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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Obrzlys, PDB code: 6abl 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)	35.06 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.671, 44.281, 72.654, 90.00, 118.43, 90.00
R / Rfree (%)	15.7 / 19.3

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

Bromine

(Br)

2 atoms

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


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 Obrzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.5 occ:1.00 O2B A:ATP504 2.1 21.0 1.0 O A:HOH726 2.1 24.7 1.0 O2G A:ATP504 2.1 21.3 1.0 O A:HOH746 2.1 29.2 1.0 O A:HOH646 2.2 25.2 1.0 O A:HOH675 2.2 24.3 1.0 PG A:ATP504 3.3 21.5 1.0 PB A:ATP504 3.3 21.2 1.0 O3B A:ATP504 3.5 20.8 1.0 O1G A:ATP504 3.8 26.1 1.0 NH1 A:ARG330 3.9 20.4 1.0 NE2 A:HIS338 4.0 21.1 1.0 O A:HOH837 4.1 48.9 1.0 OE2 A:GLU332 4.2 21.6 1.0 O3A A:ATP504 4.3 19.7 1.0 O1B A:ATP504 4.4 22.1 1.0 OE1 A:GLU332 4.4 26.4 1.0 CD2 A:HIS338 4.5 20.1 1.0 O3G A:ATP504 4.5 20.9 1.0 OE1 A:GLN287 4.5 63.4 1.0 N7 A:ATP504 4.7 17.9 1.0 NE2 A:GLN287 4.7 72.4 1.0 O A:HOH810 4.8 39.2 1.0 CD A:GLU332 4.8 23.9 1.0 O A:HOH796 5.0 45.0 1.0

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


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 Obrzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.5 occ:1.00 OG A:SER399 2.1 22.2 1.0 O1B A:ATP504 2.2 22.1 1.0 OE2 A:GLU396 2.2 21.5 1.0 O A:HOH674 2.2 25.7 1.0 O A:HOH793 2.2 29.1 1.0 O1A A:ATP504 2.2 22.7 1.0 CD A:GLU396 3.1 20.1 1.0 CB A:SER399 3.2 21.4 1.0 MG A:MG503 3.3 26.4 1.0 PA A:ATP504 3.3 20.4 1.0 PB A:ATP504 3.3 21.2 1.0 OE1 A:GLU396 3.4 23.6 1.0 O3A A:ATP504 3.5 19.7 1.0 O A:HOH684 4.0 39.8 1.0 OD2 A:ASP389 4.0 29.8 1.0 O3B A:ATP504 4.1 20.8 1.0 OD1 A:ASP389 4.2 27.0 1.0 O2A A:ATP504 4.2 21.2 1.0 O A:HOH810 4.2 39.2 1.0 O A:HOH796 4.3 45.0 1.0 CA A:SER399 4.3 19.4 1.0 O3' A:ATP504 4.3 18.7 1.0 N A:SER399 4.3 17.6 1.0 CG A:GLU396 4.4 21.9 1.0 CG A:ASP389 4.5 41.8 1.0 O5' A:ATP504 4.5 19.3 1.0 O2B A:ATP504 4.6 21.0 1.0 O A:9VL505 4.7 42.2 0.2 C3' A:ATP504 4.7 17.1 1.0 O1G A:ATP504 4.7 26.1 1.0 C5' A:ATP504 4.7 20.1 1.0 C A:SER398 4.9 18.6 1.0 O A:HOH771 4.9 37.3 1.0

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


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 Obrzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:26.4 occ:1.00 O A:HOH771 2.1 37.3 1.0 O1G A:ATP504 2.1 26.1 1.0 O A:HOH796 2.2 45.0 1.0 OE1 A:GLU396 2.3 23.6 1.0 O A:HOH674 2.3 25.7 1.0 O1B A:ATP504 2.4 22.1 1.0 CD A:GLU396 3.3 20.1 1.0 MG A:MG502 3.3 23.5 1.0 PG A:ATP504 3.4 21.5 1.0 PB A:ATP504 3.4 21.2 1.0 O3B A:ATP504 3.5 20.8 1.0 OE2 A:GLU396 3.5 21.5 1.0 O A:HOH720 3.6 26.7 1.0 O A:HOH810 4.2 39.2 1.0 OD2 A:ASP389 4.2 29.8 1.0 O A:HOH793 4.2 29.1 1.0 O2B A:ATP504 4.3 21.0 1.0 O3G A:ATP504 4.3 20.9 1.0 O A:HOH655 4.3 48.8 1.0 O2G A:ATP504 4.5 21.3 1.0 O A:HOH746 4.5 29.2 1.0 CG A:GLU396 4.7 21.9 1.0 O3A A:ATP504 4.7 19.7 1.0 O A:HOH684 4.8 39.8 1.0 O A:HOH877 4.9 53.3 1.0 OG A:SER399 5.0 22.2 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