Magnesium in PDB 6a46: Structure of TREX2 in Complex with A Nucleotide (Dcmp)

All present enzymatic activity of Structure of TREX2 in Complex with A Nucleotide (Dcmp):
3.1.11.2;

The structure of Structure of TREX2 in Complex with A Nucleotide (Dcmp), PDB code: 6a46 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)	28.86 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.808, 54.773, 88.716, 90.00, 100.76, 90.00
R / Rfree (%)	19.3 / 22.8

The structure of Structure of TREX2 in Complex with A Nucleotide (Dcmp) also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Structure of TREX2 in Complex with A Nucleotide (Dcmp) (pdb code 6a46). 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 Nucleotide (Dcmp), PDB code: 6a46:
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 Nucleotide (Dcmp)


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 Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:20.9 occ:1.00 O A:HOH407 2.2 31.0 1.0 O A:HOH412 2.2 32.0 1.0 O A:HOH457 2.2 37.8 1.0 O A:HOH430 2.2 38.3 1.0 O1P A:DCM303 2.7 95.6 1.0 OD1 A:ASP14 2.8 44.5 1.0 CG A:ASP14 3.3 36.5 1.0 OD2 A:ASP14 3.4 34.9 1.0 H5'1 A:DCM303 3.5 49.4 1.0 MG A:MG302 3.5 20.1 1.0 H5'2 A:DCM303 3.5 49.4 1.0 OD2 A:ASP123 3.7 32.2 1.0 H A:LEU15 3.7 32.5 1.0 C5' A:DCM303 3.9 41.2 1.0 O A:LEU15 3.9 30.1 1.0 OD1 A:ASP123 3.9 36.3 1.0 O A:HOH427 4.0 20.8 1.0 P A:DCM303 4.0 97.0 1.0 HA A:ASP14 4.2 33.4 1.0 O A:HOH414 4.2 48.2 1.0 CG A:ASP123 4.3 32.5 1.0 O5' A:DCM303 4.3 43.1 1.0 O A:HIS117 4.3 32.9 1.0 N A:LEU15 4.5 27.1 1.0 O A:HOH410 4.5 33.8 1.0 CB A:ASP14 4.6 31.6 1.0 HB3 A:ASP193 4.6 35.7 1.0 OD2 A:ASP193 4.7 30.4 1.0 HD2 A:TYR122 4.8 36.8 1.0 HB3 A:HIS117 4.8 33.5 1.0 O2P A:DCM303 4.8 97.4 1.0 CA A:ASP14 4.8 27.9 1.0 C A:LEU15 4.9 30.9 1.0

Magnesium binding site 2 out of 4 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


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 Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:20.1 occ:1.00 OD2 A:ASP193 1.9 30.4 1.0 OD2 A:ASP14 2.0 34.9 1.0 OE1 A:GLU16 2.1 38.8 1.0 O1P A:DCM303 2.7 95.6 1.0 CG A:ASP193 2.9 30.1 1.0 CG A:ASP14 2.9 36.5 1.0 HB2 A:ASP193 3.0 35.7 1.0 O2P A:DCM303 3.0 97.4 1.0 CD A:GLU16 3.1 37.6 1.0 CB A:ASP193 3.3 29.8 1.0 OD1 A:ASP14 3.3 44.5 1.0 HB3 A:ASP193 3.4 35.7 1.0 P A:DCM303 3.4 97.0 1.0 MG A:MG301 3.5 20.9 1.0 OE2 A:GLU16 3.5 37.3 1.0 HA A:HIS188 3.5 64.0 1.0 H5'2 A:DCM303 3.6 49.4 1.0 O A:HOH430 3.6 38.3 1.0 O A:LEU15 3.7 30.1 1.0 HA A:ALA190 3.8 37.6 1.0 OD1 A:ASP193 4.0 28.4 1.0 HG2 A:GLU16 4.1 42.9 1.0 O A:SER189 4.2 33.9 1.0 CG A:GLU16 4.2 35.8 1.0 CB A:ASP14 4.3 31.6 1.0 HB3 A:ASP14 4.3 37.9 1.0 CA A:HIS188 4.3 53.3 1.0 C5' A:DCM303 4.4 41.2 1.0 C A:HIS188 4.4 49.9 1.0 O5' A:DCM303 4.4 43.1 1.0 C A:SER189 4.5 34.6 1.0 O A:HOH414 4.5 48.2 1.0 C A:LEU15 4.5 30.9 1.0 O A:HOH407 4.5 31.0 1.0 O3P A:DCM303 4.6 99.1 1.0 CA A:ALA190 4.6 31.3 1.0 H A:HIS188 4.6 65.3 1.0 H A:LEU15 4.7 32.5 1.0 O A:HIS188 4.7 53.0 1.0 N A:ALA190 4.7 33.2 1.0 H5'1 A:DCM303 4.7 49.4 1.0 HA A:GLU16 4.7 38.2 1.0 H A:ASP193 4.7 36.6 1.0 N A:SER189 4.8 42.9 1.0 HG3 A:GLU16 4.8 42.9 1.0 CA A:ASP193 4.8 29.7 1.0 HD1 A:HIS188 4.8 67.1 1.0 HB2 A:ASP14 4.8 37.9 1.0 N A:LEU15 4.9 27.1 1.0 H3' A:DCM303 4.9 51.5 1.0 N A:HIS188 5.0 54.5 1.0 O A:HOH457 5.0 37.8 1.0

