Magnesium in PDB 5yws: Crystal Structure of TREX1 in Complex with A Y Structured Dna

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Y Structured Dna:
3.1.11.2;

The structure of Crystal Structure of TREX1 in Complex with A Y Structured Dna, PDB code: 5yws 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)	29.33 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.532, 96.604, 101.112, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.6

The binding sites of Magnesium atom in the Crystal Structure of TREX1 in Complex with A Y Structured Dna (pdb code 5yws). 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 TREX1 in Complex with A Y Structured Dna, PDB code: 5yws:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 TREX1 in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:26.8 occ:1.00 OD2 A:ASP200 2.1 31.6 1.0 OP1 C:DC22 2.3 25.9 1.0 OE1 A:GLU20 2.3 27.4 1.0 OD2 A:ASP18 2.4 26.0 1.0 HA A:HIS195 2.9 41.9 1.0 HB2 A:ASP200 3.1 27.2 1.0 CD A:GLU20 3.1 26.0 1.0 CG A:ASP200 3.2 27.5 1.0 CG A:ASP18 3.2 25.5 1.0 OD1 A:ASP18 3.3 26.9 1.0 OE2 A:GLU20 3.3 26.0 1.0 CB A:ASP200 3.5 24.3 1.0 MG A:MG302 3.6 31.2 1.0 HB3 A:ASP200 3.6 27.2 1.0 P C:DC22 3.7 26.7 1.0 O A:LEU19 3.8 22.4 1.0 CA A:HIS195 3.8 31.7 1.0 H5'' C:DC22 4.0 29.3 1.0 HA A:ALA197 4.1 24.8 1.0 H A:HIS195 4.1 39.9 1.0 O A:HOH526 4.2 25.2 1.0 ND1 A:HIS195 4.2 36.0 1.0 C A:HIS195 4.2 30.3 1.0 OD1 A:ASP200 4.3 27.2 1.0 O A:THR196 4.3 25.0 1.0 O5' C:DC22 4.4 26.4 1.0 OP2 C:DC22 4.4 27.5 1.0 N A:HIS195 4.5 30.7 1.0 CG A:GLU20 4.5 23.7 1.0 HG2 A:GLU20 4.6 29.7 1.0 C A:THR196 4.6 24.9 1.0 N A:THR196 4.6 29.1 1.0 CB A:ASP18 4.6 23.3 1.0 C A:LEU19 4.6 22.7 1.0 C5' C:DC22 4.7 25.4 1.0 O A:HOH417 4.7 23.5 1.0 HB3 A:HIS195 4.7 46.0 1.0 CB A:HIS195 4.7 33.9 1.0 HA A:GLU20 4.7 25.7 1.0 O3' C:DT21 4.7 22.1 1.0 O A:HIS195 4.8 30.1 1.0 HB3 A:ASP18 4.8 28.4 1.0 H A:LEU19 4.8 27.0 1.0 H A:ASP200 4.8 20.7 1.0 H A:THR196 4.8 37.1 1.0 CG A:HIS195 4.9 35.6 1.0 CA A:ALA197 4.9 23.0 1.0 N A:ALA197 5.0 23.2 1.0 CA A:ASP200 5.0 22.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 TREX1 in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.2 occ:1.00 OD1 A:ASP18 2.2 26.9 1.0 O A:HOH465 2.2 25.8 1.0 OP1 C:DC22 2.3 25.9 1.0 O A:HOH526 2.4 25.2 1.0 O A:HOH417 2.4 23.5 1.0 O3' C:DT21 2.6 22.1 1.0 P C:DC22 3.0 26.7 1.0 CG A:ASP18 3.3 25.5 1.0 H4' C:DT21 3.5 27.1 1.0 MG A:MG301 3.6 26.8 1.0 C3' C:DT21 3.8 23.4 1.0 H5'' C:DT21 3.8 24.9 1.0 H A:LEU19 3.9 27.0 1.0 OD2 A:ASP18 3.9 26.0 1.0 H5'' C:DC22 4.0 29.3 1.0 OP2 C:DC22 4.0 27.5 1.0 H5' C:DC22 4.0 29.3 1.0 O A:HOH436 4.0 21.4 1.0 C4' C:DT21 4.0 23.8 1.0 O A:LEU19 4.0 22.4 1.0 O5' C:DC22 4.1 26.4 1.0 OD2 A:ASP130 4.2 28.2 1.0 C5' C:DC22 4.3 25.4 1.0 O C:HOH217 4.3 24.5 1.0 OD1 A:ASP130 4.3 28.6 1.0 HA A:ASP18 4.3 24.4 1.0 H3' C:DT21 4.4 26.5 1.0 O A:HOH513 4.4 22.9 1.0 C5' C:DT21 4.4 22.9 1.0 O A:HIS124 4.5 22.0 1.0 H2'' C:DT21 4.5 28.1 1.0 CB A:ASP18 4.5 23.3 1.0 HB3 A:HIS124 4.6 25.2 1.0 N A:LEU19 4.6 22.7 1.0 HB2 A:ASP18 4.7 28.4 1.0 CG A:ASP130 4.7 27.7 1.0 HB3 A:ASP200 4.7 27.2 1.0 OD2 A:ASP200 4.7 31.6 1.0 C2' C:DT21 4.8 24.3 1.0 CA A:ASP18 4.9 21.