Magnesium in PDB 6aad: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mtmdzlys, PDB code: 6aad 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 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.917, 43.782, 72.475, 90.00, 119.05, 90.00
R / Rfree (%)	17.1 / 19.5

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


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 Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:19.1 occ:1.00 O2B A:ATP504 2.0 19.5 1.0 O A:HOH724 2.1 23.6 1.0 O A:HOH635 2.1 18.8 1.0 O2G A:ATP504 2.1 20.0 1.0 O A:HOH708 2.1 21.1 1.0 O A:HOH768 2.2 26.2 1.0 PG A:ATP504 3.2 18.8 1.0 PB A:ATP504 3.3 18.2 1.0 O3B A:ATP504 3.5 18.8 1.0 O1G A:ATP504 3.8 21.1 1.0 NH1 A:ARG330 3.9 17.9 1.0 NE2 A:HIS338 4.0 19.9 1.0 OE2 A:GLU332 4.1 19.3 1.0 O A:HOH874 4.2 44.9 1.0 O A:HOH831 4.2 37.9 1.0 O A:HOH664 4.3 40.1 1.0 O3A A:ATP504 4.3 17.1 1.0 O1B A:ATP504 4.4 19.6 1.0 OE1 A:GLU332 4.4 25.2 1.0 CD2 A:HIS338 4.5 18.8 1.0 O3G A:ATP504 4.5 19.5 1.0 OE1 A:GLN287 4.5 39.6 1.0 NE2 A:GLN287 4.6 43.9 1.0 N7 A:ATP504 4.7 15.8 1.0 O A:HOH797 4.7 32.1 1.0 CD A:GLU332 4.7 22.3 1.0 O A:HOH604 4.8 43.4 1.0

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


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 Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.4 occ:1.00 O1A A:ATP504 2.0 19.2 1.0 OG A:SER399 2.1 19.9 1.0 OE2 A:GLU396 2.1 19.3 1.0 O1B A:ATP504 2.1 19.6 1.0 O A:HOH746 2.1 23.4 1.0 O A:HOH642 2.2 22.2 1.0 CD A:GLU396 3.1 20.4 1.0 CB A:SER399 3.1 19.2 1.0 PA A:ATP504 3.2 17.5 1.0 MG A:MG503 3.3 20.2 1.0 PB A:ATP504 3.3 18.2 1.0 OE1 A:GLU396 3.4 20.5 1.0 O3A A:ATP504 3.4 17.1 1.0 OD2 A:ASP389 4.0 23.3 1.0 OD1 A:ASP389 4.1 21.6 1.0 O A:HOH797 4.1 32.1 1.0 O2A A:ATP504 4.1 19.1 1.0 O A:HOH686 4.1 34.6 1.0 O3B A:ATP504 4.1 18.8 1.0 CA A:SER399 4.2 16.5 1.0 O A:HOH620 4.2 36.1 1.0 N A:SER399 4.3 15.9 1.0 O3' A:ATP504 4.3 16.0 1.0 O A:HOH714 4.3 55.5 1.0 CG A:GLU396 4.4 17.6 1.0 CG A:ASP389 4.4 21.6 1.0 O5' A:ATP504 4.5 16.7 1.0 O2B A:ATP504 4.5 19.5 1.0 O A:HOH604 4.6 43.4 1.0 C3' A:ATP504 4.7 15.6 1.0 C5' A:ATP504 4.7 15.5 1.0 O1G A:ATP504 4.8 21.1 1.0 C A:SER398 4.9 16.2 1.0 O A:HOH747 5.0 25.7 1.0

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


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 Mtmdzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:20.2 occ:1.00 O A:HOH604 1.7 43.4 1.0 O1G A:ATP504 2.1 21.1 1.0 O A:HOH747 2.1 25.7 1.0 OE1 A:GLU396 2.1 20.5 1.0 O A:HOH642 2.2 22.2 1.0 O1B A:ATP504 2.2 19.6 1.0 CD A:GLU396 3.1 20.4 1.0 O A:HOH714 3.1 55.5 1.0 MG A:MG502 3.3 18.4 1.0 PB A:ATP504 3.3 18.2 1.0 PG A:ATP504 3.3 18.8 1.0 OE2 A:GLU396 3.4 19.3 1.0 O3B A:ATP504 3.4 18.8 1.0 O A:HOH773 3.6 21.9 1.0 O A:HOH664 3.7 40.1 1.0 OD2 A:ASP389 4.1 23.3 1.0 O2B A:ATP504 4.1 19.5 1.0 O3G A:ATP504 4.1 19.5 1.0 O A:HOH746 4.2 23.4 1.0 O A:HOH797 4.2 32.1 1.0 O A:HOH641 4.4 36.6 1.0 O2G A:ATP504 4.4 20.0 1.0 O A:HOH768 4.5 26.2 1.0 CG A:GLU396 4.5 17.6 1.0 O3A A:ATP504 4.6 17.1 1.0 O A:HOH850 4.8 39.0 1.0 CB A:GLU396 4.9 17.5 1.0 OG A:SER399 4.9 19.9 1.0 O1A A:ATP504 4.9 19.2 1.0 O A:HOH686 5.0 34.6 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