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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Bcnlys, PDB code: 6aaq 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 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.981, 44.244, 72.660, 90.00, 118.28, 90.00
R / Rfree (%)	17.5 / 20

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


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 Bcnlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K506 b:55.4 occ:1.00 O A:HOH609 2.5 31.7 1.0 O A:ASN203 2.9 24.8 1.0 O A:HOH736 3.0 32.1 1.0 O A:HOH852 3.0 38.4 1.0 O A:ASP206 3.3 33.2 1.0 O A:PRO204 3.6 32.5 1.0 CD2 A:LEU202 3.7 25.7 1.0 CG A:LEU202 3.7 20.4 1.0 C A:ASN203 3.9 26.4 1.0 CA A:PRO204 3.9 22.5 1.0 C A:PRO204 4.0 28.2 1.0 C A:ASP206 4.1 41.1 1.0 CD1 A:LEU202 4.1 19.7 1.0 CB A:ASP206 4.2 24.4 1.0 N A:ASP206 4.3 26.2 1.0 N A:PRO204 4.3 22.7 1.0 CA A:ASP206 4.4 29.6 1.0 O A:HOH658 4.8 43.3 1.0 O A:HOH796 4.8 23.9 1.0 N A:ASN203 4.9 20.7 1.0 N A:LYS205 4.9 29.7 1.0 CA A:ASN203 5.0 22.0 1.0

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


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 Bcnlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K507 b:61.2 occ:1.00 OE1 A:GLU341 2.7 20.3 1.0 O A:ARG442 2.8 24.3 1.0 O A:HOH775 3.5 28.4 1.0 CD A:GLU341 3.7 18.8 1.0 CB A:GLU341 3.7 13.7 1.0 C A:ARG442 3.8 25.1 1.0 CB A:ARG442 3.9 16.8 1.0 CG A:GLU341 3.9 16.0 1.0 O A:HOH882 4.1 36.2 1.0 O A:GLU341 4.1 15.8 1.0 CA A:ARG442 4.3 13.0 1.0 N A:ARG442 4.4 16.4 1.0 O A:HOH700 4.4 18.0 1.0 CB A:ALA441 4.6 19.3 1.0 CA A:GLU341 4.7 14.7 1.0 N A:SER443 4.8 28.5 1.0 OE2 A:GLU341 4.8 17.3 1.0 C A:GLU341 4.8 13.2 1.0 N A:GLU341 5.0 16.4 1.0

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


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 Bcnlys within 5.0Å range: probe atom residue distance (Å) B Occ A:K508 b:69.6 occ:1.00 O A:TYR446 2.7 22.0 1.0 O A:ALA441 2.8 23.9 1.0 O A:HOH605 3.1 27.2 1.0 N A:SER443 3.8 28.5 1.0 C A:TYR446 3.8 16.2 1.0 C A:ALA441 3.9 19.6 1.0 O A:SER443 3.9 31.3 1.0 CB A:SER443 4.0 38.6 1.0 O A:HOH771 4.0 26.9 1.0 CA A:ARG442 4.3 13.0 1.0 CA A:SER443 4.3 28.9 1.0 C A:ARG442 4.3 25.1 1.0 CA A:TYR447 4.4 14.5 1.0 O A:HOH677 4.5 29.2 1.0 C A:SER443 4.5 25.4 1.0 N A:ARG442 4.5 16.4 1.0 N A:TYR447 4.5 17.2 1.0 ND2 A:ASN241 4.6 23.8 1.0 N A:ASN448 4.7 18.5 1.0 CA A:TYR446 4.8 18.9 1.0 CB A:TYR446 4.9 21.2 1.0 N A:ALA441 5.0 19.3 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