Magnesium in PDB 6ab8: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys, PDB code: 6ab8 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)	42.28 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.134, 43.893, 62.070, 90.00, 98.83, 90.00
R / Rfree (%)	17.2 / 21.3

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zlys 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 Zlys (pdb code 6ab8). 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 Zlys, PDB code: 6ab8:
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 Zlys


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 Zlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.5 occ:1.00 O A:HOH697 2.0 24.0 1.0 O2B A:ATP504 2.0 21.1 1.0 O A:HOH704 2.1 24.3 1.0 O2G A:ATP504 2.1 20.9 1.0 O A:HOH743 2.2 26.3 1.0 O A:HOH613 2.2 18.7 1.0 PB A:ATP504 3.3 21.8 1.0 PG A:ATP504 3.3 20.7 1.0 O3B A:ATP504 3.5 19.7 1.0 NH1 A:ARG330 3.8 19.0 1.0 O1G A:ATP504 3.8 24.4 1.0 OE2 A:GLU332 4.1 18.9 1.0 NE2 A:HIS338 4.1 21.7 1.0 O A:HOH781 4.1 39.5 1.0 O A:HOH771 4.2 38.1 1.0 O3A A:ATP504 4.3 17.3 1.0 O A:HOH784 4.4 40.3 1.0 O1B A:ATP504 4.4 19.0 1.0 OE1 A:GLU332 4.5 24.9 1.0 OE1 A:GLN287 4.5 34.5 1.0 O A:HOH736 4.5 34.1 1.0 O3G A:ATP504 4.6 19.8 1.0 CD2 A:HIS338 4.6 21.2 1.0 N7 A:ATP504 4.6 19.9 1.0 NE2 A:GLN287 4.7 26.1 1.0 CD A:GLU332 4.7 26.4 1.0

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


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 Zlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.1 occ:1.00 OG A:SER399 2.0 19.1 1.0 O1B A:ATP504 2.0 19.0 1.0 OE2 A:GLU396 2.1 21.7 1.0 O1A A:ATP504 2.1 19.3 1.0 O A:HOH656 2.2 20.6 1.0 O A:HOH703 2.2 21.0 1.0 CD A:GLU396 3.0 29.4 1.0 CB A:SER399 3.1 24.3 1.0 PA A:ATP504 3.2 21.4 1.0 MG A:MG503 3.2 27.1 1.0 PB A:ATP504 3.3 21.8 1.0 OE1 A:GLU396 3.3 21.2 1.0 O3A A:ATP504 3.4 17.3 1.0 O A:HOH670 3.9 26.5 1.0 O3B A:ATP504 4.1 19.7 1.0 O2A A:ATP504 4.1 20.5 1.0 OD2 A:ASP389 4.1 31.1 1.0 O A:HOH736 4.1 34.1 1.0 OD1 A:ASP389 4.2 24.3 1.0 CA A:SER399 4.2 17.9 1.0 O3' A:ATP504 4.3 18.4 1.0 CG A:GLU396 4.3 19.6 1.0 N A:SER399 4.4 18.0 1.0 O5' A:ATP504 4.4 17.2 1.0 CG A:ASP389 4.5 28.7 1.0 O2B A:ATP504 4.5 21.1 1.0 C5' A:ATP504 4.6 18.4 1.0 C3' A:ATP504 4.7 17.2 1.0 O1G A:ATP504 4.9 24.4 1.0 O A:9VC505 4.9 49.9 0.6 C A:SER398 4.9 23.4 1.0

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


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 Zlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:27.1 occ:1.00 O A:HOH656 2.3 20.6 1.0 OE1 A:GLU396 2.3 21.2 1.0 O1G A:ATP504 2.3 24.4 1.0 O A:HOH769 2.4 29.4 1.0 O1B A:ATP504 2.4 19.0 1.0 MG A:MG502 3.2 20.1 1.0 CD A:GLU396 3.3 29.4 1.0 PB A:ATP504 3.4 21.8 1.0 O3B A:ATP504 3.4 19.7 1.0 PG A:ATP504 3.5 20.7 1.0 OE2 A:GLU396 3.5 21.7 1.0 O A:HOH724 3.7 27.0 1.0 O A:HOH736 3.9 34.1 1.0 O A:HOH780 4.0 37.8 1.0 O2B A:ATP504 4.2 21.1 1.0 OD2 A:ASP389 4.2 31.1 1.0 OD2 A:ASP379 4.3 56.1 1.0 O A:HOH703 4.3 21.0 1.0 O3G A:ATP504 4.3 19.8 1.0 O2G A:ATP504 4.6 20.9 1.0 O3A A:ATP504 4.6 17.3 1.0 CG A:GLU396 4.7 19.6 1.0 O A:HOH743 4.7 26.3 1.0 O A:HOH670 4.7 26.5 1.0 OG A:SER399 4.8 19.1 1.0 O1A A:ATP504 5.0 19.3 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