Manganese in PDB 6k1d: Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp

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

The structure of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp, PDB code: 6k1d 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)	49.35 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.528, 73.931, 132.543, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.7

The binding sites of Manganese atom in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp (pdb code 6k1d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp, PDB code: 6k1d:
Jump to Manganese binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:71.1 occ:1.00 O A:HOH402 2.2 58.1 1.0 OD1 A:ASP108 2.3 64.7 1.0 O A:HOH405 2.6 0.6 1.0 O A:HOH410 2.6 87.9 1.0 O A:HOH404 2.6 47.7 1.0 O A:HOH408 2.9 34.5 1.0 CG A:ASP108 3.3 61.0 1.0 OD2 A:ASP108 3.5 58.6 1.0 MN A:MN302 3.7 64.0 1.0 O A:CYS109 4.2 29.7 1.0 O A:HOH406 4.4 38.0 1.0 O B:HOH407 4.4 77.5 1.0 OD2 A:ASP171 4.5 69.0 1.0 N A:CYS109 4.6 48.2 1.0 OD1 A:ASP171 4.6 74.2 1.0 CB A:ASP108 4.6 44.5 1.0 O A:VAL166 4.7 52.8 1.0 CA A:ASP108 5.0 42.2 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:64.0 occ:1.00 OD2 A:ASP108 2.2 58.6 1.0 OE2 A:GLU110 2.3 57.6 1.0 OD2 B:ASP246 2.5 61.2 1.0 O A:HOH405 2.6 0.6 1.0 O B:HOH407 2.6 77.5 1.0 O A:HOH408 3.2 34.5 1.0 CG A:ASP108 3.3 61.0 1.0 CD A:GLU110 3.4 56.1 1.0 CG B:ASP246 3.5 58.3 1.0 OD1 A:ASP108 3.6 64.7 1.0 MN A:MN301 3.7 71.1 1.0 CB B:ASP246 3.9 49.1 1.0 OE1 A:GLU110 4.0 56.7 1.0 O A:CYS109 4.2 29.7 1.0 CE2 B:TYR242 4.4 62.3 1.0 OD1 B:ASP246 4.5 60.1 1.0 OH B:TYR242 4.6 79.3 1.0 NE2 A:GLN125 4.6 30.6 1.0 CB A:ASP108 4.6 44.5 1.0 CG A:GLU110 4.6 29.4 1.0 CZ B:TYR242 4.8 73.6 1.0 O A:HOH410 4.8 87.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:58.4 occ:1.00 O B:HOH404 1.9 83.2 1.0 OD2 B:ASP108 2.1 48.5 1.0 OE2 B:GLU110 2.2 46.1 1.0 O B:HOH403 2.2 0.6 1.0 OD2 A:ASP246 2.6 72.2 1.0 CG B:ASP108 3.1 47.5 1.0 O B:HOH406 3.1 14.1 1.0 CD B:GLU110 3.4 55.7 1.0 OD1 B:ASP108 3.5 52.6 1.0 CG A:ASP246 3.6 79.0 1.0 CB A:ASP246 3.9 68.7 1.0 OE1 B:GLU110 4.0 67.0 1.0 MN B:MN301 4.0 61.1 1.0 O B:CYS109 4.1 43.5 1.0 CE2 A:TYR242 4.3 68.0 1.0 CB B:ASP108 4.4 42.0 1.0 OH A:TYR242 4.5 69.5 1.0 CG B:GLU110 4.5 49.0 1.0 OD1 A:ASP246 4.7 89.6 1.0 CZ A:TYR242 4.7 65.6 1.0 O B:HOH408 4.8 38.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of EXD2 Exonuclease Domain Soaked in Mn and Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:61.1 occ:1.00 O B:HOH403 2.3 0.6 1.0 OD1 B:ASP108 2.3 52.6 1.0 O B:HOH401 2.7 70.1 1.0 O B:HOH408 2.7 38.5 1.0 O B:HOH406 2.9 14.1 1.0 CG B:ASP108 3.3 47.5 1.0 OD2 B:ASP108 3.7 48.5 1.0 MN A:MN303 4.0 58.4 1.0 O B:CYS109 4.2 43.5 1.0 O B:HOH402 4.3 51.9 1.0 OD2 B:ASP171 4.3 90.8 1.0 O B:VAL166 4.3 45.0 1.0 O B:HOH404 4.4 83.2 1.0 OD1 B:ASP171 4.5 71.1 1.0 N B:CYS109 4.5 44.2 1.0 CB B:ASP108 4.6 42.0 1.0 CG B:ASP171 4.8 77.7 1.0 CA B:ASP108 4.8 24.0 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