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Fluorine in PDB 4q8x: Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II

Enzymatic activity of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II

All present enzymatic activity of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II, PDB code: 4q8x was solved by D.P.Martin, S.M.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.130, 41.316, 71.830, 90.00, 104.38, 90.00
R / Rfree (%) 16.3 / 20.1

Other elements in 4q8x:

The structure of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II also contains other interesting chemical elements:

Mercury (Hg) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II (pdb code 4q8x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II, PDB code: 4q8x:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 1 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:23.5
occ:0.50
 F1 A:7FH304 0.0 23.5 0.5
F3 A:7FH304 1.1 29.5 0.5
C6 A:7FH304 1.3 23.4 0.5
C6 A:7FH304 2.0 22.5 0.5
F1 A:7FH304 2.2 30.8 0.5
F3 A:7FH304 2.2 27.0 0.5
F2 A:7FH304 2.2 19.9 0.5
C4 A:7FH304 2.3 19.1 0.5
F2 A:7FH304 2.9 26.9 0.5
C4 A:7FH304 3.0 18.6 0.5
C3 A:7FH304 3.1 19.4 0.5
C5 A:7FH304 3.1 13.9 0.5
C3 A:7FH304 3.2 13.3 0.5
O A:HOH559 3.3 33.4 1.0
CZ A:PHE131 3.4 12.1 1.0
CE2 A:PHE131 3.9 12.4 1.0
CD1 A:LEU198 3.9 8.3 1.0
C5 A:7FH304 4.2 15.9 0.5
C2 A:7FH304 4.3 17.3 0.5
N1 A:7FH304 4.3 12.9 0.5
CD2 A:LEU198 4.4 11.4 1.0
CE1 A:PHE131 4.5 8.9 1.0
O A:HOH408 4.5 31.1 1.0
C2 A:7FH304 4.6 10.4 0.5
C1 A:7FH304 4.8 14.6 0.5
CG A:LEU198 4.9 5.6 1.0
O A:HOH570 4.9 24.6 1.0

Fluorine binding site 2 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 2 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:30.8
occ:0.50
 F1 A:7FH304 0.0 30.8 0.5
F3 A:7FH304 0.9 27.0 0.5
C6 A:7FH304 1.3 22.5 0.5
C6 A:7FH304 1.4 23.4 0.5
C4 A:7FH304 1.8 19.1 0.5
C3 A:7FH304 1.8 19.4 0.5
F1 A:7FH304 2.2 23.5 0.5
F3 A:7FH304 2.2 29.5 0.5
F2 A:7FH304 2.2 26.9 0.5
C4 A:7FH304 2.3 18.6 0.5
F2 A:7FH304 2.6 19.9 0.5
C3 A:7FH304 2.9 13.3 0.5
C5 A:7FH304 3.2 13.9 0.5
C2 A:7FH304 3.2 17.3 0.5
NE2 A:GLN92 3.3 11.6 1.0
C5 A:7FH304 3.3 15.9 0.5
O A:HOH408 3.3 31.1 1.0
O A:HOH570 3.6 24.6 1.0
CZ A:PHE131 3.7 12.1 1.0
N1 A:7FH304 4.1 12.9 0.5
C1 A:7FH304 4.1 14.6 0.5
C2 A:7FH304 4.2 10.4 0.5
CE1 A:PHE131 4.3 8.9 1.0
CD A:GLN92 4.4 5.9 1.0
CE2 A:PHE131 4.5 12.4 1.0
N1 A:7FH304 4.5 11.1 0.5
CG1 A:VAL121 4.6 3.9 1.0
C1 A:7FH304 4.9 6.7 0.5
CG A:GLN92 4.9 5.1 1.0
CG2 A:VAL121 4.9 4.4 1.0

Fluorine binding site 3 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 3 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:19.9
occ:0.50
 F2 A:7FH304 0.0 19.9 0.5
C6 A:7FH304 1.3 23.4 0.5
F1 A:7FH304 2.2 23.5 0.5
F3 A:7FH304 2.2 27.0 0.5
C4 A:7FH304 2.3 19.1 0.5
C3 A:7FH304 2.3 13.3 0.5
F3 A:7FH304 2.6 29.5 0.5
F1 A:7FH304 2.6 30.8 0.5
C5 A:7FH304 2.6 13.9 0.5
C6 A:7FH304 2.9 22.5 0.5
C4 A:7FH304 2.9 18.6 0.5
O A:HOH570 3.3 24.6 1.0
C2 A:7FH304 3.4 10.4 0.5
C3 A:7FH304 3.5 19.4 0.5
N1 A:7FH304 4.0 12.9 0.5
F2 A:7FH304 4.2 26.9 0.5
C5 A:7FH304 4.3 15.9 0.5
OG1 A:THR200 4.4 10.5 1.0
C2 A:7FH304 4.6 17.3 0.5
O A:HOH559 4.6 33.4 1.0
O A:HOH408 4.7 31.1 1.0
C1 A:7FH304 4.7 6.7 0.5
C1 A:7FH304 4.8 14.6 0.5
O1 A:7FH304 4.8 9.6 0.5
NE2 A:GLN92 4.9 11.6 1.0
CD1 A:LEU198 4.9 8.3 1.0
O A:HOH466 5.0 14.4 1.0

