Magnesium in PDB 8hcg: Crystal Structure of MTREX1-Damp Complex

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

The structure of Crystal Structure of MTREX1-Damp Complex, PDB code: 8hcg 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)	27.64 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.585, 92.585, 67.44, 90, 90, 120
R / Rfree (%)	16.5 / 19.2

The structure of Crystal Structure of MTREX1-Damp Complex also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

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

Magnesium binding site 1 out of 2 in the Crystal Structure of MTREX1-Damp 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-Damp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg307 b:139.4 occ:1.00 H2 A:HOH468 1.8 30.9 1.0 H1 A:HOH412 1.8 23.6 1.0 O1P A:D5M306 1.9 24.7 1.0 O A:HOH468 2.1 25.8 1.0 O A:HOH409 2.1 41.8 1.0 OD1 A:ASP18 2.2 33.5 1.0 O A:HOH412 2.4 19.7 1.0 H1 A:HOH468 2.8 30.9 1.0 CG A:ASP18 2.9 24.0 1.0 OD2 A:ASP18 2.9 29.2 1.0 H131 A:1PE301 3.0 59.7 1.0 H2 A:HOH412 3.1 23.6 1.0 P A:D5M306 3.2 23.9 1.0 MG A:MG308 3.3 26.9 1.0 O3P A:D5M306 3.9 24.2 1.0 O A:HOH445 3.9 26.8 1.0 C13 A:1PE301 3.9 49.7 1.0 H5'1 A:D5M306 3.9 27.2 1.0 O5' A:D5M306 4.0 22.7 1.0 H5'2 A:D5M306 4.0 27.2 1.0 H A:LEU19 4.1 21.7 1.0 OD2 A:ASP130 4.1 30.9 1.0 H132 A:1PE301 4.1 59.7 1.0 O A:LEU19 4.2 24.2 1.0 H241 A:1PE301 4.2 38.9 1.0 O2P A:D5M306 4.2 22.4 1.0 H242 A:1PE301 4.2 38.9 1.0 C5' A:D5M306 4.2 22.6 1.0 O A:HOH481 4.3 26.9 1.0 OD1 A:ASP130 4.3 27.5 1.0 O A:HOH420 4.4 19.5 1.0 O A:HIS124 4.4 21.1 1.0 CB A:ASP18 4.4 16.2 1.0 HB3 A:ASP200 4.4 32.0 1.0 HB3 A:HIS124 4.4 28.9 1.0 H232 A:1PE301 4.5 63.5 1.0 OD2 A:ASP200 4.5 27.1 1.0 HA A:ASP18 4.6 22.6 1.0 H231 A:1PE301 4.6 63.5 1.0 C24 A:1PE301 4.6 32.4 1.0 C23 A:1PE301 4.6 52.9 1.0 CG A:ASP130 4.6 28.9 1.0 HB2 A:ASP18 4.7 19.5 1.0 N A:LEU19 4.8 18.1 1.0 OH4 A:1PE301 4.8 39.1 1.0 HB2 A:ASP200 4.9 32.0 1.0 HD2 A:HIS124 4.9 42.0 1.0 HB3 A:ASP18 4.9 19.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of MTREX1-Damp 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-Damp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg308 b:26.9 occ:1.00 OD2 A:ASP18 2.1 29.2 1.0 OD2 A:ASP200 2.2 27.1 1.0 OE2 A:GLU20 2.3 23.1 1.0 O1P A:D5M306 2.4 24.7 1.0 O2P A:D5M306 2.7 22.4 1.0 HB2 A:ASP200 3.0 32.0 1.0 HA A:HIS195 3.1 31.5 1.0 P A:D5M306 3.1 23.9 1.0 CG A:ASP200 3.2 37.8 1.0 CD A:GLU20 3.2 25.4 1.0 MG A:MG307 3.3 139.4 1.0 CG A:ASP18 3.3 24.0 1.0 CB A:ASP200 3.4 26.7 1.0 OE1 A:GLU20 3.5 23.3 1.0 HB3 A:ASP200 3.5 32.0 1.0 O A:HOH468 3.7 25.8 1.0 HA A:ALA197 3.8 22.1 1.0 H2 A:HOH468 3.8 30.9 1.0 OD1 A:ASP18 3.9 33.5 1.0 O A:THR196 3.9 23.3 1.0 H5'2 A:D5M306 3.9 27.2 1.0 O A:LEU19 3.9 24.2 1.0 O3P A:D5M306 4.0 24.2 1.0 CA A:HIS195 4.0 26.3 1.0 H A:HIS195 4.1 29.2 1.0 HD1 A:HIS195 4.1 39.0 1.0 H1 A:HOH412 4.1 23.6 1.0 H1 A:HOH468 4.2 30.9 1.0 O A:HOH412 4.3 19.7 1.0 C A:THR196 4.3 23.8 1.0 OD1 A:ASP200 4.3 29.4 1.0 C A:HIS195 4.3 26.4 1.0 HB3 A:ASP18 4.3 19.5 1.0 O A:HOH445 4.4 26.8 1.0 O5' A:D5M306 4.4 22.7 1.0 CB A:ASP18 4.5 16.2 1.0 HG2 A:GLU20 4.5 25.2 1.0 CG A:GLU20 4.5 21.0 1.0 N A:THR196 4.5 22.5 1.0 N A:HIS195 4.5 24.3 1.0 CA A:ALA197 4.6 18.4 1.0 C5' A:D5M306 4.6 22.6 1.0 H A:THR196 4.7 27.0 1.0 N A:ALA197 4.7 23.1 1.0 C A:LEU19 4.7 25.3 1.0 H A:ASP200 4.8 25.7 1.0 H A:LEU19 4.8 21.7 1.0 ND1 A:HIS195 4.8 32.5 1.0 HA A:GLU20 4.8 20.4 1.0 O A:HOH462 4.9 38.0 1.0 CA A:ASP200 4.9 20.7 1.0 O A:HIS195 4.9 24.7 1.0 H2 A:HOH412 5.0 23.6 1.0 HB2 A:ASP18 5.0 19.5 1.0 HB3 A:HIS195 5.0 31.4 1.0 HG3 A:GLU20 5.0 25.2 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