Gadolinium in PDB 5fis: Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation

The structure of Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation, PDB code: 5fis was solved by Z.Yang, K.M.Chen, R.R.Pandey, D.Homolka, M.Reuter, B.K.Rodino Janeiro, R.Sachidanandam, M.O.Fauvarque, A.A.Mccarthy, R.S.Pillai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.860, 135.700, 51.460, 90.00, 90.00, 90.00
R / Rfree (%)	15.69 / 18.245

The binding sites of Gadolinium atom in the Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation (pdb code 5fis). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 3 binding sites of Gadolinium where determined in the Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation, PDB code: 5fis:
Jump to Gadolinium binding site number: 1; 2; 3;

Gadolinium binding site 1 out of 3 in the Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1316 b:17.2 occ:1.00 OE1 A:GLU266 2.4 21.3 1.0 O A:HOH2093 2.4 18.1 1.0 O A:HOH2005 2.4 20.1 1.0 O A:HOH2094 2.4 20.0 1.0 O A:HOH2006 2.4 20.1 1.0 OD1 B:ASP113 2.4 19.5 1.0 OD2 A:ASP138 2.4 18.2 1.0 OD1 A:ASP138 2.5 15.7 1.0 OD2 B:ASP113 2.5 18.7 1.0 CG B:ASP113 2.8 17.6 1.0 CG A:ASP138 2.8 15.9 1.0 CD A:GLU266 3.4 28.1 1.0 OE2 A:GLU266 3.9 31.2 1.0 O B:HOH2041 4.1 34.0 1.0 CB B:ASP113 4.3 17.5 1.0 O A:HOH2092 4.4 19.9 1.0 CB A:ASP138 4.4 15.7 1.0 NZ A:LYS81 4.4 31.4 1.0 ND1 A:HIS263 4.4 21.4 1.0 O A:HOH2012 4.5 22.9 1.0 CE A:LYS81 4.6 37.2 1.0 CD2 A:HIS262 4.7 25.8 1.0 CG A:GLU266 4.8 25.2 1.0 O A:HOH2095 4.8 24.5 1.0 O B:HOH2047 4.8 36.5 1.0

Gadolinium binding site 2 out of 3 in the Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd1317 b:20.9 occ:0.50 O A:HOH2040 2.2 47.8 1.0 OE2 A:GLU104 2.3 17.5 1.0 O A:HOH2039 2.5 29.9 1.0 O A:HOH2038 2.6 32.6 1.0 OE1 A:GLU104 2.9 29.5 1.0 CD A:GLU104 2.9 33.4 1.0 O A:HOH2055 4.1 38.8 1.0 CG A:GLU104 4.3 25.4 1.0 O A:HOH2050 4.3 24.8 1.0

Gadolinium binding site 3 out of 3 in the Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Exonuclease Domain-Containing 1 (EXD1) in the Gd Bound Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd1316 b:17.1 occ:1.00 O A:HOH2064 2.4 19.3 1.0 O B:HOH2068 2.4 20.5 1.0 OE1 B:GLU266 2.4 21.9 1.0 O A:HOH2066 2.4 19.4 1.0 OD1 A:ASP113 2.5 20.0 1.0 OD2 B:ASP138 2.5 17.2 1.0 OD1 B:ASP138 2.5 15.8 1.0 OD2 A:ASP113 2.5 18.3 1.0 O A:HOH2065 2.5 18.7 1.0 CG A:ASP113 2.8 17.2 1.0 CG B:ASP138 2.9 17.9 1.0 CD B:GLU266 3.5 27.5 1.0 OE2 B:GLU266 3.9 30.1 1.0 O A:HOH2056 4.2 28.7 1.0 O B:HOH2067 4.3 22.0 1.0 CB A:ASP113 4.4 17.4 1.0 CB B:ASP138 4.4 17.1 1.0 ND1 B:HIS263 4.4 21.6 1.0 NZ B:LYS81 4.5 34.0 1.0 O B:HOH2007 4.6 22.8 1.0 CE B:LYS81 4.6 36.1 1.0 ND1 B:HIS262 4.7 28.9 1.0 CG B:GLU266 4.8 25.8 1.0 O B:HOH2069 4.8 27.7 1.0 O A:HOH2067 4.9 36.6 1.0

Z.Yang, K.M.Chen, R.R.Pandey, D.Homolka, M.Reuter, B.K.Rodino Janeiro, R.Sachidanandam, M.O.Fauvarque, A.A.Mccarthy, R.S.Pillai. Piwi Slicing and EXD1 Drive Biogenesis of Nuclear Pirnas From Cytosolic Targets of the Mouse Pirna Pathway Mol.Cell V. 61 138 2016.
ISSN: ISSN 1097-2765
PubMed: 26669262
DOI: 10.1016/J.MOLCEL.2015.11.009