Fluorine binding site 4 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 4 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:26.9
occ:0.50
 F2 A:7FH304 0.0 26.9 0.5
C6 A:7FH304 1.3 22.5 0.5
C3 A:7FH304 1.4 19.4 0.5
C2 A:7FH304 2.2 17.3 0.5
F1 A:7FH304 2.2 30.8 0.5
F3 A:7FH304 2.2 29.5 0.5
C4 A:7FH304 2.3 18.6 0.5
C4 A:7FH304 2.3 19.1 0.5
C5 A:7FH304 2.6 15.9 0.5
C6 A:7FH304 2.9 23.4 0.5
F1 A:7FH304 2.9 23.5 0.5
F3 A:7FH304 3.1 27.0 0.5
C1 A:7FH304 3.2 14.6 0.5
C5 A:7FH304 3.3 13.9 0.5
CG1 A:VAL121 3.3 3.9 1.0
C3 A:7FH304 3.6 13.3 0.5
CZ A:PHE131 3.6 12.1 1.0
CD2 A:LEU198 3.7 11.4 1.0
N1 A:7FH304 3.7 12.9 0.5
CE1 A:PHE131 3.7 8.9 1.0
CD1 A:LEU141 3.9 8.4 1.0
N1 A:7FH304 4.0 11.1 0.5
F2 A:7FH304 4.2 19.9 0.5
CG2 A:VAL121 4.2 4.4 1.0
CB A:VAL121 4.4 3.1 1.0
NE2 A:GLN92 4.6 11.6 1.0
S1 A:7FH304 4.6 17.3 0.5
C2 A:7FH304 4.7 10.4 0.5
CE2 A:PHE131 4.8 12.4 1.0
O1 A:7FH304 4.8 12.2 0.5
C1 A:7FH304 4.9 6.7 0.5
CD1 A:LEU198 4.9 8.3 1.0
CG A:LEU198 4.9 5.6 1.0
O1 A:7FH304 5.0 9.6 0.5

Fluorine binding site 5 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 5 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:27.0
occ:0.50
 F3 A:7FH304 0.0 27.0 0.5
F1 A:7FH304 0.9 30.8 0.5
C6 A:7FH304 1.3 23.4 0.5
C6 A:7FH304 2.1 22.5 0.5
F1 A:7FH304 2.2 23.5 0.5
F2 A:7FH304 2.2 19.9 0.5
C4 A:7FH304 2.3 19.1 0.5
F3 A:7FH304 2.6 29.5 0.5
C3 A:7FH304 2.7 19.4 0.5
O A:HOH408 2.8 31.1 1.0
C4 A:7FH304 2.9 18.6 0.5
F2 A:7FH304 3.1 26.9 0.5
C3 A:7FH304 3.1 13.3 0.5
O A:HOH570 3.2 24.6 1.0
NE2 A:GLN92 3.3 11.6 1.0
C5 A:7FH304 3.5 13.9 0.5
CZ A:PHE131 4.0 12.1 1.0
C2 A:7FH304 4.0 17.3 0.5
C5 A:7FH304 4.0 15.9 0.5
C2 A:7FH304 4.4 10.4 0.5
CE2 A:PHE131 4.5 12.4 1.0
CD A:GLN92 4.5 5.9 1.0
N1 A:7FH304 4.6 12.9 0.5
CE1 A:PHE131 4.7 8.9 1.0
C1 A:7FH304 4.8 14.6 0.5

Fluorine binding site 6 out of 6 in 4q8x

Go back to Fluorine Binding Sites List in 4q8x
Fluorine binding site 6 out of 6 in the Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of 1-Hydroxy-5-(Trifluoromethyl)Pyridine-2(1H)- Thione Bound to Human Carbonic Anhydrase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F304

b:29.5
occ:0.50
 F3 A:7FH304 0.0 29.5 0.5
F1 A:7FH304 1.1 23.5 0.5
C6 A:7FH304 1.3 22.5 0.5
C6 A:7FH304 1.6 23.4 0.5
C4 A:7FH304 1.7 19.1 0.5
F1 A:7FH304 2.2 30.8 0.5
F2 A:7FH304 2.2 26.9 0.5
C4 A:7FH304 2.3 18.6 0.5
C3 A:7FH304 2.4 19.4 0.5
C5 A:7FH304 2.5 13.9 0.5
F3 A:7FH304 2.6 27.0 0.5
F2 A:7FH304 2.6 19.9 0.5
C3 A:7FH304 2.8 13.3 0.5
C5 A:7FH304 3.4 15.9 0.5
C2 A:7FH304 3.4 17.3 0.5
CD1 A:LEU198 3.4 8.3 1.0
CD2 A:LEU198 3.5 11.4 1.0
N1 A:7FH304 3.5 12.9 0.5
CZ A:PHE131 3.6 12.1 1.0
C1 A:7FH304 3.9 14.6 0.5
O A:HOH559 3.9 33.4 1.0
CG A:LEU198 4.1 5.6 1.0
C2 A:7FH304 4.1 10.4 0.5
CE2 A:PHE131 4.4 12.4 1.0
CE1 A:PHE131 4.5 8.9 1.0
O1 A:7FH304 4.6 9.6 0.5
N1 A:7FH304 4.6 11.1 0.5
CB A:LEU198 4.8 5.2 1.0
CD1 A:LEU141 4.8 8.4 1.0
C1 A:7FH304 4.9 6.7 0.5

Reference:

D.P.Martin, P.G.Blachly, J.A.Mccammon, S.M.Cohen. Exploring the Influence of the Protein Environment on Metal-Binding Pharmacophores. J.Med.Chem. V. 57 7126 2014.
ISSN: ISSN 0022-2623
PubMed: 25116076
DOI: 10.1021/JM500984B
Page generated: Thu Aug 1 05:08:51 2024

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