Potassium in PDB 6ab8: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys, PDB code: 6ab8 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)	42.28 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.134, 43.893, 62.070, 90.00, 98.83, 90.00
R / Rfree (%)	17.2 / 21.3

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys 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 Zlys (pdb code 6ab8). 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 Zlys, PDB code: 6ab8:
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 Zlys


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 Zlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K507 b:67.0 occ:1.00 O A:PRO204 2.6 37.9 1.0 O A:ASP206 2.7 40.0 1.0 O A:HOH710 2.7 41.6 1.0 C A:PRO204 3.7 34.2 1.0 OE1 A:GLU207 3.7 58.4 1.0 O A:HOH759 3.8 38.5 1.0 C A:ASP206 3.9 46.6 1.0 CD A:GLU207 4.1 68.7 1.0 CA A:PRO204 4.3 32.7 1.0 OE2 A:GLU207 4.3 59.0 1.0 N A:ASP206 4.4 47.4 1.0 O A:ASN203 4.5 32.1 1.0 C A:LYS205 4.5 50.7 1.0 N A:LYS205 4.6 38.8 1.0 CA A:ASP206 4.7 39.1 1.0 NZ A:LYS435 4.8 41.0 1.0 CA A:LYS205 4.8 47.7 1.0 N A:GLU207 4.9 43.8 1.0 O A:LYS205 5.0 52.5 1.0 CA A:GLU207 5.0 50.1 1.0

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


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 Zlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K508 b:70.5 occ:1.00 O A:ARG442 2.8 25.7 1.0 O A:GLU341 2.9 16.5 1.0 O A:HOH756 3.0 30.7 1.0 OE1 A:GLU341 3.3 21.3 1.0 O A:HOH646 3.4 20.2 1.0 CB A:GLU341 3.5 13.9 1.0 CB A:ALA441 3.7 22.7 1.0 N A:ARG442 3.8 17.7 1.0 C A:ARG442 3.8 23.7 1.0 CG A:GLU341 3.8 13.0 1.0 CB A:ARG442 3.8 23.5 1.0 C A:GLU341 3.9 12.8 1.0 CA A:ARG442 4.0 17.6 1.0 CD A:GLU341 4.0 21.3 1.0 CA A:GLU341 4.1 12.7 1.0 N A:GLU341 4.4 15.0 1.0 C A:ALA441 4.5 21.0 1.0 O A:HOH686 4.5 26.4 1.0 CA A:ALA441 4.6 16.5 1.0 O A:HOH798 4.7 36.3 1.0 OG A:SER443 4.7 27.6 0.4 CG A:ARG442 4.8 22.9 1.0 CD2 A:LEU339 4.9 18.7 1.0 CB A:LEU339 4.9 20.2 1.0 CD1 A:LEU339 4.9 21.6 1.0 N A:SER443 5.0 21.4 0.4 N A:SER443 5.0 21.2 0.6

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