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Fluorine in PDB 7u0r: Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp

Enzymatic activity of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp

All present enzymatic activity of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp:
6.1.1.26;

Protein crystallography data

The structure of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp, PDB code: 7u0r was solved by C.V.Swenson, L.T.Roe, R.C.B.Fricke, S.S.Smaga, C.L.Gee, A.Schepartz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.37 / 1.80
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 108.958, 108.958, 112.26, 90, 90, 90
R / Rfree (%) 18 / 21.1

Other elements in 7u0r:

The structure of Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp (pdb code 7u0r). 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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp, PDB code: 7u0r:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 1 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:57.6
occ:1.00
 F13 A:LE0401 0.0 57.6 1.0
C12 A:LE0401 1.4 55.0 1.0
F15 A:LE0401 2.2 60.7 1.0
F14 A:LE0401 2.2 60.9 1.0
C08 A:LE0401 2.4 46.2 1.0
C07 A:LE0401 2.8 53.3 1.0
CD1 A:LEU125 3.3 38.1 1.0
CA A:ALA122 3.4 36.0 1.0
CB A:ALA166 3.5 29.1 1.0
N A:ALA122 3.7 31.3 1.0
C09 A:LE0401 3.7 51.5 1.0
CB A:ALA122 3.7 37.5 1.0
CB A:LEU125 3.8 32.0 1.0
CG A:LEU125 4.0 36.1 1.0
C A:LEU121 4.1 40.8 1.0
C06 A:LE0401 4.2 46.0 1.0
O A:LEU121 4.3 37.2 1.0
O18 A:LE0401 4.4 49.7 1.0
CB A:LEU121 4.6 29.8 1.0
C A:ALA122 4.6 33.4 1.0
O A:LEU167 4.7 34.4 1.0
C16 A:LE0401 4.8 50.5 1.0
CA A:ALA166 4.8 29.9 1.0
O A:ALA122 4.8 34.4 1.0
C10 A:LE0401 4.8 51.1 1.0
CA A:LEU121 4.9 37.2 1.0
O17 A:LE0401 4.9 57.4 1.0

Fluorine binding site 2 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 2 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:60.9
occ:1.00
 F14 A:LE0401 0.0 60.9 1.0
C12 A:LE0401 1.4 55.0 1.0
F15 A:LE0401 2.2 60.7 1.0
F13 A:LE0401 2.2 57.6 1.0
C08 A:LE0401 2.4 46.2 1.0
C09 A:LE0401 2.9 51.5 1.0
C07 A:LE0401 3.6 53.3 1.0
CB A:ALA168 3.9 30.2 1.0
CB A:ALA122 4.2 37.5 1.0
CA A:ALA122 4.3 36.0 1.0
C10 A:LE0401 4.3 51.1 1.0
CB A:LEU125 4.3 32.0 1.0
CZ3 A:TRP239 4.5 51.7 1.0
CD1 A:LEU125 4.5 38.1 1.0
O A:LEU167 4.5 34.4 1.0
CA A:GLY241 4.7 32.3 1.0
C06 A:LE0401 4.8 46.0 1.0
CH2 A:TRP239 4.9 52.1 1.0
O A:ALA122 5.0 34.4 1.0

Fluorine binding site 3 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 3 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:60.7
occ:1.00
 F15 A:LE0401 0.0 60.7 1.0
C12 A:LE0401 1.4 55.0 1.0
F13 A:LE0401 2.2 57.6 1.0
F14 A:LE0401 2.2 60.9 1.0
C08 A:LE0401 2.5 46.2 1.0
O A:LEU167 2.7 34.4 1.0
C07 A:LE0401 3.3 53.3 1.0
C09 A:LE0401 3.3 51.5 1.0
C A:LEU167 3.3 35.4 1.0
CB A:ALA168 3.5 30.2 1.0
CD1 A:LEU125 3.7 38.1 1.0
CB A:ALA166 3.8 29.1 1.0
N A:LEU167 3.9 30.9 1.0
N A:ALA168 3.9 32.5 1.0
CA A:GLY241 4.0 32.3 1.0
N A:ALA242 4.0 31.6 1.0
CA A:ALA168 4.0 32.6 1.0
CA A:LEU167 4.2 25.5 1.0
C A:ALA166 4.2 34.5 1.0
O A:ALA242 4.2 35.9 1.0
C A:GLY241 4.4 40.6 1.0
CA A:ALA166 4.5 29.9 1.0
C06 A:LE0401 4.6 46.0 1.0
C10 A:LE0401 4.6 51.1 1.0
CB A:LEU125 4.7 32.0 1.0
C A:ALA242 4.7 36.1 1.0
O A:ALA166 4.8 32.5 1.0
CG A:LEU125 4.9 36.1 1.0

