Potassium in PDB 6ab0: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys, PDB code: 6ab0 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)	35.07 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.506, 44.280, 72.671, 90.00, 118.58, 90.00
R / Rfree (%)	17 / 19.9

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys 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 Pampylys (pdb code 6ab0). 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 Pampylys, PDB code: 6ab0:
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 Pampylys


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:K506 b:66.3 occ:1.00 O A:HOH606 2.6 32.4 1.0 O A:ASN203 2.9 26.8 1.0 O A:HOH783 2.9 35.4 1.0 O A:HOH853 2.9 43.7 1.0 O A:ASP206 3.2 33.2 1.0 CD2 A:LEU202 3.5 30.0 1.0 O A:HOH845 3.5 55.5 1.0 CG A:LEU202 3.6 24.8 1.0 O A:PRO204 3.8 34.0 1.0 C A:ASN203 3.8 26.8 1.0 CA A:PRO204 3.9 23.5 1.0 C A:PRO204 4.0 28.9 1.0 C A:ASP206 4.0 39.0 1.0 CD1 A:LEU202 4.0 24.1 1.0 CB A:ASP206 4.1 26.1 1.0 N A:ASP206 4.2 27.8 1.0 N A:PRO204 4.3 24.2 1.0 CA A:ASP206 4.4 32.8 1.0 O A:HOH668 4.6 41.9 1.0 O A:HOH797 4.8 26.7 1.0 N A:ASN203 4.8 21.8 1.0 N A:LYS205 4.9 28.6 1.0 CA A:ASN203 4.9 25.3 1.0 CB A:LEU202 5.0 23.4 1.0

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


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:K507 b:77.3 occ:1.00 O A:ARG442 2.8 25.4 1.0 OE1 A:GLU341 2.8 22.9 1.0 O A:HOH799 3.0 30.0 1.0 O A:HOH877 3.4 48.9 1.0 CB A:GLU341 3.5 16.8 1.0 O A:GLU341 3.7 17.8 1.0 CD A:GLU341 3.7 20.5 1.0 C A:ARG442 3.8 23.4 1.0 CG A:GLU341 3.8 19.5 1.0 CB A:ARG442 3.9 18.8 1.0 O A:HOH882 4.0 44.2 1.0 O A:HOH688 4.2 19.8 1.0 CA A:ARG442 4.3 18.4 1.0 N A:ARG442 4.3 19.8 1.0 CB A:ALA441 4.4 23.2 1.0 CA A:GLU341 4.4 17.4 1.0 C A:GLU341 4.5 17.1 1.0 N A:GLU341 4.6 17.5 1.0 OG A:SER443 4.7 26.0 0.3 N A:SER443 4.9 27.8 0.7 N A:SER443 4.9 28.2 0.3 OE2 A:GLU341 4.9 19.2 1.0

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


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:K508 b:97.4 occ:1.00 O A:GLY335 2.7 47.9 1.0 O A:HIS338 2.7 19.7 1.0 CE A:LYS438 3.2 67.7 1.0 CD A:LYS438 3.3 75.8 1.0 O A:HOH884 3.4 49.3 1.0 CG A:LYS438 3.6 73.0 1.0 OD1 A:ASN436 3.7 44.8 1.0 CG2 A:ILE437 3.8 23.8 1.0 C A:HIS338 3.9 19.3 1.0 C A:GLY335 3.9 57.2 1.0 CD2 A:LEU339 4.1 20.7 1.0 NZ A:LYS438 4.3 63.6 1.0 N A:GLY335 4.4 51.5 1.0 N A:HIS338 4.6 19.5 1.0 CG A:ASN436 4.6 63.0 1.0 N A:LYS438 4.7 27.3 1.0 N A:LEU339 4.7 18.4 1.0 CA A:LEU339 4.7 18.1 1.0 O A:HOH762 4.8 36.7 1.0 ND2 A:ASN436 4.8 65.1 1.0 CA A:GLY335 4.8 38.3 1.0 N A:LYS336 4.8 49.9 1.0 CA A:HIS338 4.9 18.7 1.0 CB A:LYS438 4.9 33.0 1.0 CA A:LYS336 4.9 26.6 1.0 CG A:LEU339 5.0 19.1 1.0 C A:LYS336 5.0 34.8 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