Magnesium in PDB 6a47: Structure of TREX2 in Complex with A Y Structured Dsdna

All present enzymatic activity of Structure of TREX2 in Complex with A Y Structured Dsdna:
3.1.11.2;

The structure of Structure of TREX2 in Complex with A Y Structured Dsdna, PDB code: 6a47 was solved by Y.Y.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.666, 48.404, 90.593, 90.00, 97.36, 90.00
R / Rfree (%)	16.3 / 19.1

The structure of Structure of TREX2 in Complex with A Y Structured Dsdna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Structure of TREX2 in Complex with A Y Structured Dsdna (pdb code 6a47). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of TREX2 in Complex with A Y Structured Dsdna, PDB code: 6a47:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of TREX2 in Complex with A Y Structured Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of TREX2 in Complex with A Y Structured Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:40.8 occ:1.00 OE2 A:GLU16 2.2 44.3 1.0 OD2 A:ASP193 2.4 35.2 1.0 OP1 C:DT23 2.4 29.7 1.0 OD2 A:ASP14 2.6 33.5 1.0 HA A:HIS188 2.8 61.2 1.0 HB2 A:ASP193 3.1 32.7 1.0 CD A:GLU16 3.1 43.0 1.0 CG A:ASP193 3.3 34.6 1.0 CG A:ASP14 3.3 30.4 1.0 OD1 A:ASP14 3.4 27.4 1.0 OE1 A:GLU16 3.4 43.8 1.0 CB A:ASP193 3.5 27.3 1.0 HB3 A:ASP193 3.5 32.7 1.0 CA A:HIS188 3.7 51.0 1.0 MG C:MG101 3.8 30.7 1.0 P C:DT23 3.8 28.9 1.0 H A:HIS188 3.8 58.5 1.0 H5'' C:DT23 3.9 35.6 1.0 HA A:ALA190 3.9 34.6 1.0 ND1 A:HIS188 4.0 55.4 1.0 O A:LEU15 4.2 27.1 1.0 N A:HIS188 4.3 48.8 1.0 C A:HIS188 4.4 51.6 1.0 O A:HOH502 4.4 30.7 1.0 O A:SER189 4.4 36.3 1.0 O A:HOH488 4.4 40.5 1.0 OD1 A:ASP193 4.5 36.9 1.0 CG A:GLU16 4.5 31.9 1.0 OP2 C:DT23 4.5 26.9 1.0 O5' C:DT23 4.5 28.4 1.0 HG2 A:GLU16 4.5 38.2 1.0 CG A:HIS188 4.6 54.3 1.0 CB A:HIS188 4.6 53.2 1.0 O A:HOH437 4.6 25.3 1.0 C5' C:DT23 4.7 29.7 1.0 CE1 A:HIS188 4.7 54.0 1.0 C A:SER189 4.7 39.9 1.0 HA A:GLU16 4.8 31.3 1.0 CB A:ASP14 4.8 23.4 1.0 HE1 A:HIS188 4.8 64.8 1.0 CA A:ALA190 4.8 28.9 1.0 HO3' C:DT23 4.8 31.6 1.0 HB3 A:HIS188 4.8 63.8 1.0 O A:HIS188 4.8 46.7 1.0 N A:SER189 4.8 57.2 1.0 O3' C:DT22 4.9 25.6 1.0 C A:LEU15 4.9 23.4 1.0 H A:ASP193 4.9 31.7 1.0 HG3 A:GLU16 5.0 38.2 1.0 HB3 A:ASP14 5.0 28.1 1.0 CA A:ASP193 5.0 25.1 1.0 N A:ALA190 5.0 31.0 1.0

Magnesium binding site 2 out of 4 in the Structure of TREX2 in Complex with A Y Structured Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of TREX2 in Complex with A Y Structured Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:50.6 occ:1.00 OE2 B:GLU16 2.0 70.4 1.0 OD2 B:ASP193 2.4 42.1 1.0 OP1 D:DT23 2.4 31.6 1.0 OD2 B:ASP14 2.7 38.5 1.0 CD B:GLU16 3.0 64.7 1.0 OE1 B:GLU16 3.2 67.0 1.0 HB2 B:ASP193 3.3 38.1 1.0 OD1 B:ASP14 3.4 32.7 1.0 CG B:ASP193 3.4 40.0 1.0 CG B:ASP14 3.4 31.0 1.0 P D:DT23 3.7 33.5 1.0 H5'' D:DT23 3.7 35.4 1.0 CB B:ASP193 3.8 31.7 1.0 MG D:MG101 3.8 32.1 1.0 HB3 B:ASP193 3.9 38.1 1.0 HA B:ALA190 4.0 35.3 1.0 O B:LEU15 4.3 28.1 1.0 CG B:GLU16 4.3 46.4 1.0 O5' D:DT23 4.3 32.2 1.0 HG2 B:GLU16 4.4 55.6 1.0 OP2 D:DT23 4.4 33.0 1.0 HO3' D:DT23 4.5 36.5 1.0 C5' D:DT23 4.5 29.5 1.0 OD1 B:ASP193 4.5 39.0 1.0 O B:HOH526 4.5 32.2 1.0 HA B:GLU16 4.6 34.0 1.0 O B:HOH448 4.7 26.2 1.0 HG3 B:GLU16 4.8 55.6 1.0 O3' D:DT22 4.8 35.2 1.0 CB B:ASP14 4.9 25.4 1.0 C B:LEU15 4.9 28.1 1.0 CA B:ALA190 4.9 29.4 1.0 H3' D:DT23 5.0 38.0 1.0

