Potassium in PDB 6aaz: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS

All present enzymatic activity of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS:
6.1.1.26;

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS, PDB code: 6aaz 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)	39.52 / 1.84
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.378, 44.107, 72.673, 90.00, 118.63, 90.00
R / Rfree (%)	23.1 / 27.5

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Potassium atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS (pdb code 6aaz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS, PDB code: 6aaz:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:K507 b:42.1 occ:1.00 O A:ARG442 2.6 23.4 1.0 O A:HOH761 2.7 24.0 1.0 OE1 A:GLU341 2.7 16.9 1.0 O A:HOH786 3.3 22.3 1.0 CB A:GLU341 3.4 13.3 1.0 CB A:ARG442 3.5 18.4 1.0 CD A:GLU341 3.6 14.5 1.0 C A:ARG442 3.6 22.1 1.0 CG A:GLU341 3.6 13.5 1.0 O A:GLU341 3.6 15.8 1.0 O A:HOH718 3.7 23.7 1.0 CA A:ARG442 3.9 17.2 1.0 O A:HOH697 3.9 14.8 1.0 N A:ARG442 3.9 20.0 1.0 CB A:ALA441 4.3 21.9 1.0 C A:GLU341 4.4 12.8 1.0 CA A:GLU341 4.4 14.5 1.0 CG A:ARG442 4.6 16.4 1.0 OG A:SER443 4.7 24.2 0.4 OE2 A:GLU341 4.7 14.8 1.0 N A:GLU341 4.7 17.2 1.0 N A:SER443 4.8 22.1 1.0 C A:ALA441 4.8 20.2 1.0 CD A:ARG442 4.9 14.3 1.0 NZ A:LYS438 4.9 42.5 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:K508 b:78.9 occ:1.00 OE1 A:GLU218 2.9 38.4 1.0 NE A:ARG217 3.2 36.1 1.0 CG A:GLU218 3.5 32.6 1.0 CD A:GLU218 3.6 37.9 1.0 CD A:ARG217 3.6 35.9 1.0 CG A:ARG217 4.1 30.0 1.0 CZ A:ARG217 4.3 36.8 1.0 NH2 A:ARG217 4.5 35.5 1.0 OE2 A:GLU218 4.8 36.6 1.0 CB A:GLU218 4.9 30.5 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:K509 b:58.4 occ:1.00 O A:HOH792 3.1 36.7 1.0 O A:ASP433 3.1 20.6 1.0 CG A:LYS435 3.6 31.4 1.0 C A:ASP433 4.2 25.1 1.0 O A:HOH843 4.3 31.8 1.0 CB A:PRO204 4.4 28.8 1.0 CD A:LYS435 4.4 34.6 1.0 CB A:ASP433 4.4 26.7 1.0 N A:LYS435 4.6 24.1 1.0 CG A:PRO204 4.7 29.5 1.0 CB A:LYS435 4.8 29.2 1.0 CA A:LYS435 4.9 25.7 1.0 CA A:ASP433 4.9 22.0 1.0 C A:PHE434 4.9 26.1 1.0 CA A:PRO204 5.0 30.7 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