Magnesium in PDB 4zib: Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp

All present enzymatic activity of Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp:
6.1.1.26;

The structure of Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp, PDB code: 4zib was solved by A.Nakamura, L.T.Guo, Y.S.Wang, D.Soll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 2.05
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	105.140, 105.140, 70.920, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.8

The binding sites of Magnesium atom in the Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp (pdb code 4zib). 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 the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp, PDB code: 4zib:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp


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 the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:41.8 occ:1.00 O A:HOH660 2.0 42.1 1.0 O A:HOH662 2.1 39.7 1.0 O2B A:ATP504 2.1 40.8 1.0 O2G A:ATP504 2.1 39.2 1.0 O A:HOH607 2.1 35.8 1.0 O A:HOH693 2.2 44.0 1.0 PG A:ATP504 3.3 44.1 1.0 PB A:ATP504 3.3 41.3 1.0 O3B A:ATP504 3.4 41.9 1.0 NH1 A:ARG330 3.8 36.5 1.0 O3G A:ATP504 3.8 45.9 1.0 OE2 A:GLU332 4.1 38.8 1.0 NE2 A:HIS338 4.2 44.5 1.0 O1B A:ATP504 4.3 49.6 1.0 O3A A:ATP504 4.4 46.2 1.0 OE1 A:GLN287 4.5 54.1 1.0 OE1 A:GLU332 4.5 41.9 1.0 CD2 A:HIS338 4.5 40.1 1.0 O1G A:ATP504 4.5 38.2 1.0 OE1 A:GLU283 4.6 75.9 1.0 OE2 A:GLU283 4.6 72.4 1.0 N7 A:ATP504 4.6 38.0 1.0 NE2 A:GLN287 4.6 50.2 1.0 O A:HOH659 4.6 64.9 1.0 CD A:GLU332 4.7 48.6 1.0 CD A:GLU283 4.9 75.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp


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 the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:48.4 occ:1.00 O A:HOH686 2.1 52.7 1.0 O1B A:ATP504 2.2 49.6 1.0 OG A:SER399 2.2 45.0 1.0 O A:HOH702 2.2 51.2 1.0 O1A A:ATP504 2.3 42.9 1.0 OE2 A:GLU396 2.4 45.7 1.0 CB A:SER399 3.2 45.7 1.0 CD A:GLU396 3.3 51.5 1.0 PB A:ATP504 3.3 41.3 1.0 PA A:ATP504 3.3 41.8 1.0 O3A A:ATP504 3.3 46.2 1.0 OE1 A:GLU396 3.4 60.9 1.0 MG A:MG503 3.4 57.5 1.0 O A:HOH651 3.9 55.5 1.0 O A:HOH659 4.1 64.9 1.0 O2A A:ATP504 4.2 42.0 1.0 O3B A:ATP504 4.2 41.9 1.0 OD2 A:ASP389 4.4 74.7 1.0 CA A:SER399 4.4 46.0 1.0 O2B A:ATP504 4.5 40.8 1.0 OD1 A:ASP389 4.5 62.6 1.0 O5' A:ATP504 4.6 38.5 1.0 CG A:GLU396 4.6 44.7 1.0 N A:SER399 4.7 41.3 1.0 O3' A:ATP504 4.7 40.5 1.0 O3G A:ATP504 4.7 45.9 1.0 C5' A:ATP504 4.8 35.2 1.0 CG A:ASP389 4.8 67.2 1.0 C3' A:ATP504 4.9 34.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp


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 the C-Terminal Domain of Pylrs Mutant Bound with 3-Benzothienyl-L-Alanine and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:57.5 occ:1.00 O3G A:ATP504 2.1 45.9 1.0 O A:HOH659 2.4 64.9 1.0 O1B A:ATP504 2.4 49.6 1.0 O A:HOH726 2.5 65.7 1.0 OE1 A:GLU396 2.5 60.9 1.0 O A:HOH686 2.6 52.7 1.0 MG A:MG502 3.4 48.4 1.0 PG A:ATP504 3.5 44.1 1.0 PB A:ATP504 3.5 41.3 1.0 CD A:GLU396 3.5 51.5 1.0 O3B A:ATP504 3.6 41.9 1.0 OE2 A:GLU396 3.8 45.7 1.0 O A:HOH609 3.9 57.9 1.0 O1G A:ATP504 4.3 38.2 1.0 O A:HOH693 4.4 44.0 1.0 O2B A:ATP504 4.4 40.8 1.0 OD2 A:ASP389 4.5 74.7 1.0 O A:HOH702 4.5 51.2 1.0 O2G A:ATP504 4.5 39.2 1.0 O3A A:ATP504 4.8 46.2 1.0 CG A:GLU396 4.9 44.7 1.0

M.Englert, A.Nakamura, Y.S.Wang, D.Eiler, D.Soll, L.T.Guo. Probing the Active Site Tryptophan of Staphylococcus Aureus Thioredoxin with An Analog. Nucleic Acids Res. V. 43 11061 2015.
ISSN: ESSN 1362-4962
PubMed: 26582921
DOI: 10.1093/NAR/GKV1255