Sodium 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:

Magnesium

(Mg)

2 atoms

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

Sodium binding site 1 out of 2 in the Crystal Structure of MTREX1-Damp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of MTREX1-Damp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:77.5 occ:1.00 H A:GLY234 2.4 50.3 1.0 HH12 A:ARG28 3.2 100.5 1.0 N A:GLY234 3.3 41.9 1.0 HB2 A:TYR233 3.5 34.9 1.0 HH11 A:ARG28 3.5 100.5 1.0 HA3 A:GLY234 3.6 86.7 1.0 HA A:TYR233 3.6 35.9 1.0 NH1 A:ARG28 3.7 83.8 1.0 CA A:GLY234 4.0 72.3 1.0 CA A:TYR233 4.2 29.9 1.0 C A:TYR233 4.2 31.5 1.0 CB A:TYR233 4.2 29.1 1.0 HB3 A:TYR233 4.6 34.9 1.0 O A:GLY234 4.6 132.4 1.0 HA2 A:GLY234 4.7 86.7 1.0 C A:GLY234 4.8 116.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of MTREX1-Damp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of MTREX1-Damp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:36.7 occ:1.00 H A:LEU24 2.3 28.1 1.0 HG A:SER78 2.8 60.3 1.0 HA3 A:GLY23 3.1 28.8 1.0 N A:LEU24 3.2 23.4 1.0 HB3 A:SER78 3.2 39.3 1.0 HB3 A:SER27 3.3 36.8 1.0 HB2 A:LEU24 3.4 33.8 1.0 HA2 A:GLY23 3.4 28.8 1.0 OG A:SER78 3.5 50.2 1.0 HB2 A:SER78 3.6 39.3 1.0 CA A:GLY23 3.6 24.0 1.0 CB A:SER78 3.6 32.8 1.0 HG A:LEU24 3.6 31.3 1.0 HD12 A:LEU24 3.7 40.0 1.0 H2 A:D5M306 3.8 51.2 1.0 C A:GLY23 3.9 24.1 1.0 CB A:LEU24 4.0 28.2 1.0 CB A:SER27 4.1 30.6 1.0 OG A:SER27 4.1 30.8 1.0 HG A:SER27 4.1 37.0 1.0 CG A:LEU24 4.2 26.1 1.0 CA A:LEU24 4.2 23.5 1.0 HB2 A:SER27 4.4 36.8 1.0 CD1 A:LEU24 4.4 33.3 1.0 O A:HOH459 4.6 31.8 1.0 C2 A:D5M306 4.6 42.7 1.0 O A:LEU24 4.7 24.9 1.0 N3 A:D5M306 4.7 28.9 1.0 HD11 A:LEU24 4.9 40.0 1.0 C A:LEU24 4.9 24.7 1.0 H A:SER27 4.9 31.9 1.0 HB3 A:LEU24 4.9 33.8 1.0 O A:THR22 4.9 25.1 1.0 HA A:LEU24 4.9 28.1 1.0 N A:GLY23 5.0 21.5 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