Magnesium binding site 3 out of 4 in the Structure of TREX2 in Complex with A Y Structured Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of TREX2 in Complex with A Y Structured Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:30.7 occ:1.00 OD1 A:ASP14 2.3 27.4 1.0 O A:HOH437 2.3 25.3 1.0 O A:HOH414 2.4 25.0 1.0 O A:HOH502 2.4 30.7 1.0 OP1 C:DT23 2.4 29.7 1.0 O3' C:DT22 2.7 25.6 1.0 P C:DT23 3.1 28.9 1.0 CG A:ASP14 3.4 30.4 1.0 H4' C:DT22 3.6 31.9 1.0 MG A:MG301 3.8 40.8 1.0 C3' C:DT22 3.9 28.8 1.0 H5'' C:DT22 3.9 31.4 1.0 H5'' C:DT23 3.9 35.6 1.0 O A:HOH441 3.9 22.0 1.0 OD2 A:ASP14 4.0 33.5 1.0 H5' C:DT23 4.0 35.6 1.0 H A:LEU15 4.0 26.3 1.0 C4' C:DT22 4.1 26.6 1.0 OD2 A:ASP123 4.1 28.4 1.0 O A:HOH462 4.2 27.9 1.0 OD1 A:ASP123 4.2 29.3 1.0 OP2 C:DT23 4.2 26.9 1.0 O5' C:DT23 4.2 28.4 1.0 C5' C:DT23 4.3 29.7 1.0 O A:LEU15 4.3 27.1 1.0 HA A:ASP14 4.3 25.9 1.0 O C:HOH208 4.4 34.3 1.0 H2'' C:DT22 4.5 36.0 1.0 H3' C:DT22 4.5 34.6 1.0 C5' C:DT22 4.5 26.2 1.0 O A:HIS117 4.6 26.2 1.0 CB A:ASP14 4.6 23.4 1.0 CG A:ASP123 4.6 27.6 1.0 HB3 A:HIS117 4.7 34.7 1.0 HD2 A:TYR122 4.7 31.4 1.0 HB2 A:ASP14 4.7 28.1 1.0 HB3 A:ASP193 4.7 32.7 1.0 N A:LEU15 4.8 21.9 1.0 C2' C:DT22 4.8 30.0 1.0 CA A:ASP14 4.9 21.6 1.0

Magnesium binding site 4 out of 4 in the Structure of TREX2 in Complex with A Y Structured Dsdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of TREX2 in Complex with A Y Structured Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:32.1 occ:1.00 OD1 B:ASP14 2.3 32.7 1.0 O B:HOH448 2.3 26.2 1.0 O B:HOH416 2.3 27.7 1.0 OP1 D:DT23 2.3 31.6 1.0 O B:HOH526 2.5 32.2 1.0 O3' D:DT22 2.6 35.2 1.0 P D:DT23 3.1 33.5 1.0 CG B:ASP14 3.5 31.0 1.0 H4' D:DT22 3.6 39.5 1.0 MG B:MG301 3.8 50.6 1.0 H5'' D:DT23 3.8 35.4 1.0 C3' D:DT22 3.9 34.1 1.0 H5'' D:DT22 3.9 37.4 1.0 H5' D:DT23 3.9 35.4 1.0 O B:HOH474 4.0 28.0 1.0 H B:LEU15 4.0 28.1 1.0 OD2 B:ASP14 4.0 38.5 1.0 OD2 B:ASP123 4.1 28.1 1.0 OD1 B:ASP123 4.1 33.4 1.0 C4' D:DT22 4.1 32.9 1.0 O5' D:DT23 4.2 32.2 1.0 C5' D:DT23 4.2 29.5 1.0 OP2 D:DT23 4.2 33.0 1.0 O B:HOH520 4.2 31.2 1.0 HA B:ASP14 4.2 29.7 1.0 O B:LEU15 4.3 28.1 1.0 O D:HOH207 4.4 39.5 1.0 H2'' D:DT22 4.4 40.3 1.0 H3' D:DT22 4.5 41.0 1.0 C5' D:DT22 4.6 31.2 1.0 CG B:ASP123 4.6 31.9 1.0 CB B:ASP14 4.6 25.4 1.0 HB3 B:ASP193 4.6 38.1 1.0 O B:HIS117 4.7 31.9 1.0 HB2 B:ASP14 4.7 30.4 1.0 N B:LEU15 4.7 23.4 1.0 C2' D:DT22 4.8 33.6 1.0 HD2 B:TYR122 4.8 40.5 1.0 CA B:ASP14 4.9 24.8 1.0 HB3 B:HIS117 4.9 32.0 1.0 OD2 B:ASP193 5.0 42.1 1.0

H.L.Cheng, C.T.Lin, K.W.Huang, S.Wang, Y.T.Lin, S.I.Toh, Y.Y.Hsiao. Structural Insights Into the Duplex Dna Processing of TREX2 Nucleic Acids Res. V. 46 12166 2018.
ISSN: ESSN 1362-4962
PubMed: 30357414
DOI: 10.1093/NAR/GKY970