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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Ptmdzlys, PDB code: 6abm 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 / 1.37
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.604, 44.209, 72.553, 90.00, 118.48, 90.00
R / Rfree (%)	16.2 / 19.9

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Ptmdzlys 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 Ptmdzlys (pdb code 6abm). 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 Ptmdzlys, PDB code: 6abm:
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 Ptmdzlys


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 Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:73.4 occ:1.00 F5 A:9VR505 0.0 73.4 1.0 C4 A:9VR505 1.3 72.5 1.0 F6 A:9VR505 2.1 74.6 1.0 F7 A:9VR505 2.2 74.8 1.0 C3 A:9VR505 2.4 65.2 1.0 SD A:MET276 2.6 28.2 0.5 C9 A:9VR505 2.7 55.6 1.0 CE A:MET276 2.9 43.0 0.5 C8 A:9VR505 2.9 57.6 1.0 N1 A:9VR505 3.4 65.3 1.0 N2 A:9VR505 3.7 65.2 1.0 C10 A:9VR505 3.9 53.0 1.0 CE1 A:PHE384 4.0 39.8 1.0 CD2 A:LEU407 4.1 33.0 1.0 CB A:ALA302 4.2 22.9 1.0 CG A:MET276 4.2 35.0 0.5 CZ A:PHE384 4.2 31.8 1.0 C27 A:9VR505 4.3 52.5 1.0 CG A:MET276 4.4 33.3 0.5 NE1 A:TRP411 4.5 25.0 1.0 C A:ALA302 4.5 19.2 1.0 N A:PRO303 4.5 20.1 1.0 CA A:PRO303 4.6 23.0 1.0 CG A:LEU407 4.6 35.6 1.0 CE2 A:TRP411 4.6 26.4 1.0 O A:ALA302 4.6 20.9 1.0 CD1 A:TRP411 4.7 29.2 1.0 SD A:MET276 4.7 50.7 0.5 CB A:ALA306 4.7 18.8 1.0 CG A:TRP411 4.8 28.0 1.0 CD2 A:TRP411 4.9 25.2 1.0 CA A:ALA302 5.0 16.5 1.0

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


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 Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:74.6 occ:1.00 F6 A:9VR505 0.0 74.6 1.0 C4 A:9VR505 1.3 72.5 1.0 F5 A:9VR505 2.1 73.4 1.0 F7 A:9VR505 2.2 74.8 1.0 C3 A:9VR505 2.3 65.2 1.0 CD1 A:TRP411 2.8 29.2 1.0 N1 A:9VR505 2.8 65.3 1.0 NE1 A:TRP411 2.8 25.0 1.0 N2 A:9VR505 2.8 65.2 1.0 CG A:LEU407 3.0 35.6 1.0 CD2 A:LEU407 3.1 33.0 1.0 SD A:MET276 3.2 28.2 0.5 CG A:TRP411 3.4 28.0 1.0 CE2 A:TRP411 3.5 26.4 1.0 C8 A:9VR505 3.7 57.6 1.0 CD2 A:TRP411 3.8 25.2 1.0 CD1 A:LEU407 4.0 27.6 1.0 CB A:LEU407 4.1 32.9 1.0 CE A:MET276 4.1 43.0 0.5 C9 A:9VR505 4.1 55.6 1.0 CB A:TRP411 4.3 23.7 1.0 O A:LEU407 4.3 27.6 1.0 CZ2 A:TRP411 4.4 23.4 1.0 CG A:MET276 4.4 35.0 0.5 CG A:MET276 4.6 33.3 0.5 CA A:MET276 4.7 30.4 0.5 CA A:MET276 4.7 30.5 0.5 C A:LEU407 4.7 30.9 1.0 C27 A:9VR505 4.8 52.5 1.0 CE3 A:TRP411 4.9 27.8 1.0 O A:ARG275 4.9 50.6 1.0

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


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 Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:F505 b:74.8 occ:1.00 F7 A:9VR505 0.0 74.8 1.0 C4 A:9VR505 1.3 72.5 1.0 F6 A:9VR505 2.2 74.6 1.0 F5 A:9VR505 2.2 73.4 1.0 C3 A:9VR505 2.4 65.2 1.0 CD2 A:TRP411 3.0 25.2 1.0 C8 A:9VR505 3.0 57.6 1.0 CG A:TRP411 3.0 28.0 1.0 N2 A:9VR505 3.1 65.2 1.0 CB A:ALA306 3.2 18.8 1.0 C9 A:9VR505 3.2 55.6 1.0 CE2 A:TRP411 3.3 26.4 1.0 CD1 A:TRP411 3.4 29.2 1.0 SD A:MET276 3.4 28.2 0.5 NE1 A:TRP411 3.5 25.0 1.0 CE3 A:TRP411 3.6 27.8 1.0 N1 A:9VR505 3.6 65.3 1.0 CB A:TRP411 3.7 23.7 1.0 CZ2 A:TRP411 4.1 23.4 1.0 CA A:PRO303 4.1 23.0 1.0 C27 A:9VR505 4.2 52.5 1.0 CZ3 A:TRP411 4.3 29.2 1.0 C10 A:9VR505 4.4 53.0 1.0 O A:ALA302 4.4 20.9 1.0 CH2 A:TRP411 4.5 25.1 1.0 CE A:MET276 4.5 43.0 0.5 N A:PRO303 4.6 20.1 1.0 CA A:ALA306 4.7 17.6 1.0 C A:ALA302 4.7 19.2 1.0 CB A:PRO303 4.7 22.7 1.0 O A:PRO303 4.8 18.6 1.0 CG A:MET276 4.9 35.0 0.5 C A:PRO303 4.9 18.6 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