Magnesium in PDB 5k1p: Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp

All present enzymatic activity of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp:
6.1.1.26;

The structure of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp, PDB code: 5k1p was solved by A.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.28 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.493, 44.358, 64.314, 90.00, 99.92, 90.00
R / Rfree (%)	16.5 / 19.6

The binding sites of Magnesium atom in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp (pdb code 5k1p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp, PDB code: 5k1p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:23.2 occ:1.00 O A:HOH784 2.1 41.8 1.0 O A:HOH642 2.2 40.2 1.0 O1B A:ANP501 2.3 34.4 0.9 OG A:SER399 2.3 28.3 1.0 OE2 A:GLU396 2.5 26.1 1.0 O1A A:ANP501 2.5 29.2 0.9 OE1 A:GLU396 2.5 30.5 1.0 CD A:GLU396 2.9 31.4 1.0 O A:HOH666 3.1 45.1 1.0 PB A:ANP501 3.4 30.4 0.9 HNB1 A:ANP501 3.4 33.2 0.9 CB A:SER399 3.5 25.5 1.0 HB2 A:SER399 3.5 30.6 1.0 PA A:ANP501 3.6 28.1 0.9 O3A A:ANP501 3.6 30.5 0.9 HB3 A:SER399 3.9 30.6 1.0 N3B A:ANP501 3.9 27.7 0.9 HO3' A:ANP501 4.0 27.1 0.9 O A:HOH762 4.0 59.9 1.0 OD1 A:ASP389 4.1 31.0 1.0 O A:HOH604 4.1 36.8 1.0 CG A:GLU396 4.4 23.3 1.0 O2A A:ANP501 4.4 26.5 0.9 H5'2 A:ANP501 4.5 31.3 0.9 H3' A:ANP501 4.6 23.7 0.9 CA A:SER399 4.6 19.6 1.0 CG A:ASP389 4.7 30.5 1.0 HG2 A:GLU396 4.7 27.9 1.0 HG3 A:GLU396 4.7 27.9 1.0 O3' A:ANP501 4.7 22.6 0.9 OD2 A:ASP389 4.7 38.2 1.0 O2B A:ANP501 4.7 31.6 0.9 HG1 A:THR387 4.8 48.7 1.0 HA A:SER399 4.8 23.6 1.0 N A:SER399 4.8 20.9 1.0 O5' A:ANP501 4.8 24.4 0.9 H A:SER399 4.9 25.0 1.0

Magnesium binding site 2 out of 2 in the Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Polyspecific Pyrrolysyl-Trna Synthetase Mutant N346A/C348A in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:23.2 occ:1.00 O A:HOH725 2.1 32.1 1.0 O2G A:ANP501 2.1 28.1 0.9 O A:HOH722 2.2 34.8 1.0 O2B A:ANP501 2.2 31.6 0.9 O A:HOH670 2.2 26.4 1.0 HE2 A:HIS338 3.3 31.6 1.0 PG A:ANP501 3.5 29.2 0.9 PB A:ANP501 3.6 30.4 0.9 HH21 A:ARG330 3.6 27.7 1.0 HE22 A:GLN287 3.9 43.7 1.0 N3B A:ANP501 4.0 27.7 0.9 NE2 A:HIS338 4.0 26.3 1.0 HD2 A:HIS338 4.0 28.3 1.0 O1G A:ANP501 4.1 35.3 0.9 HH22 A:ARG330 4.2 27.7 1.0 NH2 A:ARG330 4.2 23.1 1.0 O A:HOH829 4.3 45.1 1.0 OE2 A:GLU332 4.3 27.3 1.0 CD2 A:HIS338 4.3 23.6 1.0 O1B A:ANP501 4.4 34.4 0.9 OE1 A:GLN287 4.5 41.3 1.0 OE1 A:GLU332 4.6 34.5 1.0 O3A A:ANP501 4.6 30.5 0.9 NE2 A:GLN287 4.7 36.4 1.0 O3G A:ANP501 4.7 35.0 0.9 HNB1 A:ANP501 4.8 33.2 0.9 HD3 A:ARG330 4.8 28.3 1.0 CD A:GLU332 4.9 30.5 1.0 N7 A:ANP501 4.9 20.2 0.9 HD2 A:ARG330 5.0 28.3 1.0

Y.J.Lee, M.J.Schmidt, J.M.Tharp, A.Weber, A.L.Koenig, H.Zheng, J.Gao, M.L.Waters, D.Summerer, W.R.Liu. Genetically Encoded Fluorophenylalanines Enable Insights Into the Recognition of Lysine Trimethylation By An Epigenetic Reader. Chem.Commun.(Camb.) V. 52 12606 2016.
ISSN: ESSN 1364-548X
PubMed: 27711380
DOI: 10.1039/C6CC05959G