Magnesium in PDB 4bw9: Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp

All present enzymatic activity of Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp:
6.1.1.26;

The structure of Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp, PDB code: 4bw9 was solved by S.Schneider, M.Vrabel, M.J.Gattner, V.Fluegel, V.Lopez-Carillo, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.29 / 2.35
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.742, 105.742, 69.674, 90.00, 90.00, 120.00
R / Rfree (%)	17.444 / 20.372

The binding sites of Magnesium atom in the Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp (pdb code 4bw9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp, PDB code: 4bw9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:54.1 occ:1.00 O1B A:ANP900 1.8 61.4 1.0 O1A A:ANP900 2.0 55.9 1.0 O A:HOH2036 2.0 55.7 1.0 O A:HOH2035 2.0 61.8 1.0 OG A:SER399 2.2 50.7 1.0 OE2 A:GLU396 2.3 60.0 1.0 CD A:GLU396 3.0 65.7 1.0 PB A:ANP900 3.1 52.3 1.0 OE1 A:GLU396 3.2 79.7 1.0 PA A:ANP900 3.2 56.7 1.0 CB A:SER399 3.2 48.3 1.0 O3A A:ANP900 3.5 56.7 1.0 N3B A:ANP900 3.8 51.0 1.0 O2 A:EDO1458 3.9 84.7 1.0 O2A A:ANP900 3.9 59.3 1.0 O A:HOH2044 4.1 67.1 1.0 OD1 A:ASP389 4.2 65.6 1.0 O2B A:ANP900 4.3 48.2 1.0 OD2 A:ASP389 4.4 80.7 1.0 CA A:SER399 4.4 50.1 1.0 CG A:GLU396 4.4 61.2 1.0 O5' A:ANP900 4.5 55.0 1.0 N A:SER399 4.6 51.2 1.0 O3' A:ANP900 4.6 54.0 1.0 CG A:ASP389 4.6 69.3 1.0 C5' A:ANP900 4.7 54.3 1.0 C3' A:ANP900 4.9 51.4 1.0

Magnesium binding site 2 out of 2 in the Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pylrs Y306G, Y384F, I405R Mutant in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:49.1 occ:1.00 O2G A:ANP900 1.8 54.8 1.0 O A:HOH2017 2.0 49.3 1.0 O A:HOH2024 2.1 44.7 1.0 O A:HOH2018 2.1 49.0 1.0 O2B A:ANP900 2.1 48.2 1.0 O A:HOH2043 2.2 51.6 1.0 PG A:ANP900 3.1 60.5 1.0 PB A:ANP900 3.4 52.3 1.0 N3B A:ANP900 3.7 51.0 1.0 O3G A:ANP900 3.7 69.7 1.0 NH1 A:ARG330 3.9 50.3 1.0 NE2 A:HIS338 3.9 61.5 1.0 OE2 A:GLU332 4.1 49.7 1.0 O3A A:ANP900 4.2 56.7 1.0 O1G A:ANP900 4.3 56.9 1.0 OE1 A:GLU332 4.4 55.6 1.0 CD2 A:HIS338 4.5 58.6 1.0 O1B A:ANP900 4.5 61.4 1.0 NE2 A:GLN287 4.6 61.1 1.0 OE1 A:GLN287 4.6 65.7 1.0 CD A:GLU332 4.7 55.7 1.0 N7 A:ANP900 4.7 53.4 1.0 CE1 A:HIS338 5.0 59.9 1.0

S.Schneider, M.J.Gattner, M.Vrabel, V.Flugel, V.Lopez-Carrillo, S.Prill, T.Carell. Structural Insights Into Incorporation of Norbornene Amino Acids For Click Modification of Proteins Chem.Bio.Chem. V. 14 2114 2013.
ISSN: ISSN 1439-4227
PubMed: 24027216
DOI: 10.1002/CBIC.201300435