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 TREX1 in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:23.1 occ:1.00 OP1 D:DC22 2.1 23.2 1.0 OD2 B:ASP200 2.1 28.0 1.0 OD2 B:ASP18 2.2 23.7 1.0 OE1 B:GLU20 2.3 22.8 1.0 CG B:ASP18 3.0 22.9 1.0 OD1 B:ASP18 3.1 23.9 1.0 CD B:GLU20 3.1 21.5 1.0 HA B:HIS195 3.1 36.5 1.0 CG B:ASP200 3.2 25.7 1.0 HB2 B:ASP200 3.2 28.9 1.0 OE2 B:GLU20 3.4 21.6 1.0 MG B:MG302 3.5 29.3 1.0 CB B:ASP200 3.6 23.1 1.0 P D:DC22 3.6 23.4 1.0 HB3 B:ASP200 3.6 28.9 1.0 O B:LEU19 3.7 20.9 1.0 H5'' D:DC22 3.8 24.7 1.0 HA B:ALA197 4.0 22.3 1.0 CA B:HIS195 4.0 28.0 1.0 O B:HOH542 4.2 20.8 1.0 O5' D:DC22 4.2 22.3 1.0 O B:THR196 4.3 20.9 1.0 OD1 B:ASP200 4.3 25.1 1.0 HG2 B:GLU20 4.3 20.5 1.0 H B:HIS195 4.3 35.7 1.0 C B:HIS195 4.3 27.5 1.0 CG B:GLU20 4.4 19.3 1.0 OP2 D:DC22 4.4 25.0 1.0 O B:HOH424 4.4 22.3 1.0 CB B:ASP18 4.4 20.4 1.0 C5' D:DC22 4.5 22.0 1.0 O3' D:DT21 4.5 18.2 1.0 C B:THR196 4.5 21.7 1.0 C B:LEU19 4.6 20.3 1.0 N B:THR196 4.6 26.0 1.0 HB3 B:ASP18 4.6 23.6 1.0 N B:HIS195 4.7 27.6 1.0 HA B:GLU20 4.8 22.3 1.0 H B:LEU19 4.8 23.2 1.0 H B:THR196 4.8 31.1 1.0 ND1 B:HIS195 4.8 33.6 1.0 CA B:ALA197 4.8 21.0 1.0 O D:HOH226 4.9 23.2 1.0 HB2 B:ASP18 4.9 23.6 1.0 N B:ALA197 4.9 20.6 1.0 O B:HIS195 4.9 28.7 1.0 H5' D:DC22 4.9 24.7 1.0 HG3 B:GLU20 4.9 20.5 1.0 HB3 B:HIS195 5.0 39.3 1.0 H B:ASP200 5.0 24.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 TREX1 in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:29.3 occ:1.00 O B:HOH447 2.2 19.7 1.0 OD1 B:ASP18 2.3 23.9 1.0 O B:HOH424 2.4 22.3 1.0 O3' D:DT21 2.4 18.2 1.0 O B:HOH542 2.4 20.8 1.0 OP1 D:DC22 2.5 23.2 1.0 P D:DC22 3.0 23.4 1.0 H4' D:DT21 3.3 27.2 1.0 CG B:ASP18 3.5 22.9 1.0 MG B:MG301 3.5 23.1 1.0 H5'' D:DT21 3.6 28.8 1.0 C3' D:DT21 3.6 21.0 1.0 C4' D:DT21 3.8 22.5 1.0 H5' D:DC22 3.9 24.7 1.0 H5'' D:DC22 4.0 24.7 1.0 OD2 B:ASP18 4.0 23.7 1.0 O B:HOH432 4.0 15.8 1.0 OP2 D:DC22 4.1 25.0 1.0 H B:LEU19 4.1 23.2 1.0 O D:HOH226 4.1 23.2 1.0 O5' D:DC22 4.2 22.3 1.0 O B:HOH540 4.2 24.9 1.0 O B:LEU19 4.2 20.9 1.0 C5' D:DT21 4.2 23.3 1.0 OD1 B:ASP130 4.2 27.9 1.0 OD2 B:ASP130 4.2 24.0 1.0 H3' D:DT21 4.2 24.5 1.0 C5' D:DC22 4.2 22.0 1.0 H2'' D:DT21 4.3 26.4 1.0 HA B:ASP18 4.4 20.2 1.0 O B:HIS124 4.4 18.2 1.0 HB3 B:HIS124 4.4 17.8 1.0 C2' D:DT21 4.6 22.1 1.0 OD2 B:ASP200 4.7 28.0 1.0 CG B:ASP130 4.7 24.7 1.0 HB3 B:ASP200 4.7 28.9 1.0 CB B:ASP18 4.7 20.4 1.0 N B:LEU19 4.8 19.9 1.0 HB2 B:ASP18 4.8 23.6 1.0 H5' D:DT21 4.8 28.8 1.0

K.W.Huang, T.C.Liu, R.Y.Liang, L.Y.Chu, H.L.Cheng, J.W.Chu, Y.Y.Hsiao. Structural Basis For Overhang Excision and Terminal Unwinding of Dna Duplexes By TREX1 Plos Biol. V. 16 05653 2018.
ISSN: ESSN 1545-7885
PubMed: 29734329
DOI: 10.1371/JOURNAL.PBIO.2005653