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Fluorine in PDB 4i7s: T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound

Enzymatic activity of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound

All present enzymatic activity of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound:
3.2.1.17;

Protein crystallography data

The structure of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound, PDB code: 4i7s was solved by M.Merski, B.K.Shoichet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.51 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.580, 75.590, 52.600, 90.00, 93.13, 90.00
R / Rfree (%) 16.9 / 19.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound (pdb code 4i7s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound, PDB code: 4i7s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 1 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:9.2
occ:1.00
 FAB A:1DV202 0.0 9.2 1.0
CAJ A:1DV202 1.3 10.6 1.0
FAC A:1DV202 2.2 11.0 1.0
FAD A:1DV202 2.2 10.3 1.0
CAI A:1DV202 2.4 10.2 1.0
NAF A:1DV202 3.3 11.4 1.0
CB A:ALA99 3.3 6.0 1.0
CAE A:1DV202 3.3 12.9 1.0
CA A:TYR88 3.5 8.1 1.0
CD1 A:LEU91 3.5 9.1 1.0
N A:TYR88 3.5 6.8 1.0
CB A:TYR88 3.7 6.7 1.0
CG1 A:VAL87 3.8 6.9 1.0
C A:VAL87 4.1 7.5 1.0
CB A:VAL87 4.2 7.8 1.0
NAG A:1DV202 4.3 10.1 1.0
CAH A:1DV202 4.3 13.4 1.0
CD1 A:TYR88 4.3 8.2 1.0
O A:LEU84 4.4 7.8 1.0
O A:VAL87 4.5 7.3 1.0
CA A:ALA99 4.5 5.4 1.0
CG A:TYR88 4.5 7.2 1.0
CG A:LEU91 4.6 7.9 1.0
CA A:VAL87 4.8 7.5 1.0
C A:TYR88 4.9 8.2 1.0

Fluorine binding site 2 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 2 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:11.0
occ:1.00
 FAC A:1DV202 0.0 11.0 1.0
CAJ A:1DV202 1.3 10.6 1.0
FAD A:1DV202 2.1 10.3 1.0
FAB A:1DV202 2.2 9.2 1.0
CAI A:1DV202 2.3 10.2 1.0
NAF A:1DV202 2.8 11.4 1.0
CB A:ALA99 3.5 6.0 1.0
CAE A:1DV202 3.5 12.9 1.0
CD1 A:ILE78 4.0 6.8 1.0
NAG A:1DV202 4.0 10.1 1.0
CG1 A:ILE78 4.0 5.7 1.0
CB A:LEU84 4.1 6.3 1.0
CD2 A:LEU84 4.2 7.3 1.0
CB A:TYR88 4.2 6.7 1.0
CG2 A:ILE78 4.2 8.5 1.0
O A:LEU84 4.3 7.8 1.0
CAH A:1DV202 4.3 13.4 1.0
CD1 A:LEU84 4.4 8.1 1.0
CG A:LEU84 4.4 6.9 1.0
CA A:ALA99 4.4 5.4 1.0
CD1 A:TYR88 4.5 8.2 1.0
CG2 A:VAL103 4.6 7.3 1.0
CG1 A:VAL111 4.7 9.2 1.0
CA A:TYR88 4.7 8.1 1.0
O A:ALA99 4.7 5.2 1.0
CA A:LEU84 4.7 9.3 1.0
N A:TYR88 4.7 6.8 1.0
C A:ALA99 4.8 6.2 1.0
CB A:ILE78 4.8 6.2 1.0
C A:LEU84 4.8 8.2 1.0
CG A:TYR88 4.9 7.2 1.0

Fluorine binding site 3 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 3 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:10.3
occ:1.00
 FAD A:1DV202 0.0 10.3 1.0
CAJ A:1DV202 1.3 10.6 1.0
FAC A:1DV202 2.1 11.0 1.0
FAB A:1DV202 2.2 9.2 1.0
CAI A:1DV202 2.3 10.2 1.0
CAE A:1DV202 2.8 12.9 1.0
O A:LEU84 3.4 7.8 1.0
CB A:VAL87 3.5 7.8 1.0
CG1 A:VAL87 3.5 6.9 1.0
CD2 A:LEU84 3.5 7.3 1.0
NAF A:1DV202 3.5 11.4 1.0
CA A:LEU84 3.8 9.3 1.0
CB A:LEU84 3.8 6.3 1.0
N A:TYR88 3.9 6.8 1.0
CAH A:1DV202 4.0 13.4 1.0
C A:LEU84 4.0 8.2 1.0
CD2 A:LEU118 4.1 22.7 1.0
CG A:LEU84 4.2 6.9 1.0
NAG A:1DV202 4.3 10.1 1.0
C A:VAL87 4.4 7.5 1.0
CG2 A:VAL87 4.5 8.6 1.0
CA A:VAL87 4.5 7.5 1.0
CA A:TYR88 4.5 8.1 1.0
CB A:TYR88 4.5 6.7 1.0
CD1 A:LEU84 4.9 8.1 1.0
N A:VAL87 5.0 7.5 1.0

