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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Metzlys, PDB code: 6aan 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)	35.00 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.484, 44.072, 72.474, 90.00, 118.62, 90.00
R / Rfree (%)	18.3 / 20.6

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


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 Metzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:39.5 occ:1.00 O2B A:ATP504 1.7 41.7 1.0 O A:HOH620 2.0 41.7 1.0 O2G A:ATP504 2.0 38.5 1.0 O A:HOH633 2.1 52.6 1.0 O A:HOH613 2.2 32.7 1.0 O A:HOH643 2.3 48.6 1.0 PB A:ATP504 3.1 45.3 1.0 PG A:ATP504 3.1 52.1 1.0 O3B A:ATP504 3.3 46.6 1.0 O1G A:ATP504 3.6 61.1 1.0 NE2 A:HIS338 4.0 33.3 1.0 OE1 A:GLU332 4.0 51.8 1.0 O1B A:ATP504 4.1 53.0 1.0 O3A A:ATP504 4.1 55.1 1.0 OE2 A:GLU332 4.1 38.9 1.0 NH1 A:ARG330 4.2 27.1 1.0 CD2 A:HIS338 4.4 30.9 1.0 O3G A:ATP504 4.5 48.2 1.0 CD A:GLU332 4.5 44.9 1.0 N7 A:ATP504 4.7 22.9 1.0 MG A:MG503 4.8 52.8 1.0

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


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 Metzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.8 occ:1.00 O1B A:ATP504 1.9 53.0 1.0 OG A:SER399 2.2 36.7 1.0 O1A A:ATP504 2.3 40.9 1.0 OE2 A:GLU396 2.4 33.3 1.0 MG A:MG503 3.1 52.8 1.0 PB A:ATP504 3.1 45.3 1.0 CD A:GLU396 3.3 40.1 1.0 CB A:SER399 3.3 31.3 1.0 OE1 A:GLU396 3.4 46.5 1.0 PA A:ATP504 3.5 31.9 1.0 O3A A:ATP504 3.6 55.1 1.0 O3B A:ATP504 3.8 46.6 1.0 O5' A:ATP504 4.1 30.6 1.0 O1G A:ATP504 4.3 61.1 1.0 O2B A:ATP504 4.4 41.7 1.0 O3' A:ATP504 4.4 26.8 1.0 CA A:SER399 4.4 23.6 1.0 O A:9TX505 4.4 53.3 1.0 C5' A:ATP504 4.5 29.0 1.0 OD1 A:ASP389 4.6 42.1 1.0 N A:SER399 4.6 21.5 1.0 O A:HOH644 4.7 46.1 1.0 CG A:GLU396 4.7 27.3 1.0 C3' A:ATP504 4.7 25.2 1.0 PG A:ATP504 4.8 52.1 1.0 O2A A:ATP504 4.8 32.8 1.0 OD2 A:ASP389 4.9 61.3 1.0

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


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 Metzlys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:52.8 occ:1.00 O A:HOH644 2.0 46.1 1.0 O1G A:ATP504 2.0 61.1 1.0 O1B A:ATP504 2.5 53.0 1.0 OE1 A:GLU396 2.6 46.5 1.0 MG A:MG502 3.1 39.8 1.0 PG A:ATP504 3.3 52.1 1.0 PB A:ATP504 3.5 45.3 1.0 CD A:GLU396 3.6 40.1 1.0 O3B A:ATP504 3.6 46.6 1.0 OE2 A:GLU396 3.7 33.3 1.0 O A:HOH633 3.7 52.6 1.0 O A:HOH779 4.0 57.8 1.0 O2B A:ATP504 4.1 41.7 1.0 O3G A:ATP504 4.3 48.2 1.0 O A:HOH724 4.3 43.6 1.0 O2G A:ATP504 4.3 38.5 1.0 OD2 A:ASP389 4.5 61.3 1.0 MG A:MG501 4.8 39.5 1.0 OG A:SER399 4.9 36.7 1.0 CG A:GLU396 5.0 27.3 1.0 O3A A:ATP504 5.0 55.1 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