Magnesium in PDB 8hch: Crystal Structure of MTREX1-Uridine Complex

All present enzymatic activity of Crystal Structure of MTREX1-Uridine Complex:
3.1.11.2;

The structure of Crystal Structure of MTREX1-Uridine Complex, PDB code: 8hch was solved by Y.Y.Hsiao, K.W.Huang, C.Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.69 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.632, 81.149, 93.653, 90, 103.51, 90
R / Rfree (%)	18.7 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of MTREX1-Uridine Complex (pdb code 8hch). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of MTREX1-Uridine Complex, PDB code: 8hch:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of MTREX1-Uridine Complex


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 MTREX1-Uridine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:51.3 occ:1.00 O A:HOH435 2.2 38.5 1.0 O A:HOH477 2.2 40.1 1.0 O A:HOH462 2.2 51.2 1.0 O A:HOH460 2.2 33.2 1.0 O A:HOH513 2.2 53.4 1.0 OD1 A:ASP18 2.3 35.6 1.0 CG A:ASP18 3.4 35.5 1.0 O A:HOH515 3.9 45.0 1.0 O A:HOH512 3.9 51.6 1.0 OE2 A:GLU20 4.0 36.5 1.0 O A:LEU19 4.0 30.5 1.0 OD2 A:ASP18 4.0 33.2 1.0 OD2 A:ASP130 4.1 38.2 1.0 OD2 A:ASP200 4.1 43.8 1.0 H5'1 A:URI302 4.2 48.3 1.0 H A:LEU19 4.2 36.4 1.0 O A:HIS124 4.2 27.0 1.0 O A:HOH434 4.2 27.5 1.0 OD1 A:ASP130 4.3 35.8 1.0 HA A:ASP18 4.4 32.7 1.0 O5' A:URI302 4.4 41.1 1.0 HB3 A:ASP200 4.4 32.9 1.0 HB3 A:HIS124 4.5 35.7 1.0 CB A:ASP18 4.6 26.9 1.0 H5'2 A:URI302 4.6 48.3 1.0 C5' A:URI302 4.6 40.2 1.0 HB2 A:ASP18 4.7 32.3 1.0 CG A:ASP130 4.7 35.3 1.0 O A:HOH470 4.7 28.6 1.0 N A:LEU19 4.8 30.3 1.0 HO5' A:URI302 4.9 49.4 1.0 CD A:GLU20 5.0 31.3 1.0 CA A:ASP18 5.0 27.2 1.0 CG A:ASP200 5.0 38.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of MTREX1-Uridine Complex


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 MTREX1-Uridine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:48.3 occ:1.00 O B:HOH473 2.2 39.5 1.0 O B:HOH468 2.2 51.2 1.0 O B:HOH420 2.2 34.2 1.0 O B:HOH464 2.2 48.3 1.0 O B:HOH499 2.2 55.0 1.0 OD1 B:ASP18 2.3 36.2 1.0 CG B:ASP18 3.5 35.7 1.0 OD2 B:ASP200 4.0 43.5 1.0 O B:HOH433 4.1 25.7 1.0 OD2 B:ASP18 4.1 32.9 1.0 OD2 B:ASP130 4.2 38.3 1.0 O B:HIS124 4.2 32.6 1.0 OE2 B:GLU20 4.2 30.6 1.0 H B:LEU19 4.2 33.4 1.0 O B:LEU19 4.3 34.2 1.0 OD1 B:ASP130 4.3 35.6 1.0 HB3 B:ASP200 4.3 35.2 1.0 O B:HOH482 4.4 29.9 1.0 H5'1 B:URI302 4.4 45.8 1.0 HB3 B:HIS124 4.5 38.4 1.0 O5' B:URI302 4.5 38.0 1.0 HA B:ASP18 4.5 32.2 1.0 HO5' B:URI302 4.6 45.7 1.0 CB B:ASP18 4.7 25.6 1.0 CG B:ASP130 4.7 32.6 1.0 HB2 B:ASP18 4.7 30.7 1.0 H5'2 B:URI302 4.8 45.8 1.0 C5' B:URI302 4.8 38.1 1.0 CG B:ASP200 4.9 38.2 1.0 CB B:ASP200 5.0 29.3 1.0 N B:LEU19 5.0 27.7 1.0 HB2 B:ASP200 5.0 35.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of MTREX1-Uridine Complex