Fluorine binding site 4 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 4 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:9.9
occ:1.00
 FAB B:1DV202 0.0 9.9 1.0
CAJ B:1DV202 1.3 9.9 1.0
FAC B:1DV202 2.1 9.1 1.0
FAD B:1DV202 2.2 9.3 1.0
CAI B:1DV202 2.3 8.7 1.0
NAF B:1DV202 3.2 9.6 1.0
CB B:ALA99 3.2 5.1 1.0
CAE B:1DV202 3.3 13.3 1.0
CD1 B:LEU91 3.5 8.6 1.0
CA B:TYR88 3.5 7.9 1.0
N B:TYR88 3.6 6.1 1.0
CB B:TYR88 3.8 6.0 1.0
CG1 B:VAL87 3.9 7.2 1.0
C B:VAL87 4.2 4.6 1.0
CD1 B:TYR88 4.2 6.8 1.0
NAG B:1DV202 4.2 8.6 1.0
CAH B:1DV202 4.3 14.4 1.0
CB B:VAL87 4.4 8.4 1.0
O B:LEU84 4.4 6.5 1.0
CA B:ALA99 4.5 4.0 1.0
CG B:TYR88 4.5 5.7 1.0
O B:VAL87 4.6 7.1 1.0
CG B:LEU91 4.6 7.3 1.0
CA B:VAL87 4.9 8.1 1.0
C B:TYR88 5.0 8.0 1.0

Fluorine binding site 5 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 5 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:9.1
occ:1.00
 FAC B:1DV202 0.0 9.1 1.0
CAJ B:1DV202 1.3 9.9 1.0
FAB B:1DV202 2.1 9.9 1.0
FAD B:1DV202 2.2 9.3 1.0
CAI B:1DV202 2.3 8.7 1.0
NAF B:1DV202 2.8 9.6 1.0
CB B:ALA99 3.4 5.1 1.0
CAE B:1DV202 3.6 13.3 1.0
CD1 B:ILE78 3.9 5.6 1.0
CG1 B:ILE78 3.9 5.2 1.0
CG2 B:ILE78 4.0 8.4 1.0
NAG B:1DV202 4.0 8.6 1.0
CB B:LEU84 4.0 9.4 1.0
CB B:TYR88 4.2 6.0 1.0
CD2 B:LEU84 4.3 8.7 1.0
O B:LEU84 4.3 6.5 1.0
CD1 B:TYR88 4.3 6.8 1.0
CAH B:1DV202 4.3 14.4 1.0
CA B:ALA99 4.4 4.0 1.0
CD1 B:LEU84 4.4 9.8 1.0
CG B:LEU84 4.5 8.3 1.0
CB B:ILE78 4.6 5.8 1.0
CA B:TYR88 4.6 7.9 1.0
CA B:LEU84 4.7 6.9 1.0
N B:TYR88 4.7 6.1 1.0
CG2 B:VAL103 4.7 5.2 1.0
O B:ALA99 4.7 7.4 1.0
CG1 B:VAL111 4.7 4.8 1.0
CG B:TYR88 4.8 5.7 1.0
C B:ALA99 4.8 6.1 1.0
C B:LEU84 4.8 7.1 1.0

Fluorine binding site 6 out of 6 in 4i7s

Go back to Fluorine Binding Sites List in 4i7s
Fluorine binding site 6 out of 6 in the T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of T4 Lysozyme L99A/M102H with 3-Trifluoromethyl-5-Methyl Pyrazole Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:9.3
occ:1.00
 FAD B:1DV202 0.0 9.3 1.0
CAJ B:1DV202 1.3 9.9 1.0
FAC B:1DV202 2.2 9.1 1.0
FAB B:1DV202 2.2 9.9 1.0
CAI B:1DV202 2.4 8.7 1.0
CAE B:1DV202 2.8 13.3 1.0
O B:LEU84 3.3 6.5 1.0
CB B:VAL87 3.5 8.4 1.0
NAF B:1DV202 3.6 9.6 1.0
CG1 B:VAL87 3.6 7.2 1.0
CD2 B:LEU84 3.6 8.7 1.0
CA B:LEU84 3.7 6.9 1.0
CB B:LEU84 3.8 9.4 1.0
N B:TYR88 3.8 6.1 1.0
C B:LEU84 3.9 7.1 1.0
CAH B:1DV202 4.1 14.4 1.0
CG B:LEU84 4.2 8.3 1.0
CD2 B:LEU118 4.3 20.8 1.0
C B:VAL87 4.3 4.6 1.0
NAG B:1DV202 4.4 8.6 1.0
CA B:VAL87 4.4 8.1 1.0
CA B:TYR88 4.4 7.9 1.0
CG2 B:VAL87 4.4 9.7 1.0
CB B:TYR88 4.5 6.0 1.0
CD1 B:LEU84 4.9 9.8 1.0
N B:VAL87 4.9 9.0 1.0
N B:LEU84 5.0 7.8 1.0

Reference:

M.Merski, B.K.Shoichet. The Impact of Introducing A Histidine Into An Apolar Cavity Site on Docking and Ligand Recognition. J.Med.Chem. V. 56 2874 2013.
ISSN: ISSN 0022-2623
PubMed: 23473072
DOI: 10.1021/JM301823G
Page generated: Thu Aug 1 02:16:35 2024

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