Chlorine in PDB 6ab2: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys, PDB code: 6ab2 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)	35.07 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.419, 43.887, 72.386, 90.00, 119.45, 90.00
R / Rfree (%)	17 / 19.8

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

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

The binding sites of Chlorine atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys (pdb code 6ab2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys, PDB code: 6ab2:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:67.7 occ:0.42 CL A:9V6505 0.0 67.7 0.4 CL A:9V6506 0.5 68.4 0.5 C16 A:9V6506 1.4 59.3 0.5 C16 A:9V6505 1.8 58.2 0.4 C18 A:9V6506 2.3 54.6 0.5 C15 A:9V6506 2.6 50.4 0.5 O13 A:9V6505 2.7 37.8 0.4 C18 A:9V6505 2.7 54.2 0.4 C15 A:9V6505 2.7 48.8 0.4 O13 A:9V6506 3.0 38.6 0.5 C14 A:9V6505 3.1 43.4 0.4 C14 A:9V6506 3.1 44.7 0.5 CB A:ALA302 3.2 20.8 1.0 CE1 A:PHE384 3.4 46.6 1.0 C11 A:9V6506 3.4 36.9 0.5 C19 A:9V6506 3.6 51.9 0.5 NZ A:9V6506 3.6 32.9 0.5 CZ A:PHE384 3.8 42.5 1.0 C21 A:9V6506 3.8 48.8 0.5 CE A:MET276 3.8 42.8 1.0 O A:ALA302 3.8 19.7 1.0 CD A:9V6506 3.8 36.4 0.5 CA A:ALA302 4.0 17.8 1.0 C11 A:9V6505 4.0 33.4 0.4 C A:ALA302 4.0 19.4 1.0 C19 A:9V6505 4.0 51.6 0.4 C21 A:9V6505 4.0 47.9 0.4 C20 A:9V6506 4.2 49.7 0.5 O12 A:9V6506 4.2 39.0 0.5 CE A:9V6506 4.4 33.1 0.5 CB A:ALA306 4.4 18.3 1.0 NZ A:9V6505 4.4 33.5 0.4 SD A:MET276 4.5 34.3 1.0 C20 A:9V6505 4.5 48.9 0.4 CD1 A:PHE384 4.6 70.9 1.0 N A:PRO303 4.8 17.6 1.0 CH2 A:TRP417 4.8 24.8 1.0 O12 A:9V6505 5.0 30.4 0.4

Chlorine binding site 2 out of 2 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oclzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:68.4 occ:0.47 CL A:9V6506 0.0 68.4 0.5 CL A:9V6505 0.5 67.7 0.4 C16 A:9V6506 1.7 59.3 0.5 C16 A:9V6505 1.8 58.2 0.4 O13 A:9V6505 2.2 37.8 0.4 C15 A:9V6505 2.5 48.8 0.4 O13 A:9V6506 2.7 38.6 0.5 C14 A:9V6505 2.7 43.4 0.4 C18 A:9V6506 2.7 54.6 0.5 C15 A:9V6506 2.7 50.4 0.5 C18 A:9V6505 2.9 54.2 0.4 C14 A:9V6506 3.1 44.7 0.5 C11 A:9V6506 3.1 36.9 0.5 CB A:ALA302 3.2 20.8 1.0 NZ A:9V6506 3.2 32.9 0.5 CE1 A:PHE384 3.3 46.6 1.0 CD A:9V6506 3.3 36.4 0.5 C11 A:9V6505 3.5 33.4 0.4 CZ A:PHE384 3.6 42.5 1.0 C21 A:9V6505 3.9 47.9 0.4 CA A:ALA302 3.9 17.8 1.0 CE A:9V6506 3.9 33.1 0.5 O A:ALA302 3.9 19.7 1.0 NZ A:9V6505 3.9 33.5 0.4 O12 A:9V6506 4.0 39.0 0.5 C19 A:9V6506 4.0 51.9 0.5 C21 A:9V6506 4.0 48.8 0.5 C A:ALA302 4.1 19.4 1.0 CE A:MET276 4.1 42.8 1.0 C19 A:9V6505 4.1 51.6 0.4 CD1 A:PHE384 4.4 70.9 1.0 O12 A:9V6505 4.5 30.4 0.4 C20 A:9V6505 4.5 48.9 0.4 CH2 A:TRP417 4.5 24.8 1.0 C20 A:9V6506 4.5 49.7 0.5 CG A:9V6506 4.6 38.0 0.5 CB A:ALA306 4.7 18.3 1.0 SD A:MET276 4.9 34.3 1.0 CZ2 A:TRP417 4.9 22.3 1.0 CZ3 A:TRP417 4.9 20.8 1.0 CE2 A:PHE384 5.0 44.9 1.0 N A:PRO303 5.0 17.6 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