Magnesium in PDB 6ab1: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oazzlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oazzlys, PDB code: 6ab1 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 / 1.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.435, 44.314, 72.713, 90.00, 118.47, 90.00
R / Rfree (%)	17.5 / 19.6

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

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Oazzlys (pdb code 6ab1). 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 Oazzlys, PDB code: 6ab1:
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 Oazzlys


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 Oazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.3 occ:1.00 O2B A:ATP504 2.0 21.1 1.0 O A:HOH757 2.1 26.4 1.0 O2G A:ATP504 2.1 20.7 1.0 O A:HOH681 2.1 19.9 1.0 O A:HOH728 2.1 24.6 1.0 O A:HOH692 2.2 23.4 1.0 PG A:ATP504 3.2 19.8 1.0 PB A:ATP504 3.3 19.1 1.0 O3B A:ATP504 3.5 18.5 1.0 O1G A:ATP504 3.8 25.1 1.0 NH1 A:ARG330 3.9 19.6 1.0 NE2 A:HIS338 4.0 20.0 1.0 OE2 A:GLU332 4.2 19.3 1.0 O3A A:ATP504 4.3 18.6 1.0 O1B A:ATP504 4.4 20.3 1.0 OE1 A:GLU332 4.4 25.7 1.0 O3G A:ATP504 4.5 20.7 1.0 CD2 A:HIS338 4.5 18.8 1.0 OE1 A:GLN287 4.5 45.3 1.0 NE2 A:GLN287 4.7 37.9 1.0 N7 A:ATP504 4.7 16.4 1.0 O A:HOH741 4.8 49.1 1.0 CD A:GLU332 4.8 23.7 1.0 O A:HOH828 4.9 33.2 1.0

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


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 Oazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.3 occ:1.00 O1B A:ATP504 2.1 20.3 1.0 OG A:SER399 2.1 21.1 1.0 O1A A:ATP504 2.2 21.7 1.0 O A:HOH670 2.2 22.8 1.0 O A:HOH807 2.2 25.0 1.0 OE2 A:GLU396 2.2 20.1 1.0 CD A:GLU396 3.1 19.1 1.0 CB A:SER399 3.2 20.4 1.0 MG A:MG503 3.3 23.9 1.0 PA A:ATP504 3.3 19.1 1.0 PB A:ATP504 3.3 19.1 1.0 OE1 A:GLU396 3.4 22.0 1.0 O3A A:ATP504 3.4 18.6 1.0 O A:HOH727 4.0 27.0 1.0 OD2 A:ASP389 4.0 26.9 1.0 O3B A:ATP504 4.1 18.5 1.0 O2A A:ATP504 4.2 20.0 1.0 OD1 A:ASP389 4.2 23.2 1.0 CA A:SER399 4.3 18.5 1.0 O A:HOH828 4.3 33.2 1.0 O A:9V0505 4.3 32.0 0.4 O3' A:ATP504 4.3 18.8 1.0 N A:SER399 4.4 17.4 1.0 CG A:GLU396 4.4 18.7 1.0 CG A:ASP389 4.5 23.4 1.0 O5' A:ATP504 4.5 18.2 1.0 O2B A:ATP504 4.6 21.1 1.0 C3' A:ATP504 4.7 17.9 1.0 C5' A:ATP504 4.8 18.6 1.0 O1G A:ATP504 4.8 25.1 1.0 C A:SER398 4.9 20.0 1.0

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


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 Oazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.9 occ:1.00 O A:HOH834 2.2 29.9 1.0 O A:HOH828 2.2 33.2 1.0 O1G A:ATP504 2.2 25.1 1.0 OE1 A:GLU396 2.3 22.0 1.0 O1B A:ATP504 2.3 20.3 1.0 O A:HOH670 2.3 22.8 1.0 MG A:MG502 3.3 20.3 1.0 CD A:GLU396 3.3 19.1 1.0 PB A:ATP504 3.4 19.1 1.0 O3B A:ATP504 3.4 18.5 1.0 PG A:ATP504 3.4 19.8 1.0 OE2 A:GLU396 3.5 20.1 1.0 O A:HOH754 3.6 25.2 1.0 O A:HOH751 3.9 50.4 1.0 O A:HOH864 4.1 57.8 1.0 O2B A:ATP504 4.2 21.1 1.0 O A:HOH807 4.2 25.0 1.0 OD2 A:ASP389 4.2 26.9 1.0 O3G A:ATP504 4.3 20.7 1.0 O A:HOH741 4.5 49.1 1.0 O A:HOH682 4.5 38.7 1.0 O2G A:ATP504 4.5 20.7 1.0 O A:HOH757 4.6 26.4 1.0 CG A:GLU396 4.6 18.7 1.0 O3A A:ATP504 4.7 18.6 1.0 O A:HOH727 4.7 27.0 1.0 OG A:SER399 4.9 21.1 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