Potassium 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:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	3 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Ptmdzlys, PDB code: 6abm:
Jump to Potassium binding site number: 1; 2;

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


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 Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K506 b:68.5 occ:1.00 O A:HOH714 2.6 29.9 1.0 O A:PRO204 2.7 30.0 1.0 O A:ASP206 2.7 63.7 1.0 O A:HOH866 2.7 49.7 1.0 O A:HOH863 2.9 70.1 1.0 C A:PRO204 3.7 35.6 1.0 C A:ASP206 4.0 50.2 1.0 O A:HOH791 4.0 36.6 1.0 CA A:PRO204 4.2 25.2 1.0 O A:HOH864 4.3 42.0 1.0 O A:ASN203 4.5 24.4 1.0 N A:ASP206 4.6 25.6 1.0 N A:LYS205 4.8 27.2 1.0 C A:LYS205 4.8 27.5 1.0 CA A:GLU207 4.8 54.1 1.0 N A:GLU207 4.8 39.0 1.0 CA A:ASP206 4.9 25.2 1.0

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


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 Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K508 b:70.1 occ:1.00 O A:ILE372 2.6 20.4 1.0 OD1 A:ASN368 2.8 28.8 1.0 O A:HOH623 2.8 56.5 1.0 O A:HOH828 2.9 47.8 1.0 C A:ILE372 3.3 21.0 1.0 CA A:ASP373 3.7 20.9 1.0 N A:ASP373 3.8 21.0 1.0 OD1 A:ASP373 3.8 61.9 1.0 CG A:ASN368 3.9 29.4 1.0 O A:LEU367 3.9 19.4 1.0 N A:ASN368 4.0 17.4 1.0 CA A:ASN368 4.0 21.2 1.0 C A:LEU367 4.0 19.0 1.0 CD1 A:PHE374 4.1 20.6 1.0 N A:ILE372 4.2 19.1 1.0 CE1 A:PHE374 4.2 20.3 1.0 CA A:ILE372 4.4 20.4 1.0 CB A:LEU367 4.5 17.8 1.0 CB A:ASN368 4.6 20.8 1.0 C A:ASP373 4.6 20.7 1.0 N A:PHE374 4.7 19.9 1.0 CG A:ASP373 4.7 55.1 1.0 CB A:ASP373 4.8 23.7 1.0 O A:HOH719 4.8 47.7 1.0 C A:GLY371 4.9 34.0 1.0 CA A:LEU367 4.9 17.1 1.0 ND2 A:ASN368 5.0 25.3 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