Magnesium in PDB 4tqd: Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe and Atp

All present enzymatic activity of Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe and Atp:
6.1.1.26;

The structure of Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe and Atp, PDB code: 4tqd was solved by A.Nakamura, P.O'donoghue, D.Soll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.06 / 2.14
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	104.700, 104.700, 70.660, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 19.3

The structure of Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe and Atp also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe and Atp (pdb code 4tqd). 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 Ifrs Bound with 3-Iodo- L-Phe and Atp, PDB code: 4tqd:
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 Ifrs Bound with 3-Iodo- L-Phe 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 Ifrs Bound with 3-Iodo- L-Phe and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:44.4 occ:1.00 O2G A:ATP504 2.0 37.7 1.0 O A:HOH671 2.1 41.6 1.0 O2B A:ATP504 2.1 43.7 1.0 O A:HOH654 2.1 34.8 1.0 O A:HOH670 2.1 36.9 1.0 O A:HOH717 2.2 47.4 1.0 PG A:ATP504 3.3 40.3 1.0 PB A:ATP504 3.3 39.5 1.0 O3B A:ATP504 3.5 41.1 1.0 O3G A:ATP504 3.9 46.1 1.0 O A:HOH683 3.9 56.5 1.0 NH1 A:ARG330 3.9 38.0 1.0 NE2 A:HIS338 3.9 48.2 1.0 OE2 A:GLU332 4.1 38.4 1.0 O3A A:ATP504 4.3 42.4 1.0 OE1 A:GLU283 4.3 81.7 1.0 OE1 A:GLU332 4.4 37.3 1.0 OE1 A:GLN287 4.4 45.5 1.0 O1B A:ATP504 4.4 44.1 1.0 CD2 A:HIS338 4.4 40.8 1.0 OE2 A:GLU283 4.4 77.0 1.0 O A:HOH716 4.4 63.6 1.0 O1G A:ATP504 4.5 37.2 1.0 NE2 A:GLN287 4.6 46.7 1.0 N7 A:ATP504 4.7 37.1 1.0 CD A:GLU283 4.7 84.7 1.0 CD A:GLU332 4.7 45.5 1.0 CD A:GLN287 4.9 45.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe 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 Ifrs Bound with 3-Iodo- L-Phe and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.7 occ:1.00 O A:HOH663 2.1 42.7 1.0 O1B A:ATP504 2.1 44.1 1.0 OG A:SER399 2.2 43.6 1.0 O1A A:ATP504 2.3 44.2 1.0 OE2 A:GLU396 2.3 43.2 1.0 O A:HOH714 2.4 62.4 1.0 CD A:GLU396 3.1 45.9 1.0 OE1 A:GLU396 3.2 57.4 1.0 CB A:SER399 3.2 42.4 1.0 MG A:MG503 3.3 56.0 1.0 PB A:ATP504 3.4 39.5 1.0 PA A:ATP504 3.4 39.1 1.0 O3A A:ATP504 3.6 42.4 1.0 OD2 A:ASP389 4.0 70.3 1.0 O3B A:ATP504 4.2 41.1 1.0 OD1 A:ASP389 4.2 55.6 1.0 O2A A:ATP504 4.3 42.9 1.0 CA A:SER399 4.3 42.4 1.0 N A:SER399 4.4 40.5 1.0 O A:HOH716 4.5 63.6 1.0 O3' A:ATP504 4.5 37.5 1.0 CG A:GLU396 4.5 40.1 1.0 CG A:ASP389 4.5 60.2 1.0 O2B A:ATP504 4.6 43.7 1.0 O5' A:ATP504 4.6 34.4 1.0 C3' A:ATP504 4.8 34.2 1.0 O3G A:ATP504 4.8 46.1 1.0 C5' A:ATP504 4.9 31.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the C-Terminal Domain of Ifrs Bound with 3-Iodo- L-Phe 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 Ifrs Bound with 3-Iodo- L-Phe and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:56.0 occ:1.00 O3G A:ATP504 2.3 46.1 1.0 O1B A:ATP504 2.4 44.1 1.0 OE1 A:GLU396 2.5 57.4 1.0 O A:HOH715 2.5 58.2 1.0 O A:HOH716 2.7 63.6 1.0 O A:HOH714 2.8 62.4 1.0 MG A:MG502 3.3 44.7 1.0 PB A:ATP504 3.4 39.5 1.0 PG A:ATP504 3.5 40.3 1.0 O3B A:ATP504 3.5 41.1 1.0 CD A:GLU396 3.6 45.9 1.0 OE2 A:GLU396 3.9 43.2 1.0 O A:HOH682 4.1 51.7 1.0 O2B A:ATP504 4.2 43.7 1.0 O A:HOH663 4.2 42.7 1.0 O A:HOH717 4.3 47.4 1.0 OD2 A:ASP389 4.4 70.3 1.0 O1G A:ATP504 4.4 37.2 1.0 O2G A:ATP504 4.4 37.7 1.0 O3A A:ATP504 4.8 42.4 1.0 CG A:GLU396 4.9 40.1 1.0

L.T.Guo, Y.S.Wang, A.Nakamura, D.Eiler, J.Kavran, M.Wong, L.Kiessling, T.Steitz, P.O'donoghue, D.Soll. Polyspecific Pyrrolysyl-Trna Synthetases From Directed Evolution Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490