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 MTREX1-Uridine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:49.5 occ:1.00 O C:HOH449 2.2 37.3 1.0 O C:HOH427 2.2 37.3 1.0 O C:HOH479 2.2 39.2 1.0 O C:HOH477 2.2 53.1 1.0 O C:HOH499 2.2 49.3 1.0 OD1 C:ASP18 2.2 32.8 1.0 O C:HOH493 3.4 42.7 1.0 CG C:ASP18 3.4 34.6 1.0 O C:HOH506 3.9 46.4 1.0 OD2 C:ASP130 4.0 33.9 1.0 O C:HOH422 4.0 26.2 1.0 O C:HIS124 4.1 28.9 1.0 OD2 C:ASP18 4.1 33.9 1.0 O C:LEU19 4.1 30.2 1.0 HO5' C:URI302 4.1 43.6 1.0 OE2 C:GLU20 4.2 33.6 1.0 OD2 C:ASP200 4.2 43.8 1.0 H C:LEU19 4.2 32.8 1.0 OD1 C:ASP130 4.3 39.0 1.0 HA C:ASP18 4.4 35.3 1.0 HB3 C:HIS124 4.4 37.1 1.0 O5' C:URI302 4.4 36.3 1.0 HB3 C:ASP200 4.5 32.2 1.0 HB2 C:ASP18 4.5 35.4 1.0 CB C:ASP18 4.5 29.4 1.0 O C:HOH467 4.6 28.8 1.0 H5'1 C:URI302 4.6 47.8 1.0 CG C:ASP130 4.6 36.9 1.0 H5'2 C:URI302 4.9 47.8 1.0 N C:LEU19 4.9 27.3 1.0 C5' C:URI302 4.9 39.8 1.0 CA C:ASP18 5.0 29.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of MTREX1-Uridine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of MTREX1-Uridine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:55.8 occ:1.00 O D:HOH461 2.2 43.9 1.0 O D:HOH477 2.2 50.9 1.0 O D:HOH435 2.2 37.6 1.0 O D:HOH464 2.2 49.8 1.0 O D:HOH492 2.2 57.4 1.0 OD2 D:ASP18 2.3 41.1 1.0 CG D:ASP18 3.5 35.2 1.0 OD2 D:ASP130 4.0 38.8 1.0 O D:HOH414 4.1 28.0 1.0 O D:HIS124 4.1 37.9 1.0 O D:LEU19 4.1 33.0 1.0 H D:LEU19 4.2 40.6 1.0 OD2 D:ASP200 4.2 44.7 1.0 OE2 D:GLU20 4.2 39.1 1.0 OD1 D:ASP18 4.2 36.4 1.0 OD1 D:ASP130 4.2 42.0 1.0 H5'2 D:URI302 4.2 57.8 1.0 O D:HOH481 4.4 30.6 1.0 HA D:ASP18 4.4 31.6 1.0 HB3 D:ASP200 4.4 34.4 1.0 HB3 D:HIS124 4.5 44.3 1.0 CG D:ASP130 4.5 37.0 1.0 O5' D:URI302 4.5 61.3 1.0 HB2 D:ASP18 4.6 37.3 1.0 CB D:ASP18 4.6 31.0 1.0 H5'1 D:URI302 4.7 57.8 1.0 C5' D:URI302 4.7 48.1 1.0 N D:LEU19 4.9 33.8 1.0 CA D:ASP18 5.0 26.3 1.0

Y.Y.Hsiao, K.W.Huang, C.Y.Wu. Molecular Insight Into the Specific Enzymatic Properties of TREX1 Revealing the Diverse Functions in Processing Rna and Dna/Rna Hybrids. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAD910