Magnesium in PDB 4ynq: TREX1-Dsdna Complex

All present enzymatic activity of TREX1-Dsdna Complex:
3.1.11.2;

The structure of TREX1-Dsdna Complex, PDB code: 4ynq was solved by J.M.Fye, S.Harvey, F.W.Perrino, T.Hollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.142, 84.457, 103.000, 90.00, 102.15, 90.00
R / Rfree (%)	21.8 / 26.6

The binding sites of Magnesium atom in the TREX1-Dsdna Complex (pdb code 4ynq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the TREX1-Dsdna Complex, PDB code: 4ynq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the TREX1-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TREX1-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:59.3 occ:1.00 O A:HOH401 2.6 48.1 1.0 OD1 A:ASN18 2.8 48.8 1.0 OP1 E:DG24 2.8 42.0 1.0 O3' E:DC23 3.0 34.8 1.0 P E:DG24 3.4 39.1 1.0 C5' E:DC23 3.7 41.9 1.0 CG A:ASN18 3.8 42.8 1.0 O A:HIS124 3.9 51.8 1.0 C4' E:DC23 4.0 39.6 1.0 C3' E:DC23 4.0 38.4 1.0 OP2 E:DG24 4.0 37.7 1.0 CB A:HIS124 4.4 47.3 1.0 O5' E:DC23 4.4 44.3 1.0 ND2 A:ASN18 4.4 42.0 1.0 O5' E:DG24 4.8 38.4 1.0 OD1 A:ASP130 4.8 53.2 1.0 C A:HIS124 4.8 49.3 1.0 CD2 A:LEU179 4.9 38.9 1.0 OD2 A:ASP200 5.0 47.1 1.0

Magnesium binding site 2 out of 4 in the TREX1-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TREX1-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:25.2 occ:1.00 O B:HOH407 2.3 54.9 1.0 O B:HOH406 2.3 46.5 1.0 O B:HOH403 2.6 45.0 1.0 OD1 B:ASN18 2.6 36.1 1.0 CG B:ASN18 3.7 37.6 1.0 O B:HIS124 3.9 39.0 1.0 OD1 B:ASP130 4.2 50.6 1.0 OD2 B:ASP130 4.3 51.1 1.0 ND2 B:ASN18 4.3 41.2 1.0 O B:LEU19 4.5 50.0 1.0 CG B:ASP130 4.7 45.2 1.0 CB B:ASN18 4.8 38.2 1.0 C B:HIS124 5.0 40.3 1.0 CB B:HIS124 5.0 46.5 1.0

Magnesium binding site 3 out of 4 in the TREX1-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of TREX1-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:28.4 occ:1.00 O C:HOH403 1.9 47.1 1.0 OD1 C:ASN18 2.2 46.3 1.0 O C:HOH405 2.6 31.8 1.0 CG C:ASN18 3.4 41.5 1.0 ND2 C:ASN18 4.1 42.4 1.0 O C:HIS124 4.1 45.5 1.0 OD2 C:ASP130 4.2 66.1 1.0 OD1 C:ASP130 4.3 60.6 1.0 O C:LEU19 4.4 43.2 1.0 CB C:ASN18 4.6 40.9 1.0 CG C:ASP130 4.7 57.6 1.0 N C:LEU19 4.8 46.4 1.0 CA C:ASN18 4.9 41.5 1.0

Magnesium binding site 4 out of 4 in the TREX1-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of TREX1-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:46.3 occ:1.00 OD1 D:ASN18 2.6 59.4 1.0 O D:HOH401 2.8 55.5 1.0 O3' G:DC23 3.2 48.1 1.0 OP1 G:DG24 3.2 53.4 1.0 O D:HIS124 3.5 43.7 1.0 CG D:ASN18 3.7 53.0 1.0 P G:DG24 3.7 50.6 1.0 C5' G:DC23 3.9 48.9 1.0 C4' G:DC23 4.0 48.9 1.0 OD1 D:ASP130 4.1 53.4 1.0 C3' G:DC23 4.2 50.5 1.0 CB D:HIS124 4.2 44.8 1.0 OD2 D:ASP130 4.4 57.3 1.0 C D:HIS124 4.4 43.1 1.0 OP2 G:DG24 4.4 47.7 1.0 ND2 D:ASN18 4.5 54.8 1.0 CA D:HIS124 4.7 44.8 1.0 CG D:ASP130 4.7 52.3 1.0 N D:HIS124 4.7 45.5 1.0 CB D:ASN18 4.7 50.2 1.0 O5' G:DC23 4.9 47.2 1.0

J.L.Grieves, J.M.Fye, S.Harvey, J.M.Grayson, T.Hollis, F.W.Perrino. Exonuclease TREX1 Degrades Double-Stranded Dna to Prevent Spontaneous Lupus-Like Inflammatory Disease. Proc.Natl.Acad.Sci.Usa V. 112 5117 2015.
ISSN: ESSN 1091-6490
PubMed: 25848017
DOI: 10.1073/PNAS.1423804112