Magnesium in PDB 6lyb: Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp

All present enzymatic activity of Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp:
6.1.1.26;

The structure of Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp, PDB code: 6lyb was solved by J.H.Weng, M.D.Tsai, Y.S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.27 / 1.90
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.369, 105.369, 71.459, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.3

The binding sites of Magnesium atom in the Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp (pdb code 6lyb). 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 C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp, PDB code: 6lyb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.8 occ:1.00 O A:HOH649 2.0 49.2 1.0 HOA2 A:ANP501 2.0 48.5 1.0 O1B A:ANP501 2.2 43.4 1.0 OG A:SER399 2.2 35.9 1.0 O A:HOH692 2.2 46.2 1.0 O2A A:ANP501 2.3 40.4 1.0 OE2 A:GLU396 2.4 38.5 1.0 OE1 A:GLU396 3.1 48.2 1.0 CD A:GLU396 3.1 45.5 1.0 PB A:ANP501 3.2 38.1 1.0 HNB1 A:ANP501 3.3 41.7 1.0 HB2 A:SER399 3.3 44.9 1.0 CB A:SER399 3.3 37.4 1.0 PA A:ANP501 3.3 38.5 1.0 O3A A:ANP501 3.4 35.1 1.0 HB3 A:SER399 3.8 44.9 1.0 N3B A:ANP501 3.8 34.8 1.0 O A:HOH624 3.9 51.5 1.0 O1A A:ANP501 4.1 37.4 1.0 H5 A:EXR504 4.1 65.6 0.8 HO3' A:ANP501 4.1 39.9 1.0 H5'2 A:ANP501 4.3 52.2 1.0 OD1 A:ASP389 4.4 51.8 1.0 CA A:SER399 4.5 36.8 1.0 H3' A:ANP501 4.5 40.1 1.0 CG A:GLU396 4.5 40.3 1.0 O2B A:ANP501 4.5 38.1 1.0 O3' A:ANP501 4.6 33.3 1.0 H A:SER399 4.6 40.8 1.0 O5' A:ANP501 4.6 44.0 1.0 N A:SER399 4.6 34.0 1.0 H7 A:EXR504 4.6 65.6 0.8 HA A:SER399 4.7 44.2 1.0 N A:EXR504 4.7 54.7 0.8 HG2 A:GLU396 4.7 48.3 1.0 HG3 A:GLU396 4.9 48.3 1.0 C5' A:ANP501 5.0 43.5 1.0

Magnesium binding site 2 out of 2 in the Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pylrs C-Terminus Domain Mutant in Complex with 3-Benzothienyl-D- Alanine and Ampnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:34.7 occ:1.00 HOB2 A:ANP501 1.8 45.7 1.0 O2G A:ANP501 1.9 37.2 1.0 O A:HOH683 1.9 38.3 1.0 O A:HOH639 1.9 36.6 1.0 O2B A:ANP501 2.1 38.1 1.0 HOG2 A:ANP501 2.1 44.6 1.0 O A:HOH612 2.1 32.7 1.0 O A:HOH698 2.4 41.3 1.0 PG A:ANP501 3.2 38.4 1.0 HH21 A:ARG330 3.3 42.8 1.0 PB A:ANP501 3.4 38.1 1.0 N3B A:ANP501 3.7 34.8 1.0 HE22 A:GLN287 3.8 55.2 1.0 HH22 A:ARG330 3.8 42.8 1.0 NH2 A:ARG330 3.9 35.7 1.0 O3G A:ANP501 3.9 39.8 1.0 NE2 A:HIS338 4.0 38.0 1.0 HOG3 A:ANP501 4.0 47.7 1.0 HD2 A:HIS338 4.1 39.5 1.0 OE2 A:GLU332 4.1 38.4 1.0 O A:HOH745 4.2 46.1 1.0 O1B A:ANP501 4.3 43.4 1.0 O1G A:ANP501 4.3 36.1 1.0 O3A A:ANP501 4.3 35.1 1.0 CD2 A:HIS338 4.4 32.9 1.0 OE1 A:GLU332 4.4 36.3 1.0 O A:HOH659 4.4 61.1 1.0 OE1 A:GLN287 4.5 49.3 1.0 HD3 A:ARG330 4.6 39.0 1.0 HNB1 A:ANP501 4.6 41.7 1.0 NE2 A:GLN287 4.6 46.0 1.0 N7 A:ANP501 4.6 29.8 1.0 CD A:GLU332 4.7 42.4 1.0 HD2 A:ARG330 4.9 39.0 1.0 H8 A:ANP501 5.0 36.9 1.0

H.K.Jiang, Y.H.Wang, J.H.Weng, P.Kurkute, C.L.Li, M.N.Lee, P.J.Chen, H.W.Tseng, M.D.Tsai, Y.S.Wang. Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Biochemistry V. 59 2205 2020.
ISSN: ISSN 0006-2960
PubMed: 32484330
DOI: 10.1021/ACS.BIOCHEM.0C00307