Magnesium in PDB 6ab0: Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys, PDB code: 6ab0 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 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.506, 44.280, 72.671, 90.00, 118.58, 90.00
R / Rfree (%)	17 / 19.9

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Pampylys 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 Pampylys (pdb code 6ab0). 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 Pampylys, PDB code: 6ab0:
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 Pampylys


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.3 occ:1.00 O2B A:ATP504 2.0 20.5 1.0 O A:HOH728 2.1 23.9 1.0 O A:HOH730 2.1 27.4 1.0 O A:HOH655 2.1 19.6 1.0 O2G A:ATP504 2.1 21.3 1.0 O A:HOH663 2.2 24.9 1.0 PG A:ATP504 3.3 20.4 1.0 PB A:ATP504 3.3 19.2 1.0 O3B A:ATP504 3.5 18.9 1.0 O1G A:ATP504 3.8 23.7 1.0 NH1 A:ARG330 3.9 20.7 1.0 O A:HOH834 4.1 43.2 1.0 NE2 A:HIS338 4.1 21.1 1.0 OE2 A:GLU332 4.2 20.7 1.0 O A:HOH846 4.2 44.7 1.0 O3A A:ATP504 4.3 18.6 1.0 O1B A:ATP504 4.4 21.2 1.0 OE1 A:GLU332 4.4 27.8 1.0 O3G A:ATP504 4.5 21.2 1.0 CD2 A:HIS338 4.6 20.6 1.0 OE1 A:GLN287 4.6 47.3 1.0 NE2 A:GLN287 4.6 48.1 1.0 N7 A:ATP504 4.7 17.4 1.0 O A:HOH804 4.7 38.2 1.0 CD A:GLU332 4.8 27.2 1.0 O A:HOH625 4.8 45.2 1.0 O A:HOH775 4.9 33.6 1.0

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


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.8 occ:1.00 OG A:SER399 2.0 22.0 1.0 O1A A:ATP504 2.1 20.8 1.0 O A:HOH747 2.1 23.2 1.0 O1B A:ATP504 2.1 21.2 1.0 O A:HOH657 2.1 21.9 1.0 OE2 A:GLU396 2.2 21.3 1.0 CD A:GLU396 3.1 20.3 1.0 CB A:SER399 3.1 20.9 1.0 PA A:ATP504 3.2 19.3 1.0 MG A:MG503 3.3 23.9 1.0 PB A:ATP504 3.3 19.2 1.0 OE1 A:GLU396 3.4 22.6 1.0 O3A A:ATP504 3.4 18.6 1.0 O A:HOH726 4.0 28.6 1.0 OD2 A:ASP389 4.0 27.4 1.0 O2A A:ATP504 4.1 21.7 1.0 OD1 A:ASP389 4.1 22.6 1.0 O3B A:ATP504 4.1 18.9 1.0 O A:HOH804 4.2 38.2 1.0 O A:HOH775 4.2 33.6 1.0 CA A:SER399 4.2 18.0 1.0 O3' A:ATP504 4.3 20.6 1.0 N A:SER399 4.4 18.0 1.0 CG A:ASP389 4.4 23.0 1.0 CG A:GLU396 4.4 18.2 1.0 O5' A:ATP504 4.5 18.7 1.0 O2B A:ATP504 4.5 20.5 1.0 C5' A:ATP504 4.7 19.1 1.0 C3' A:ATP504 4.7 18.1 1.0 O1G A:ATP504 4.9 23.7 1.0 C A:SER398 4.9 18.6 1.0 O A:HOH791 5.0 29.4 1.0

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


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 Pampylys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.9 occ:1.00 O A:HOH775 2.0 33.6 1.0 O A:HOH791 2.1 29.4 1.0 O1G A:ATP504 2.2 23.7 1.0 O1B A:ATP504 2.2 21.2 1.0 OE1 A:GLU396 2.3 22.6 1.0 O A:HOH657 2.3 21.9 1.0 CD A:GLU396 3.3 20.3 1.0 MG A:MG502 3.3 20.8 1.0 PB A:ATP504 3.3 19.2 1.0 O3B A:ATP504 3.4 18.9 1.0 PG A:ATP504 3.4 20.4 1.0 OE2 A:GLU396 3.5 21.3 1.0 O A:HOH738 3.7 30.5 1.0 O A:HOH625 3.9 45.2 1.0 O A:HOH804 4.1 38.2 1.0 O2B A:ATP504 4.1 20.5 1.0 O A:HOH830 4.1 46.2 1.0 O A:HOH747 4.2 23.2 1.0 OD2 A:ASP389 4.2 27.4 1.0 O3G A:ATP504 4.3 21.2 1.0 O2G A:ATP504 4.4 21.3 1.0 O A:HOH730 4.4 27.4 1.0 O3A A:ATP504 4.6 18.6 1.0 O A:HOH664 4.6 39.7 1.0 CG A:GLU396 4.6 18.2 1.0 O A:HOH726 4.6 28.6 1.0 OG A:SER399 4.8 22.0 1.0 O1A A:ATP504 4.9 20.8 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