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Fluorine in PDB 3ryx: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase

Enzymatic activity of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase

All present enzymatic activity of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase:
4.2.1.1;

Protein crystallography data

The structure of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase, PDB code: 3ryx was solved by P.W.Snyder, S.Bai, A.Heroux, G.W.Whitesides, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.94 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.580, 41.781, 72.348, 90.00, 103.58, 90.00
R / Rfree (%) 16.5 / 24

Other elements in 3ryx:

The structure of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase (pdb code 3ryx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase, PDB code: 3ryx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 3ryx

Go back to Fluorine Binding Sites List in 3ryx
Fluorine binding site 1 out of 5 in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:32.8
occ:1.00
 F2'1 B:RYX1 0.0 32.8 1.0
C2' B:RYX1 1.3 35.3 1.0
C1' B:RYX1 2.1 29.6 1.0
F2'2 B:RYX1 2.3 38.1 1.0
C3' B:RYX1 2.5 38.7 1.0
F3'1 B:RYX1 2.8 42.0 1.0
N' B:RYX1 2.8 22.8 1.0
CD B:PRO202 3.0 18.5 1.0
F3'2 B:RYX1 3.1 41.7 1.0
O B:HOH263 3.3 23.3 1.0
F3'3 B:RYX1 3.4 41.5 1.0
O B:PRO201 3.9 17.9 1.0
CG B:PRO202 3.9 18.2 1.0
C7 B:RYX1 4.0 19.7 1.0
N B:PRO202 4.2 17.9 1.0
O B:HOH289 4.4 42.3 1.0
C B:PRO201 4.5 16.7 1.0
O' B:RYX1 4.6 19.7 1.0
CD1 B:LEU198 4.9 16.9 1.0

Fluorine binding site 2 out of 5 in 3ryx

Go back to Fluorine Binding Sites List in 3ryx
Fluorine binding site 2 out of 5 in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:42.0
occ:1.00
 F3'1 B:RYX1 0.0 42.0 1.0
C3' B:RYX1 1.4 38.7 1.0
F3'2 B:RYX1 2.2 41.7 1.0
C2' B:RYX1 2.3 35.3 1.0
F3'3 B:RYX1 2.3 41.5 1.0
C1' B:RYX1 2.7 29.6 1.0
F2'1 B:RYX1 2.8 32.8 1.0
F2'2 B:RYX1 3.3 38.1 1.0
O B:HOH339 3.5 50.1 1.0
N' B:RYX1 4.1 22.8 1.0
O' B:RYX1 4.7 19.7 1.0
C7 B:RYX1 4.9 19.7 1.0
CE2 B:PHE131 5.0 20.4 1.0

Fluorine binding site 3 out of 5 in 3ryx

Go back to Fluorine Binding Sites List in 3ryx
Fluorine binding site 3 out of 5 in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:38.1
occ:1.00
 F2'2 B:RYX1 0.0 38.1 1.0
C2' B:RYX1 1.3 35.3 1.0
C3' B:RYX1 2.1 38.7 1.0
F3'3 B:RYX1 2.1 41.5 1.0
F2'1 B:RYX1 2.3 32.8 1.0
C1' B:RYX1 2.5 29.6 1.0
F3'2 B:RYX1 2.5 41.7 1.0
N' B:RYX1 2.6 22.8 1.0
CD1 B:LEU198 3.1 16.9 1.0
C7 B:RYX1 3.2 19.7 1.0
F3'1 B:RYX1 3.3 42.0 1.0
CD B:PRO202 3.3 18.5 1.0
O' B:RYX1 3.7 19.7 1.0
CG B:PRO202 3.7 18.2 1.0
C1 B:RYX1 4.2 16.6 1.0
O B:HOH263 4.3 23.3 1.0
C3 B:RYX1 4.5 16.8 1.0
CD1 B:LEU204 4.5 23.7 1.0
CG B:LEU198 4.6 14.2 1.0
N B:PRO202 4.6 17.9 1.0
CG1 B:VAL135 4.8 20.3 1.0

Fluorine binding site 4 out of 5 in 3ryx

Go back to Fluorine Binding Sites List in 3ryx
Fluorine binding site 4 out of 5 in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:41.7
occ:1.00
 F3'2 B:RYX1 0.0 41.7 1.0
C3' B:RYX1 1.3 38.7 1.0
F3'3 B:RYX1 2.1 41.5 1.0
F3'1 B:RYX1 2.2 42.0 1.0
C2' B:RYX1 2.4 35.3 1.0
F2'2 B:RYX1 2.5 38.1 1.0
O B:HOH339 3.0 50.1 1.0
F2'1 B:RYX1 3.1 32.8 1.0
C1' B:RYX1 3.7 29.6 1.0
CG B:PRO202 4.0 18.2 1.0
CG2 B:VAL135 4.2 18.6 1.0
CD B:PRO202 4.3 18.5 1.0
CD1 B:LEU204 4.4 23.7 1.0
N' B:RYX1 4.6 22.8 1.0
CB B:VAL135 4.9 18.3 1.0

Fluorine binding site 5 out of 5 in 3ryx

Go back to Fluorine Binding Sites List in 3ryx
Fluorine binding site 5 out of 5 in the Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:41.5
occ:1.00
 F3'3 B:RYX1 0.0 41.5 1.0
C3' B:RYX1 1.3 38.7 1.0
C2' B:RYX1 2.1 35.3 1.0
F3'2 B:RYX1 2.1 41.7 1.0
F2'2 B:RYX1 2.1 38.1 1.0
F3'1 B:RYX1 2.3 42.0 1.0
C1' B:RYX1 2.6 29.6 1.0
CE2 B:PHE131 3.3 20.4 1.0
O' B:RYX1 3.3 19.7 1.0
F2'1 B:RYX1 3.4 32.8 1.0
N' B:RYX1 3.4 22.8 1.0
C7 B:RYX1 3.7 19.7 1.0
O B:HOH339 3.9 50.1 1.0
CG1 B:VAL135 4.0 20.3 1.0
CZ B:PHE131 4.1 18.7 1.0
CD2 B:PHE131 4.2 17.6 1.0
CG2 B:VAL135 4.3 18.6 1.0
CB B:VAL135 4.5 18.3 1.0
CD1 B:LEU198 4.8 16.9 1.0
C1 B:RYX1 5.0 16.6 1.0

Reference:

J.Mecinovic, P.W.Snyder, K.A.Mirica, S.Bai, E.T.Mack, R.L.Kwant, D.T.Moustakas, A.Heroux, G.M.Whitesides. Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the "Hydrophobic Wall" of Carbonic Anhydrase. J.Am.Chem.Soc. V. 133 14017 2011.
ISSN: ISSN 0002-7863
PubMed: 21790183
DOI: 10.1021/JA2045293
Page generated: Wed Jul 31 22:25:30 2024

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