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

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

The structure of Crystal Structure of Methanosarcina Mazei Pylrs(Y306A/Y384F) Complexed with Zaesecys, PDB code: 6aap 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)	37.04 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.797, 43.609, 72.478, 90.00, 119.67, 90.00
R / Rfree (%)	16.4 / 19.6

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


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 Zaesecys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:18.9 occ:1.00 O2B A:ATP504 2.0 18.7 1.0 O A:HOH640 2.0 18.0 1.0 O2G A:ATP504 2.1 18.7 1.0 O A:HOH691 2.1 21.2 1.0 O A:HOH750 2.1 24.9 1.0 O A:HOH682 2.2 22.6 1.0 PG A:ATP504 3.2 17.9 1.0 PB A:ATP504 3.3 17.6 1.0 O3B A:ATP504 3.5 17.4 1.0 O1G A:ATP504 3.8 18.9 1.0 NH1 A:ARG330 3.9 19.4 1.0 O A:HOH827 3.9 62.6 1.0 NE2 A:HIS338 4.0 20.4 1.0 O A:HOH822 4.1 39.9 1.0 OE2 A:GLU332 4.2 19.8 1.0 O3A A:ATP504 4.3 17.1 1.0 O1B A:ATP504 4.3 19.7 1.0 OE1 A:GLU332 4.4 27.5 1.0 CD2 A:HIS338 4.5 19.3 1.0 O3G A:ATP504 4.5 18.6 1.0 OE1 A:GLN287 4.5 37.6 1.0 O A:HOH764 4.6 27.1 1.0 NE2 A:GLN287 4.6 78.8 1.0 N7 A:ATP504 4.7 15.2 1.0 O A:HOH812 4.7 42.6 1.0 CD A:GLU332 4.7 23.3 1.0

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


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 Zaesecys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:17.8 occ:1.00 O1A A:ATP504 2.0 17.6 1.0 OG A:SER399 2.1 18.5 1.0 O A:HOH732 2.1 19.6 1.0 O1B A:ATP504 2.1 19.7 1.0 OE2 A:GLU396 2.1 17.2 1.0 O A:HOH637 2.2 19.6 1.0 CD A:GLU396 3.1 18.3 1.0 CB A:SER399 3.1 17.8 1.0 PA A:ATP504 3.2 17.0 1.0 MG A:MG503 3.2 19.7 1.0 PB A:ATP504 3.3 17.6 1.0 OE1 A:GLU396 3.4 20.2 1.0 O3A A:ATP504 3.4 17.1 1.0 O A:HOH764 4.0 27.1 1.0 OD2 A:ASP389 4.0 22.2 1.0 O2A A:ATP504 4.1 17.8 1.0 O3B A:ATP504 4.1 17.4 1.0 OD1 A:ASP389 4.1 21.3 1.0 O A:HOH603 4.2 37.9 1.0 CA A:SER399 4.2 14.9 1.0 N A:SER399 4.3 16.1 1.0 O A:HOH731 4.3 51.6 1.0 O3' A:ATP504 4.4 16.0 1.0 CG A:GLU396 4.4 15.4 1.0 CG A:ASP389 4.5 19.3 1.0 O5' A:ATP504 4.5 16.3 1.0 O2B A:ATP504 4.5 18.7 1.0 C3' A:ATP504 4.7 16.5 1.0 C5' A:ATP504 4.7 16.0 1.0 O1G A:ATP504 4.8 18.9 1.0 C A:SER398 4.9 16.4 1.0

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


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 Zaesecys within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.7 occ:1.00 O1G A:ATP504 2.1 18.9 1.0 OE1 A:GLU396 2.1 20.2 1.0 O A:HOH637 2.2 19.6 1.0 O1B A:ATP504 2.2 19.7 1.0 CD A:GLU396 3.1 18.3 1.0 MG A:MG502 3.2 17.8 1.0 PB A:ATP504 3.2 17.6 1.0 PG A:ATP504 3.3 17.9 1.0 O3B A:ATP504 3.3 17.4 1.0 OE2 A:GLU396 3.4 17.2 1.0 O A:HOH611 3.5 42.6 1.0 O A:HOH768 3.6 23.8 1.0 O2B A:ATP504 4.1 18.7 1.0 OD2 A:ASP389 4.1 22.2 1.0 O A:HOH732 4.1 19.6 1.0 O A:HOH764 4.1 27.1 1.0 O3G A:ATP504 4.2 18.6 1.0 O A:HOH633 4.3 38.8 1.0 O2G A:ATP504 4.4 18.7 1.0 O A:HOH750 4.4 24.9 1.0 CG A:GLU396 4.5 15.4 1.0 O3A A:ATP504 4.5 17.1 1.0 OG A:SER399 4.8 18.5 1.0 CB A:GLU396 4.8 16.8 1.0 O1A A:ATP504 4.9 17.6 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