Fluorine binding site 4 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 4 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:75.1
occ:1.00
 F13 B:LE0401 0.0 75.1 1.0
C12 B:LE0401 1.4 66.3 1.0
F15 B:LE0401 2.2 53.0 1.0
F14 B:LE0401 2.2 60.9 1.0
C08 B:LE0401 2.5 69.2 1.0
C09 B:LE0401 3.0 65.5 1.0
CZ3 B:TRP239 3.5 62.7 1.0
C07 B:LE0401 3.8 66.1 1.0
CB B:ALA168 3.8 41.7 1.0
O B:LEU167 4.1 38.9 1.0
CH2 B:TRP239 4.1 66.4 1.0
CA B:GLY241 4.1 42.5 1.0
CB B:ALA122 4.2 45.9 1.0
CA B:ALA122 4.4 43.2 1.0
C10 B:LE0401 4.4 62.6 1.0
CE3 B:TRP239 4.5 59.2 1.0
N B:ALA242 4.7 42.1 1.0
C B:GLY241 4.7 48.9 1.0
C B:LEU167 4.8 34.4 1.0
CA B:ALA168 4.8 39.4 1.0
CB B:ALA166 4.9 34.8 1.0
CD1 B:LEU125 4.9 39.8 1.0
N B:GLY241 4.9 46.5 1.0
OH B:TYR206 4.9 91.7 1.0
C06 B:LE0401 5.0 64.4 1.0

Fluorine binding site 5 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 5 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:60.9
occ:1.00
 F14 B:LE0401 0.0 60.9 1.0
C12 B:LE0401 1.4 66.3 1.0
F15 B:LE0401 2.1 53.0 1.0
F13 B:LE0401 2.2 75.1 1.0
C08 B:LE0401 2.5 69.2 1.0
O B:LEU167 3.0 38.9 1.0
CB B:ALA166 3.1 34.8 1.0
C07 B:LE0401 3.3 66.1 1.0
O B:ALA242 3.4 43.1 1.0
N B:LEU167 3.4 30.1 1.0
C09 B:LE0401 3.5 65.5 1.0
CA B:ALA166 3.6 31.0 1.0
C B:ALA166 3.7 34.2 1.0
N B:ALA242 3.7 42.1 1.0
C B:LEU167 3.7 34.4 1.0
C B:ALA242 3.9 43.1 1.0
CA B:LEU167 4.2 28.7 1.0
CA B:GLY241 4.2 42.5 1.0
C B:GLY241 4.3 48.9 1.0
CB B:ALA168 4.4 41.7 1.0
CA B:ALA242 4.4 44.6 1.0
CD1 B:LEU125 4.4 39.8 1.0
N B:GLY243 4.5 38.2 1.0
O B:ALA166 4.5 37.1 1.0
N B:ALA168 4.6 37.0 1.0
C06 B:LE0401 4.6 64.4 1.0
C10 B:LE0401 4.7 62.6 1.0
CA B:ALA168 4.8 39.4 1.0
CA B:GLY243 4.9 40.2 1.0

Fluorine binding site 6 out of 6 in 7u0r

Go back to Fluorine Binding Sites List in 7u0r
Fluorine binding site 6 out of 6 in the Crystal Structure of Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp


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 Methanomethylophilus Alvus Pylrs(N166A/V168A) Complexed with Meta-Trifluoromethyl-2-Benzylmalonate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:53.0
occ:1.00
 F15 B:LE0401 0.0 53.0 1.0
C12 B:LE0401 1.4 66.3 1.0
F14 B:LE0401 2.1 60.9 1.0
F13 B:LE0401 2.2 75.1 1.0
C08 B:LE0401 2.6 69.2 1.0
C07 B:LE0401 3.0 66.1 1.0
CB B:ALA166 3.3 34.8 1.0
CA B:ALA122 3.3 43.2 1.0
CB B:ALA122 3.5 45.9 1.0
N B:ALA122 3.5 39.3 1.0
C09 B:LE0401 3.8 65.5 1.0
C B:LEU121 4.1 38.9 1.0
O01 B:LE0401 4.1 61.9 1.0
CD1 B:LEU125 4.3 39.8 1.0
O03 B:LE0401 4.3 56.2 1.0
C06 B:LE0401 4.4 64.4 1.0
C02 B:LE0401 4.4 66.0 1.0
CB B:LEU121 4.5 37.8 1.0
CA B:ALA166 4.5 31.0 1.0
O B:LEU121 4.5 40.4 1.0
CB B:LEU125 4.6 41.8 1.0
C B:ALA122 4.7 35.6 1.0
CA B:LEU121 4.8 40.7 1.0
CG B:LEU125 4.9 44.9 1.0
OH B:TYR206 4.9 91.7 1.0
C B:ALA166 4.9 34.2 1.0
C10 B:LE0401 5.0 62.6 1.0

Reference:

R.Fricke, C.V.Swenson, L.T.Roe, N.X.Hamlish, B.Shah, Z.Zhang, E.Ficaretta, O.Ad, S.Smaga, C.L.Gee, A.Chatterjee, A.Schepartz. Expanding the Substrate Scope of Pyrrolysyl-Transfer Rna Synthetase Enzymes to Include Non-Alpha-Amino Acids in Vitro and in Vivo. Nat.Chem. 2023.
ISSN: ESSN 1755-4349
PubMed: 37264106
DOI: 10.1038/S41557-023-01224-Y
Page generated: Wed Jul 16 00:46:16 2025

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