Silicon in PDB 6abk: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys, PDB code: 6abk 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)	34.99 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.245, 43.906, 72.451, 90.00, 118.69, 90.00
R / Rfree (%)	15.9 / 18.9

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

Magnesium

(Mg)

3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range: probe atom residue distance (Å) B Occ A:Si505 b:23.9 occ:0.31 SI A:9VF505 0.0 23.9 0.3 NZ A:9VF505 0.7 24.7 0.3 CE A:9VF505 0.8 23.4 0.3 C7 A:9VF505 1.1 24.1 0.4 O6 A:9VF505 1.5 21.2 0.4 O8 A:9VF505 1.6 28.5 0.4 C7 A:9VF505 1.7 26.0 0.3 C4 A:9VF505 1.9 25.4 0.3 C3 A:9VF505 1.9 27.4 0.3 C5 A:9VF505 1.9 24.4 0.3 C1 A:9VF505 1.9 28.9 0.3 C5 A:9VF505 1.9 25.0 0.4 NZ A:9VF505 2.1 19.3 0.4 CG A:9VF505 2.2 21.4 0.3 O8 A:9VF505 2.3 26.7 0.3 C3 A:9VF505 2.5 27.6 0.4 SI A:9VF505 2.5 27.1 0.4 O6 A:9VF505 2.8 20.3 0.3 O6 A:9VF505 2.9 27.1 0.3 C1 A:9VF505 3.0 24.3 0.3 C7 A:9VF505 3.1 18.0 0.3 CE A:9VF505 3.1 17.8 0.4 CG A:9VF505 3.1 19.5 0.4 CD A:9VF505 3.2 19.8 0.4 CD A:9VF505 3.3 16.6 0.3 NZ A:9VF505 3.4 21.8 0.3 CB A:9VF505 3.6 20.7 0.3 O8 A:9VF505 3.8 16.2 0.3 C5 A:9VF505 3.8 23.3 0.3 SI A:9VF505 4.0 26.4 0.3 C4 A:9VF505 4.0 30.6 0.4 CZ3 A:TRP417 4.0 20.3 1.0 C1 A:9VF505 4.1 26.9 0.4 CE3 A:TRP417 4.2 16.2 1.0 CH2 A:TRP417 4.2 20.5 1.0 CB A:ALA306 4.2 18.1 1.0 CD2 A:TRP417 4.4 16.7 1.0 CZ2 A:TRP417 4.4 18.8 1.0 CA A:ALA306 4.4 14.7 1.0 CB A:9VF505 4.5 22.0 0.4 O A:ALA302 4.5 18.0 1.0 CD1 A:LEU309 4.5 18.6 1.0 CE2 A:TRP417 4.5 16.8 1.0 N A:ALA306 4.6 14.1 1.0 CE A:9VF505 4.6 21.5 0.3 C4 A:9VF505 4.7 31.4 0.3 CA A:9VF505 4.8 20.7 0.3 N A:9VF505 5.0 24.6 0.3

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


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range: probe atom residue distance (Å) B Occ A:Si505 b:27.1 occ:0.41 SI A:9VF505 0.0 27.1 0.4 O6 A:9VF505 1.1 27.1 0.3 C7 A:9VF505 1.3 26.0 0.3 C5 A:9VF505 1.3 23.3 0.3 C3 A:9VF505 1.8 27.4 0.3 O8 A:9VF505 1.8 26.7 0.3 C4 A:9VF505 1.9 30.6 0.4 C5 A:9VF505 1.9 25.0 0.4 C1 A:9VF505 1.9 26.9 0.4 C3 A:9VF505 1.9 27.6 0.4 SI A:9VF505 2.1 26.4 0.3 C1 A:9VF505 2.2 28.9 0.3 NZ A:9VF505 2.4 24.7 0.3 SI A:9VF505 2.5 23.9 0.3 C1 A:9VF505 2.6 24.3 0.3 O6 A:9VF505 2.9 21.2 0.4 C4 A:9VF505 3.0 31.4 0.3 CE A:9VF505 3.3 23.4 0.3 O8 A:9VF505 3.3 28.5 0.4 C7 A:9VF505 3.4 24.1 0.4 C3 A:9VF505 3.7 25.8 0.3 CB A:ALA306 3.9 18.1 1.0 C4 A:9VF505 3.9 25.4 0.3 C5 A:9VF505 3.9 24.4 0.3 CZ2 A:TRP417 4.1 18.8 1.0 OD1 A:ASP408 4.2 25.0 1.0 CE2 A:TRP417 4.3 16.8 1.0 CG1 A:ILE413 4.4 17.6 1.0 CH2 A:TRP417 4.6 20.5 1.0 CG A:9VF505 4.6 21.4 0.3 NZ A:9VF505 4.6 19.3 0.4 NE1 A:TRP417 4.7 20.8 1.0 CA A:ALA306 4.8 14.7 1.0 CD2 A:TRP417 4.9 16.7 1.0 CE1 A:PHE384 5.0 30.2 1.0 NZ A:9VF505 5.0 21.8 0.3

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


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 3 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Teoclys within 5.0Å range: probe atom residue distance (Å) B Occ A:Si505 b:26.4 occ:0.28 SI A:9VF505 0.0 26.4 0.3 C3 A:9VF505 1.7 27.6 0.4 C3 A:9VF505 1.8 25.8 0.3 C4 A:9VF505 1.9 31.4 0.3 C5 A:9VF505 1.9 23.3 0.3 C1 A:9VF505 1.9 24.3 0.3 SI A:9VF505 2.1 27.1 0.4 C1 A:9VF505 2.1 26.9 0.4 C4 A:9VF505 2.6 30.6 0.4 O6 A:9VF505 2.7 27.1 0.3 C1 A:9VF505 2.8 28.9 0.3 C7 A:9VF505 3.2 26.0 0.3 C3 A:9VF505 3.7 27.4 0.3 O8 A:9VF505 3.8 26.7 0.3 C5 A:9VF505 3.9 25.0 0.4 NZ A:9VF505 3.9 24.7 0.3 SI A:9VF505 4.0 23.9 0.3 CD2 A:LEU407 4.0 31.1 1.0 CE A:MET276 4.0 53.3 1.0 CE1 A:PHE384 4.1 30.2 1.0 SD A:MET276 4.3 49.0 1.0 CG A:LEU407 4.3 31.5 1.0 CD1 A:TRP411 4.4 25.7 1.0 O8 A:9VF505 4.4 28.5 0.4 CB A:ALA306 4.5 18.1 1.0 CG A:TRP411 4.6 23.4 1.0 CE A:9VF505 4.7 23.4 0.3 CB A:LEU407 4.7 34.9 1.0 O6 A:9VF505 4.8 21.2 0.4 NE1 A:TRP411 4.8 25.2 1.0 C5 A:9VF505 4.8 24.4 0.3 CD1 A:PHE384 4.8 30.1 1.0 C7 A:9VF505 4.9 24.1 0.4 CZ A:PHE384 4.9 29.7 1.0 OD1 A:ASP408 5.0 25.0 1.0 CD1 A:ILE405 5.0 31.8 1.0 CB A:TRP411 5.0 24.4 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