Magnesium in PDB 6aaz: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS

All present enzymatic activity of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS:
6.1.1.26;

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS, PDB code: 6aaz 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)	39.52 / 1.84
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.378, 44.107, 72.673, 90.00, 118.63, 90.00
R / Rfree (%)	23.1 / 27.5

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS (pdb code 6aaz). 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 PNO2ZLYS, PDB code: 6aaz:
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 PNO2ZLYS


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 PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.3 occ:1.00 O2B A:ATP504 2.0 16.0 1.0 O2G A:ATP504 2.0 18.5 1.0 O A:HOH699 2.1 16.6 1.0 O A:HOH739 2.2 21.8 1.0 O A:HOH696 2.2 21.4 1.0 O A:HOH784 2.3 23.9 1.0 PG A:ATP504 3.1 17.9 1.0 PB A:ATP504 3.2 18.2 1.0 O3B A:ATP504 3.3 19.1 1.0 O1G A:ATP504 3.7 22.5 1.0 NE2 A:HIS338 3.9 23.3 1.0 NH1 A:ARG330 4.0 16.9 1.0 O3A A:ATP504 4.2 21.3 1.0 OE2 A:GLU332 4.3 18.6 1.0 O1B A:ATP504 4.3 18.5 1.0 CD2 A:HIS338 4.4 21.7 1.0 O3G A:ATP504 4.4 16.6 1.0 OE1 A:GLU332 4.5 24.7 1.0 O A:HOH842 4.6 35.8 1.0 N7 A:ATP504 4.6 15.0 1.0 OE1 A:GLN287 4.8 34.1 1.0 CD A:GLU332 4.8 24.1 1.0 NE2 A:GLN287 4.8 30.6 1.0 O A:HOH794 4.9 27.4 1.0 CE1 A:HIS338 5.0 26.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS


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 PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.7 occ:1.00 OE2 A:GLU396 1.9 19.8 1.0 OG A:SER399 2.0 19.5 1.0 O1B A:ATP504 2.1 18.5 1.0 O1A A:ATP504 2.1 22.1 1.0 O A:HOH713 2.3 21.5 1.0 O A:HOH749 2.4 22.1 1.0 CD A:GLU396 3.0 20.0 1.0 CB A:SER399 3.1 21.3 1.0 MG A:MG503 3.2 24.5 1.0 PA A:ATP504 3.3 19.4 1.0 PB A:ATP504 3.3 18.2 1.0 OE1 A:GLU396 3.5 18.7 1.0 O3A A:ATP504 3.5 21.3 1.0 O A:HOH729 4.0 23.5 1.0 O3B A:ATP504 4.1 19.1 1.0 OD2 A:ASP389 4.1 22.7 1.0 OD1 A:ASP389 4.1 19.4 1.0 OXT A:9UC505 4.1 41.3 1.0 O2A A:ATP504 4.2 16.8 1.0 CA A:SER399 4.2 18.1 1.0 O3' A:ATP504 4.2 16.3 1.0 CG A:GLU396 4.3 19.6 1.0 O A:HOH794 4.3 27.4 1.0 N A:SER399 4.4 17.2 1.0 CG A:ASP389 4.5 19.8 1.0 O5' A:ATP504 4.5 15.5 1.0 C3' A:ATP504 4.6 17.0 1.0 O2B A:ATP504 4.6 16.0 1.0 O A:HOH676 4.6 41.8 1.0 C5' A:ATP504 4.7 15.3 1.0 O1G A:ATP504 4.8 22.5 1.0 O A:HOH710 4.8 27.0 1.0 C A:SER398 4.9 18.1 1.0 O A:SER398 5.0 17.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with PNO2ZLYS


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 PNO2ZLYS within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:24.5 occ:1.00 O1G A:ATP504 2.2 22.5 1.0 O A:HOH710 2.2 27.0 1.0 O A:HOH713 2.3 21.5 1.0 O1B A:ATP504 2.3 18.5 1.0 OE1 A:GLU396 2.3 18.7 1.0 CD A:GLU396 3.2 20.0 1.0 MG A:MG502 3.2 20.7 1.0 PB A:ATP504 3.2 18.2 1.0 OE2 A:GLU396 3.3 19.8 1.0 O3B A:ATP504 3.3 19.1 1.0 PG A:ATP504 3.4 17.9 1.0 O A:HOH687 3.6 23.0 1.0 O A:HOH676 3.9 41.8 1.0 O2B A:ATP504 4.0 16.0 1.0 O A:HOH794 4.1 27.4 1.0 O A:HOH749 4.1 22.1 1.0 O3G A:ATP504 4.2 16.6 1.0 OD2 A:ASP389 4.3 22.7 1.0 O2G A:ATP504 4.5 18.5 1.0 O A:HOH838 4.5 32.9 1.0 O A:HOH784 4.6 23.9 1.0 O3A A:ATP504 4.6 21.3 1.0 CG A:GLU396 4.6 19.6 1.0 O A:HOH729 4.7 23.5 1.0 OG A:SER399 4.8 19.5 1.0 O1A A:ATP504 4.9 22.1 1.0 OD2 A:ASP379 4.9 32.4 1.0 O A:HOH837 4.9 30.7 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