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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 6lyb

Go back to Magnesium Binding Sites List in 6lyb
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 6lyb

Go back to Magnesium Binding Sites List in 6lyb
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

Reference:

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
Page generated: Mon Jan 25 09:06:23 2021

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