Magnesium in PDB 6k1e: Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp

All present enzymatic activity of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp:
3.1.11.1;

The structure of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp, PDB code: 6k1e was solved by J.Park, C.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.496, 73.288, 134.086, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.8

The binding sites of Magnesium atom in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp (pdb code 6k1e). 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 EXD2 Exonuclease Domain Soaked in Mg and Gmp, PDB code: 6k1e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp


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 EXD2 Exonuclease Domain Soaked in Mg and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.9 occ:1.00 OD1 A:ASP108 2.3 59.0 1.0 O A:HOH402 2.4 58.2 1.0 O A:HOH405 2.5 51.2 1.0 O A:HOH409 2.5 42.2 1.0 O A:HOH403 2.5 56.0 1.0 O A:HOH401 2.7 51.4 1.0 O A:HOH406 2.7 49.3 1.0 CG A:ASP108 3.3 58.2 1.0 OD2 A:ASP108 3.6 56.9 1.0 MG A:MG302 4.3 57.9 1.0 O A:CYS109 4.3 58.0 1.0 OD2 A:ASP171 4.5 66.5 1.0 OD1 A:ASP171 4.5 68.8 1.0 CB A:ASP108 4.7 50.5 1.0 N A:CYS109 4.7 56.3 1.0 O B:HOH410 4.9 45.7 1.0 CG A:ASP171 5.0 67.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp


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 EXD2 Exonuclease Domain Soaked in Mg and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:57.9 occ:1.00 OD2 B:ASP246 2.2 96.9 1.0 O A:HOH403 2.4 56.0 1.0 OE2 A:GLU110 2.4 64.5 1.0 OD2 A:ASP108 2.7 56.9 1.0 O A:HOH405 2.8 51.2 1.0 CG B:ASP246 3.4 86.2 1.0 CD A:GLU110 3.5 54.5 1.0 OH B:TYR242 3.7 66.8 1.0 CG A:ASP108 3.8 58.2 1.0 OE1 A:GLU110 3.9 58.8 1.0 CE2 B:TYR242 3.9 51.8 1.0 CZ B:TYR242 4.0 51.6 1.0 CB B:ASP246 4.2 66.2 1.0 MG A:MG301 4.3 46.9 1.0 OD1 A:ASP108 4.3 59.0 1.0 OD1 B:ASP246 4.4 95.8 1.0 O A:CYS109 4.7 58.0 1.0 CG A:GLU110 4.8 42.5 1.0 CD2 B:TYR242 4.9 51.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp


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 EXD2 Exonuclease Domain Soaked in Mg and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:53.0 occ:1.00 OD2 A:ASP246 2.1 83.1 1.0 OE2 B:GLU110 2.1 73.3 1.0 O B:HOH407 2.5 49.9 1.0 OD2 B:ASP108 2.7 55.5 1.0 O A:HOH404 3.1 62.6 1.0 CD B:GLU110 3.2 61.7 1.0 CG A:ASP246 3.3 80.3 1.0 OH A:TYR242 3.6 74.5 1.0 OE1 B:GLU110 3.6 59.5 1.0 CG B:ASP108 3.8 58.6 1.0 CE2 A:TYR242 3.9 65.1 1.0 CZ A:TYR242 3.9 70.9 1.0 CB A:ASP246 4.2 64.9 1.0 OD1 A:ASP246 4.2 82.4 1.0 OD1 B:ASP108 4.2 64.2 1.0 MG B:MG302 4.4 47.4 1.0 CG B:GLU110 4.5 42.8 1.0 O B:CYS109 4.7 46.1 1.0 O B:HOH413 4.8 47.8 1.0 CD2 A:TYR242 4.8 63.6 1.0 CE1 A:TYR242 4.9 67.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mg and Gmp


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 EXD2 Exonuclease Domain Soaked in Mg and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:47.4 occ:1.00 O B:HOH405 2.2 49.9 1.0 O B:HOH413 2.2 47.8 1.0 O B:HOH401 2.3 51.1 1.0 OD1 B:ASP108 2.5 64.2 1.0 O B:HOH407 2.6 49.9 1.0 O A:HOH404 2.7 62.6 1.0 CG B:ASP108 3.4 58.6 1.0 OD2 B:ASP108 3.8 55.5 1.0 O A:HOH408 4.3 48.6 1.0 MG B:MG301 4.4 53.0 1.0 OD2 B:ASP171 4.5 62.4 1.0 O B:VAL166 4.6 48.2 1.0 O B:CYS109 4.7 46.1 1.0 CB B:ASP108 4.7 48.4 1.0 OD1 B:ASP171 4.9 47.9 1.0 N B:CYS109 5.0 53.8 1.0

J.Park, S.Y.Lee, H.Jeong, M.G.Kang, L.Van Haute, M.Minczuk, J.K.Seo, Y.Jun, K.Myung, H.W.Rhee, C.Lee. The Structure of Human EXD2 Reveals A Chimeric 3' to 5' Exonuclease Domain That Discriminates Substrates Via Metal Coordination. Nucleic Acids Res. V. 47 7078 2019.
ISSN: ESSN 1362-4962
PubMed: 31127291
DOI: 10.1093/NAR/GKZ454