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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Mazzlys, PDB code: 6aac 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)	35.05 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.492, 44.284, 72.637, 90.00, 118.49, 90.00
R / Rfree (%)	14.2 / 18.2

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

Potassium

(K)

1 atom

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


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 Mazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.0 occ:1.00 O2B A:ATP504 2.0 17.0 1.0 O A:HOH723 2.1 19.9 1.0 O A:HOH733 2.1 23.6 1.0 O2G A:ATP504 2.1 18.1 1.0 O A:HOH654 2.1 16.5 1.0 O A:HOH664 2.1 19.1 1.0 PG A:ATP504 3.3 17.3 1.0 PB A:ATP504 3.3 16.6 1.0 O3B A:ATP504 3.5 16.2 1.0 O1G A:ATP504 3.8 19.4 1.0 NH1 A:ARG330 3.9 16.2 1.0 NE2 A:HIS338 4.1 17.3 1.0 O A:HOH852 4.1 36.0 1.0 OE2 A:GLU332 4.2 17.8 1.0 O3A A:ATP504 4.3 15.4 1.0 O1B A:ATP504 4.4 16.7 1.0 OE1 A:GLU332 4.4 22.9 1.0 O3G A:ATP504 4.5 18.1 1.0 CD2 A:HIS338 4.5 15.8 1.0 OE1 A:GLN287 4.6 42.0 1.0 N7 A:ATP504 4.7 14.7 1.0 NE2 A:GLN287 4.7 34.9 1.0 O A:HOH800 4.7 33.6 1.0 CD A:GLU332 4.8 20.2 1.0 O A:HOH666 4.8 54.7 1.0 O A:HOH804 4.9 33.1 1.0

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


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 Mazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.4 occ:1.00 OG A:SER399 2.1 19.0 1.0 O A:HOH750 2.1 21.7 1.0 O1A A:ATP504 2.1 18.8 1.0 O1B A:ATP504 2.1 16.7 1.0 O A:HOH643 2.2 20.7 1.0 OE2 A:GLU396 2.2 17.4 1.0 CD A:GLU396 3.1 16.1 1.0 CB A:SER399 3.2 17.8 1.0 PA A:ATP504 3.3 16.1 1.0 MG A:MG503 3.3 21.7 1.0 PB A:ATP504 3.3 16.6 1.0 OE1 A:GLU396 3.4 18.4 1.0 O3A A:ATP504 3.4 15.4 1.0 O A:HOH708 3.9 23.9 1.0 OD2 A:ASP389 4.1 23.1 1.0 O3B A:ATP504 4.1 16.2 1.0 O2A A:ATP504 4.1 16.6 1.0 OD1 A:ASP389 4.2 20.4 1.0 O A:HOH800 4.2 33.6 1.0 CA A:SER399 4.2 16.6 1.0 O3' A:ATP504 4.3 15.6 1.0 N A:SER399 4.3 15.4 1.0 O A:HOH804 4.4 33.1 1.0 CG A:GLU396 4.4 16.9 1.0 O5' A:ATP504 4.5 14.6 1.0 CG A:ASP389 4.5 20.5 1.0 O2B A:ATP504 4.6 17.0 1.0 O A:9TR505 4.6 60.5 1.0 C3' A:ATP504 4.7 13.7 1.0 C5' A:ATP504 4.8 15.7 1.0 O1G A:ATP504 4.9 19.4 1.0 O A:HOH772 4.9 49.5 1.0 C A:SER398 4.9 15.6 1.0

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


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 Mazzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:21.7 occ:1.00 O A:HOH813 2.2 29.6 1.0 O A:HOH804 2.2 33.1 1.0 O1G A:ATP504 2.2 19.4 1.0 O1B A:ATP504 2.3 16.7 1.0 OE1 A:GLU396 2.3 18.4 1.0 O A:HOH643 2.3 20.7 1.0 MG A:MG502 3.3 18.4 1.0 CD A:GLU396 3.3 16.1 1.0 PB A:ATP504 3.4 16.6 1.0 PG A:ATP504 3.4 17.3 1.0 O3B A:ATP504 3.4 16.2 1.0 OE2 A:GLU396 3.5 17.4 1.0 O A:HOH728 3.6 22.6 1.0 O A:HOH695 4.0 53.4 1.0 O A:HOH800 4.1 33.6 1.0 O2B A:ATP504 4.2 17.0 1.0 OD2 A:ASP389 4.2 23.1 1.0 O A:HOH750 4.2 21.7 1.0 O3G A:ATP504 4.3 18.1 1.0 O A:HOH666 4.3 54.7 1.0 O A:HOH733 4.5 23.6 1.0 O2G A:ATP504 4.5 18.1 1.0 O A:HOH665 4.5 37.7 1.0 O A:HOH915 4.6 49.7 1.0 O3A A:ATP504 4.6 15.4 1.0 CG A:GLU396 4.7 16.9 1.0 O A:HOH708 4.7 23.9 1.0 OG A:SER399 4.9 19.0 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