Sodium in PDB 6k17: Crystal Structure of EXD2 Exonuclease Domain

All present enzymatic activity of Crystal Structure of EXD2 Exonuclease Domain:
3.1.11.1;

The structure of Crystal Structure of EXD2 Exonuclease Domain, PDB code: 6k17 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)	37.33 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.955, 72.607, 135.670, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22

The binding sites of Sodium atom in the Crystal Structure of EXD2 Exonuclease Domain (pdb code 6k17). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of EXD2 Exonuclease Domain, PDB code: 6k17:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of EXD2 Exonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:30.9 occ:1.00 O B:HOH447 2.4 29.5 1.0 OE2 A:GLU110 2.6 18.5 1.0 OD2 A:ASP108 2.6 36.9 1.0 O B:HOH454 2.9 21.0 1.0 O B:HOH411 2.9 36.7 1.0 O A:HOH452 3.1 20.4 1.0 CD A:GLU110 3.5 16.4 1.0 CG A:ASP108 3.6 17.8 1.0 OE1 A:GLU110 3.8 14.5 1.0 OD2 B:ASP246 3.8 31.5 1.0 NA A:NA302 3.9 12.6 1.0 OD1 A:ASP108 4.0 18.4 1.0 CE2 B:TYR242 4.1 11.7 1.0 OH B:TYR242 4.1 19.9 1.0 CG B:ASP246 4.2 30.1 1.0 CZ B:TYR242 4.3 15.9 1.0 O B:HOH401 4.3 20.5 1.0 O B:HOH494 4.4 28.5 1.0 O B:HOH645 4.4 35.5 1.0 CB B:ASP246 4.4 15.1 1.0 O A:CYS109 4.5 16.2 1.0 O B:HOH457 4.6 36.0 1.0 O B:TYR242 4.8 11.7 1.0 CB A:ASP108 4.9 10.9 1.0 NE2 A:GLN125 4.9 10.8 1.0 O B:ALA243 4.9 13.3 1.0 CG A:GLU110 4.9 11.5 1.0 CD2 B:TYR242 4.9 12.2 1.0 OD1 B:ASP246 5.0 32.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of EXD2 Exonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:12.6 occ:1.00 O A:HOH684 2.3 34.8 1.0 O A:HOH409 2.3 30.3 1.0 O B:HOH447 2.4 29.5 1.0 O B:HOH494 2.4 28.5 1.0 OD1 A:ASP108 2.4 18.4 1.0 O A:HOH445 2.4 28.9 1.0 O A:HOH452 2.5 20.4 1.0 CG A:ASP108 3.3 17.8 1.0 OD2 A:ASP108 3.5 36.9 1.0 NA A:NA301 3.9 30.9 1.0 O B:HOH645 4.2 35.5 1.0 OD2 A:ASP171 4.3 28.4 1.0 O A:CYS109 4.3 16.2 1.0 OD2 B:ASP246 4.5 31.5 1.0 O A:HOH581 4.5 29.9 1.0 O B:HOH677 4.5 35.5 1.0 O A:HOH574 4.6 31.6 1.0 OD1 A:ASP171 4.6 27.6 1.0 CB A:ASP108 4.7 10.9 1.0 N A:CYS109 4.8 10.9 1.0 CG A:ASP171 4.9 26.6 1.0 O B:HOH454 5.0 21.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of EXD2 Exonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:49.2 occ:1.00 O A:HOH430 2.2 31.4 1.0 OE2 B:GLU110 2.5 16.4 1.0 OD2 B:ASP108 2.6 39.3 1.0 O A:HOH444 2.7 44.0 1.0 O B:HOH436 2.9 26.5 1.0 O A:HOH459 3.1 26.0 1.0 CD B:GLU110 3.5 18.4 1.0 CG B:ASP108 3.6 22.0 1.0 OE1 B:GLU110 3.7 14.9 1.0 OD2 A:ASP246 3.8 33.5 1.0 OD1 B:ASP108 3.9 28.6 1.0 NA B:NA302 3.9 22.0 1.0 CE2 A:TYR242 4.0 11.9 1.0 OH A:TYR242 4.1 16.8 1.0 O A:HOH562 4.1 38.0 1.0 CG A:ASP246 4.3 33.1 1.0 CZ A:TYR242 4.3 15.5 1.0 O B:CYS109 4.4 16.4 1.0 O A:HOH662 4.4 34.4 1.0 O A:HOH527 4.4 35.3 1.0 CB A:ASP246 4.5 16.2 1.0 O A:HOH407 4.6 24.7 1.0 NE2 B:GLN125 4.6 10.7 1.0 O B:HOH599 4.8 36.4 1.0 CD2 A:TYR242 4.8 11.0 1.0 CG B:GLU110 4.8 10.8 1.0 CB B:ASP108 4.9 13.4 1.0 O B:HOH665 4.9 38.1 1.0 O A:TYR242 5.0 11.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of EXD2 Exonuclease Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of EXD2 Exonuclease Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:22.0 occ:1.00 O B:HOH410 2.2 22.9 1.0 O B:HOH665 2.3 38.1 1.0 O B:HOH481 2.3 26.8 1.0 O A:HOH430 2.3 31.4 1.0 O A:HOH527 2.4 35.3 1.0 OD1 B:ASP108 2.4 28.6 1.0 O B:HOH436 2.5 26.5 1.0 CG B:ASP108 3.3 22.0 1.0 OD2 B:ASP108 3.6 39.3 1.0 NA B:NA301 3.9 49.2 1.0 O A:HOH653 4.0 47.2 1.0 O B:HOH531 4.2 37.4 1.0 O B:CYS109 4.4 16.4 1.0 OD2 B:ASP171 4.4 25.6 1.0 O A:HOH598 4.4 35.0 1.0 O A:HOH662 4.4 34.4 1.0 OD2 A:ASP246 4.5 33.5 1.0 O A:HOH690 4.5 40.2 1.0 O B:HOH599 4.5 36.4 1.0 OD1 B:ASP171 4.5 30.3 1.0 O B:HOH555 4.6 33.0 1.0 CB B:ASP108 4.7 13.4 1.0 N B:CYS109 4.8 11.6 1.0 O B:HOH625 4.8 42.7 1.0 CG B:ASP171 4.9 26.2 1.0 O A:HOH444 5.0 44.0 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