Fluorine in PDB 6aad: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys

All present enzymatic activity of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys:
6.1.1.26;

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys, PDB code: 6aad was solved by T.Yanagisawa, M.Kuratani, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.02 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.917, 43.782, 72.475, 90.00, 119.05, 90.00
R / Rfree (%)	17.1 / 19.5

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Potassium	(K)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys (pdb code 6aad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys, PDB code: 6aad:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:63.4 occ:1.00 F5 A:9TU505 0.0 63.4 1.0 C4 A:9TU505 1.3 57.3 1.0 F6 A:9TU505 2.2 61.4 1.0 F7 A:9TU505 2.2 62.5 1.0 C3 A:9TU505 2.4 45.3 1.0 C9 A:9TU505 2.7 35.2 1.0 C8 A:9TU505 2.8 30.6 1.0 CB A:ALA306 3.2 18.4 1.0 SD A:MET276 3.4 33.1 0.6 O A:ALA302 3.4 19.7 1.0 N2 A:9TU505 3.7 46.4 1.0 C A:ALA302 3.7 18.3 1.0 N1 A:9TU505 3.8 44.5 1.0 CE A:MET276 3.9 38.2 0.6 CA A:PRO303 3.9 19.4 1.0 N A:PRO303 4.0 18.8 1.0 C10 A:9TU505 4.0 23.3 1.0 C27 A:9TU505 4.0 34.7 1.0 CB A:ALA302 4.0 21.4 1.0 CA A:ALA302 4.4 17.9 1.0 CA A:ALA306 4.5 16.6 1.0 CD2 A:TRP411 4.6 23.6 1.0 CG A:TRP411 4.6 22.6 1.0 N A:ALA306 4.6 16.7 1.0 CE1 A:PHE384 4.7 35.9 1.0 CE2 A:TRP411 4.8 27.1 1.0 CB A:PRO303 4.8 23.4 1.0 C25 A:9TU505 4.9 25.0 1.0 C A:PRO303 4.9 20.5 1.0 CD1 A:TRP411 4.9 27.5 1.0 CZ A:PHE384 4.9 31.8 1.0 C26 A:9TU505 4.9 35.9 1.0 O A:PRO303 4.9 18.6 1.0 C11 A:9TU505 4.9 22.6 1.0 O12 A:9TU505 4.9 27.8 1.0 CD A:PRO303 5.0 21.8 1.0 NE1 A:TRP411 5.0 28.1 1.0 CE3 A:TRP411 5.0 28.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:61.4 occ:1.00 F6 A:9TU505 0.0 61.4 1.0 C4 A:9TU505 1.3 57.3 1.0 F7 A:9TU505 2.2 62.5 1.0 F5 A:9TU505 2.2 63.4 1.0 C3 A:9TU505 2.3 45.3 1.0 N1 A:9TU505 2.8 44.5 1.0 SD A:MET276 2.9 33.1 0.6 CE A:MET276 3.0 38.2 0.6 CD2 A:LEU407 3.2 34.6 1.0 N2 A:9TU505 3.3 46.4 1.0 CE1 A:PHE384 3.4 35.9 1.0 C8 A:9TU505 3.5 30.6 1.0 C9 A:9TU505 3.8 35.2 1.0 CZ A:PHE384 3.9 31.8 1.0 CG A:LEU407 4.1 32.5 1.0 CD1 A:PHE384 4.4 32.6 1.0 CG A:MET276 4.4 37.5 0.4 CG1 A:VAL383 4.5 34.2 1.0 CG A:MET276 4.5 38.4 0.6 NE1 A:TRP411 4.6 28.1 1.0 CD1 A:TRP411 4.6 27.5 1.0 C27 A:9TU505 4.6 34.7 1.0 CB A:ALA302 4.8 21.4 1.0 CB A:MET276 5.0 37.5 0.6 SD A:MET276 5.0 39.6 0.4 CE2 A:TRP411 5.0 27.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys


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 Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:62.5 occ:1.00 F7 A:9TU505 0.0 62.5 1.0 C4 A:9TU505 1.3 57.3 1.0 F6 A:9TU505 2.2 61.4 1.0 F5 A:9TU505 2.2 63.4 1.0 C3 A:9TU505 2.3 45.3 1.0 N2 A:9TU505 2.6 46.4 1.0 CD1 A:TRP411 2.8 27.5 1.0 CG A:TRP411 2.9 22.6 1.0 NE1 A:TRP411 3.1 28.1 1.0 N1 A:9TU505 3.1 44.5 1.0 SD A:MET276 3.2 33.1 0.6 CD2 A:TRP411 3.2 23.6 1.0 CE2 A:TRP411 3.3 27.1 1.0 C8 A:9TU505 3.5 30.6 1.0 CB A:TRP411 3.7 23.1 1.0 CD2 A:LEU407 4.0 34.6 1.0 CB A:ALA306 4.0 18.4 1.0 CE3 A:TRP411 4.2 28.2 1.0 CG A:LEU407 4.2 32.5 1.0 C9 A:9TU505 4.2 35.2 1.0 CZ2 A:TRP411 4.3 28.7 1.0 C27 A:9TU505 4.3 34.7 1.0 CE A:MET276 4.4 38.2 0.6 CG A:MET276 4.7 37.5 0.4 CG A:MET276 4.7 38.4 0.6 O A:LEU407 4.8 26.0 1.0 CZ3 A:TRP411 4.9 29.5 1.0 CH2 A:TRP411 5.0 26.8 1.0

T.Yanagisawa, M.Kuratani, E.Seki, N.Hino, K.Sakamoto, S.Yokoyama. Structural Basis For Genetic-Code Expansion with Bulky Lysine Derivatives By An Engineered Pyrrolysyl-Trna Synthetase. Cell Chem Biol V. 26 936 2019.
ISSN: ESSN 2451-9456
PubMed: 31031143
DOI: 10.1016/J.CHEMBIOL.2019.03.008