Magnesium binding site 3 out of 4 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


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 Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:35.0 occ:1.00 O B:HOH414 2.2 40.2 1.0 O B:HOH401 2.2 55.2 1.0 O B:HOH404 2.2 35.9 1.0 O B:HOH409 2.2 53.9 1.0 OD1 B:ASP14 2.8 48.3 1.0 O3P B:DCM301 2.9 78.8 1.0 O2P B:DCM301 3.2 83.1 1.0 P B:DCM301 3.4 81.9 1.0 H B:LEU15 3.4 45.6 1.0 CG B:ASP14 3.5 45.3 1.0 OD2 B:ASP123 3.5 38.5 1.0 OD2 B:ASP14 3.6 47.5 1.0 O5' B:DCM301 3.7 81.5 1.0 MG B:MG303 3.7 28.5 1.0 O B:LEU15 3.7 44.0 1.0 OD1 B:ASP123 3.9 43.2 1.0 H5'1 B:DCM301 4.0 99.7 1.0 CG B:ASP123 4.1 38.6 1.0 HA B:ASP14 4.2 43.1 1.0 N B:LEU15 4.2 38.0 1.0 HD2 B:TYR122 4.3 67.4 1.0 O B:HOH426 4.3 35.0 1.0 C5' B:DCM301 4.4 83.1 1.0 O B:HIS117 4.5 33.6 1.0 CB B:ASP14 4.7 40.6 1.0 O B:HOH422 4.7 41.4 1.0 C B:LEU15 4.7 42.8 1.0 CA B:ASP14 4.8 35.9 1.0 HE2 B:TYR122 4.8 66.7 1.0 H5'2 B:DCM301 4.8 99.7 1.0 HB2 B:LEU15 4.8 49.4 1.0 CD2 B:TYR122 4.9 56.2 1.0 O1P B:DCM301 4.9 82.3 1.0 OD2 B:ASP193 4.9 37.5 1.0 HB2 B:ASP14 5.0 48.7 1.0 HB3 B:HIS117 5.0 45.1 1.0

Magnesium binding site 4 out of 4 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


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 Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:28.5 occ:1.00 O3P B:DCM301 1.8 78.8 1.0 OD2 B:ASP14 1.9 47.5 1.0 OD2 B:ASP193 1.9 37.5 1.0 OE2 B:GLU16 2.1 47.4 1.0 CG B:ASP14 2.7 45.3 1.0 OD1 B:ASP14 2.9 48.3 1.0 CG B:ASP193 3.0 37.6 1.0 HB2 B:ASP193 3.0 41.0 1.0 CD B:GLU16 3.0 47.3 1.0 P B:DCM301 3.3 81.9 1.0 CB B:ASP193 3.3 34.1 1.0 HA B:ALA190 3.3 46.0 1.0 HB3 B:ASP193 3.5 41.0 1.0 OE1 B:GLU16 3.5 48.4 1.0 O B:HOH414 3.6 40.2 1.0 MG B:MG302 3.7 35.0 1.0 O B:LEU15 3.8 44.0 1.0 O1P B:DCM301 3.9 82.3 1.0 HA B:HIS188 3.9 87.0 1.0 O5' B:DCM301 4.0 81.5 1.0 HG2 B:GLU16 4.1 55.8 1.0 CB B:ASP14 4.1 40.6 1.0 OD1 B:ASP193 4.1 39.9 1.0 O B:SER189 4.1 34.4 1.0 HB3 B:ASP14 4.2 48.7 1.0 CG B:GLU16 4.2 46.5 1.0 O2P B:DCM301 4.2 83.1 1.0 CA B:ALA190 4.2 38.3 1.0 H B:LEU15 4.3 45.6 1.0 C B:SER189 4.4 38.7 1.0 C B:LEU15 4.4 42.8 1.0 N B:ALA190 4.5 40.4 1.0 C B:HIS188 4.6 64.9 1.0 N B:LEU15 4.6 38.0 1.0 HB2 B:ASP14 4.6 48.7 1.0 CA B:HIS188 4.6 72.5 1.0 H B:ASP193 4.7 41.8 1.0 HG3 B:GLU16 4.7 55.8 1.0 O B:HIS188 4.7 67.7 1.0 HA B:GLU16 4.8 53.0 1.0 H B:HIS188 4.8 87.6 1.0 CA B:ASP193 4.8 34.4 1.0 O B:HOH401 4.9 55.2 1.0 O B:ALA190 4.9 42.6 1.0 N B:SER189 4.9 52.7 1.0 N B:GLU16 5.0 41.2 1.0 C B:ASP14 5.0 35.7 1.0 HB2 B:ALA190 5.0 45.6 1.0 H B:ALA190 5.0 48.4 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