Magnesium 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
Potassium	(K)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Ptmdzlys, PDB code: 6abm:
Jump to Magnesium binding site number: 1; 2; 3;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg501 b:18.7 occ:1.00 O1B A:ATP504 2.0 18.7 1.0 O2G A:ATP504 2.1 19.7 1.0 O A:HOH744 2.1 22.1 1.0 O A:HOH669 2.1 21.8 1.0 O A:HOH778 2.1 27.4 1.0 O A:HOH645 2.1 18.1 1.0 PG A:ATP504 3.2 19.2 1.0 PB A:ATP504 3.3 18.4 1.0 O3B A:ATP504 3.5 17.9 1.0 O3G A:ATP504 3.8 23.1 1.0 NH1 A:ARG330 3.9 18.6 1.0 NE2 A:HIS338 4.0 19.3 1.0 O A:HOH853 4.1 60.0 1.0 OE2 A:GLU332 4.2 18.9 1.0 O3A A:ATP504 4.3 17.0 1.0 O2B A:ATP504 4.4 19.1 1.0 OE1 A:GLU332 4.4 23.9 1.0 CD2 A:HIS338 4.5 18.2 1.0 O1G A:ATP504 4.5 19.9 1.0 OE1 A:GLN287 4.6 67.9 1.0 N7 A:ATP504 4.7 15.5 1.0 NE2 A:GLN287 4.7 59.7 1.0 CD A:GLU332 4.8 20.4 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg502 b:19.8 occ:1.00 OG A:SER399 2.1 19.5 1.0 O2A A:ATP504 2.1 19.7 1.0 O A:HOH772 2.1 24.6 1.0 O2B A:ATP504 2.1 19.1 1.0 OE2 A:GLU396 2.2 19.1 1.0 O A:HOH648 2.2 21.8 1.0 CD A:GLU396 3.1 23.8 1.0 CB A:SER399 3.2 18.5 1.0 PA A:ATP504 3.3 17.7 1.0 MG A:MG503 3.3 23.7 1.0 PB A:ATP504 3.3 18.4 1.0 O3A A:ATP504 3.4 17.0 1.0 OE1 A:GLU396 3.4 22.2 1.0 O A:HOH722 4.0 31.8 1.0 OD2 A:ASP389 4.1 25.5 1.0 O3B A:ATP504 4.1 17.9 1.0 O1A A:ATP504 4.2 18.0 1.0 OD1 A:ASP389 4.2 22.0 1.0 CA A:SER399 4.3 16.9 1.0 O A:HOH815 4.3 32.0 1.0 O3' A:ATP504 4.3 16.9 1.0 N A:SER399 4.3 15.6 1.0 CG A:GLU396 4.4 17.4 1.0 O5' A:ATP504 4.5 16.8 1.0 CG A:ASP389 4.5 23.7 1.0 O1B A:ATP504 4.6 18.7 1.0 C3' A:ATP504 4.7 15.7 1.0 OXT A:9VR505 4.7 62.0 1.0 C5' A:ATP504 4.7 17.6 1.0 O3G A:ATP504 4.8 23.1 1.0 C A:SER398 4.9 16.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Ptmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.7 occ:1.00 O A:HOH803 2.1 30.0 1.0 O A:HOH815 2.2 32.0 1.0 O3G A:ATP504 2.2 23.1 1.0 O2B A:ATP504 2.3 19.1 1.0 OE1 A:GLU396 2.3 22.2 1.0 O A:HOH648 2.3 21.8 1.0 CD A:GLU396 3.3 23.8 1.0 MG A:MG502 3.3 19.8 1.0 PB A:ATP504 3.3 18.4 1.0 PG A:ATP504 3.4 19.2 1.0 O3B A:ATP504 3.4 17.9 1.0 OE2 A:GLU396 3.5 19.1 1.0 O A:HOH705 3.6 27.3 1.0 O A:HOH772 4.2 24.6 1.0 O1B A:ATP504 4.2 18.7 1.0 OD2 A:ASP389 4.2 25.5 1.0 O1G A:ATP504 4.2 19.9 1.0 O A:HOH745 4.4 58.8 1.0 O A:HOH778 4.5 27.4 1.0 O2G A:ATP504 4.5 19.7 1.0 O A:HOH663 4.6 44.0 1.0 O3A A:ATP504 4.6 17.0 1.0 CG A:GLU396 4.6 17.4 1.0 O A:HOH722 4.7 31.8 1.0 O A:HOH874 4.8 45.0 1.0 OG A:SER399 4.9 19.5 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