
O X:ETF1941 2.8 40.0 1.0
CB X:CYS6 2.8 21.4 1.0
N X:CYS6 2.9 16.8 1.0
C X:CYS6 2.9 17.6 1.0
CA X:CYS6 2.9 18.0 1.0
CA X:GLU7 3.3 16.7 1.0
CB X:GLU7 3.5 19.6 1.0
C X:ARG5 3.9 18.3 1.0
C X:GLY4 3.9 19.6 1.0
O X:CYS6 4.0 18.7 1.0
N X:ARG5 4.1 19.9 1.0
O X:GLY4 4.1 18.9 1.0
CA X:GLY4 4.2 18.4 1.0
SG X:CYS6 4.3 23.1 1.0
CA X:ARG5 4.5 19.2 1.0
O X:ARG5 4.6 16.1 1.0
C X:GLU7 4.7 17.1 1.0
N X:LEU8 4.9 15.5 1.0
CG X:GLU7 5.0 21.4 1.0

Reference:

A.Deshpande, S.Nimsadkar, S.C.Mande. Effect of Alcohols on Protein Hydration: Crystallographic Analysis of Hen Egg-White Lysozyme in the Presence of Alcohols. Acta Crystallogr.,Sect.D V. 61 1005 2005.
ISSN: ISSN 0907-4449
PubMed: 15983424
DOI: 10.1107/S0907444905009364
Page generated: Wed Jul 31 13:32:47 2024

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