Bromine in PDB 6abl: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Obrzlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Obrzlys, PDB code: 6abl 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)	35.06 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.671, 44.281, 72.654, 90.00, 118.43, 90.00
R / Rfree (%)	15.7 / 19.3

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

Magnesium

(Mg)

3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Obrzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:0.7 occ:0.73 BR A:9VL505 0.0 0.7 0.7 BR A:9VL505 0.9 71.7 0.2 C16 A:9VL505 1.9 81.2 0.7 C16 A:9VL505 2.5 64.5 0.2 C18 A:9VL505 2.7 72.3 0.7 C15 A:9VL505 3.0 67.1 0.7 C18 A:9VL505 3.1 62.5 0.2 O13 A:9VL505 3.2 47.6 0.7 CB A:ALA302 3.3 24.4 1.0 CE1 A:PHE384 3.3 45.3 1.0 CE A:MET276 3.4 31.8 0.6 C14 A:9VL505 3.5 57.6 0.7 O13 A:9VL505 3.6 48.8 0.2 C15 A:9VL505 3.6 58.1 0.2 CZ A:PHE384 3.7 34.6 1.0 CE A:9VL505 3.8 34.2 0.7 NZ A:9VL505 3.8 44.2 0.2 O A:ALA302 3.9 22.5 1.0 C A:ALA302 3.9 23.1 1.0 SD A:MET276 4.0 30.0 0.6 C19 A:9VL505 4.0 66.9 0.7 C14 A:9VL505 4.1 53.0 0.2 CA A:ALA302 4.1 17.9 1.0 C11 A:9VL505 4.2 43.9 0.7 C21 A:9VL505 4.2 65.7 0.7 C11 A:9VL505 4.2 45.0 0.2 NZ A:9VL505 4.4 35.2 0.7 CB A:ALA306 4.4 20.4 1.0 C19 A:9VL505 4.4 61.2 0.2 N A:PRO303 4.5 22.9 1.0 CD1 A:PHE384 4.6 41.7 1.0 C20 A:9VL505 4.6 65.5 0.7 C21 A:9VL505 4.8 58.2 0.2 CA A:PRO303 4.9 24.1 1.0

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


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Obrzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Br505 b:71.7 occ:0.22 BR A:9VL505 0.0 71.7 0.2 BR A:9VL505 0.9 0.7 0.7 C16 A:9VL505 1.9 81.2 0.7 C16 A:9VL505 1.9 64.5 0.2 O13 A:9VL505 2.5 47.6 0.7 C15 A:9VL505 2.7 67.1 0.7 C18 A:9VL505 2.8 62.5 0.2 C18 A:9VL505 2.9 72.3 0.7 C15 A:9VL505 2.9 58.1 0.2 O13 A:9VL505 3.0 48.8 0.2 C14 A:9VL505 3.1 57.6 0.7 O A:ALA302 3.3 22.5 1.0 C14 A:9VL505 3.3 53.0 0.2 CB A:ALA302 3.3 24.4 1.0 C A:ALA302 3.6 23.1 1.0 C11 A:9VL505 3.6 43.9 0.7 CB A:ALA306 3.7 20.4 1.0 CE A:9VL505 3.7 34.2 0.7 NZ A:9VL505 3.8 44.2 0.2 CA A:ALA302 3.8 17.9 1.0 C11 A:9VL505 3.9 45.0 0.2 C21 A:9VL505 3.9 65.7 0.7 NZ A:9VL505 4.0 35.2 0.7 CE A:MET276 4.1 31.8 0.6 CE1 A:PHE384 4.1 45.3 1.0 C19 A:9VL505 4.1 66.9 0.7 C19 A:9VL505 4.1 61.2 0.2 C21 A:9VL505 4.2 58.2 0.2 N A:PRO303 4.3 22.9 1.0 CZ A:PHE384 4.3 34.6 1.0 SD A:MET276 4.4 30.0 0.6 C20 A:9VL505 4.5 65.5 0.7 CA A:PRO303 4.6 24.1 1.0 O12 A:9VL505 4.6 49.7 0.7 N A:ALA306 4.6 16.8 1.0 C20 A:9VL505 4.7 59.6 0.2 CA A:ALA306 4.7 16.7 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