Sodium in PDB 4fzy: Exonuclease X in Complex with 12BP Blunt-Ended Dsdna

The structure of Exonuclease X in Complex with 12BP Blunt-Ended Dsdna, PDB code: 4fzy was solved by T.Wang, H.Sun, F.Cheng, L.Bi, T.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.282, 78.887, 146.668, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.1

The binding sites of Sodium atom in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna (pdb code 4fzy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna, PDB code: 4fzy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exonuclease X in Complex with 12BP Blunt-Ended Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:31.0 occ:1.00 OD1 A:ASP6 2.2 14.4 1.0 O C:HOH202 2.2 23.3 1.0 O A:HOH303 2.2 25.4 1.0 O A:HOH304 2.4 16.1 1.0 OP1 C:DG12 2.4 20.1 1.0 O3' C:DA11 2.8 11.2 1.0 P C:DG12 3.2 17.0 1.0 CG A:ASP6 3.4 15.7 1.0 NA A:NA201 3.7 22.3 1.0 OD2 A:ASP85 3.7 21.7 1.0 OD1 A:ASP85 4.0 21.0 1.0 O A:THR7 4.0 15.9 1.0 OD2 A:ASP6 4.0 18.1 1.0 C3' C:DA11 4.0 11.7 1.0 O5' C:DG12 4.1 14.9 1.0 C5' C:DG12 4.1 11.6 1.0 CG A:ASP85 4.3 19.3 1.0 N A:THR7 4.3 13.3 1.0 C4' C:DA11 4.4 9.6 1.0 OP2 C:DG12 4.4 14.7 1.0 O A:HIS80 4.6 12.1 1.0 CB A:ASP6 4.6 13.1 1.0 CA A:ASP6 4.8 14.8 1.0 C2' C:DA11 4.8 10.7 1.0 CG2 A:THR7 4.8 16.4 1.0 C A:THR7 4.9 14.5 1.0

Sodium binding site 2 out of 4 in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exonuclease X in Complex with 12BP Blunt-Ended Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:22.3 occ:1.00 OD2 A:ASP139 2.1 18.2 1.0 OP1 C:DG12 2.2 20.1 1.0 OD2 A:ASP6 2.6 18.1 1.0 OE2 A:GLU8 2.6 13.9 1.0 CG A:ASP139 3.1 17.1 1.0 CG A:ASP6 3.4 15.7 1.0 OD1 A:ASP6 3.4 14.4 1.0 CD A:GLU8 3.4 17.1 1.0 OE1 A:GLU8 3.5 12.8 1.0 P C:DG12 3.6 17.0 1.0 CB A:ASP139 3.6 11.5 1.0 NA C:NA101 3.7 31.0 1.0 O C:HOH202 3.9 23.3 1.0 CA A:HIS134 4.0 15.0 1.0 CD2 A:HIS134 4.0 13.0 1.0 OD1 A:ASP139 4.2 17.0 1.0 O5' C:DG12 4.2 14.9 1.0 OP2 C:DG12 4.2 14.7 1.0 N A:ALA136 4.4 17.1 1.0 O A:THR7 4.4 15.9 1.0 O A:HOH302 4.4 31.6 1.0 C A:HIS134 4.5 15.8 1.0 CG A:HIS134 4.6 14.9 1.0 O3' C:DA11 4.7 11.2 1.0 CB A:HIS134 4.7 14.9 1.0 CA A:ALA136 4.7 14.7 1.0 N A:HIS134 4.8 14.9 1.0 N A:ARG135 4.8 18.4 1.0 CB A:ASP6 4.9 13.1 1.0 NE2 A:HIS134 4.9 21.1 1.0 CG A:GLU8 4.9 12.1 1.0 C5' C:DG12 4.9 11.6 1.0 O A:HIS134 4.9 13.7 1.0

Sodium binding site 3 out of 4 in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Exonuclease X in Complex with 12BP Blunt-Ended Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:27.0 occ:1.00 O D:HOH202 2.1 24.9 1.0 OD1 B:ASP6 2.2 20.7 1.0 O B:HOH306 2.2 25.2 1.0 O B:HOH307 2.3 19.1 1.0 OP1 D:DA12 2.6 12.4 1.0 O3' D:DC11 2.8 16.7 1.0 P D:DA12 3.3 11.9 1.0 CG B:ASP6 3.4 19.8 1.0 NA B:NA201 3.7 24.7 1.0 OD2 B:ASP6 3.9 20.0 1.0 OD2 B:ASP85 3.9 29.0 1.0 C5' D:DA12 3.9 16.9 1.0 O B:THR7 4.0 17.3 1.0 C3' D:DC11 4.0 12.1 1.0 O B:HOH301 4.1 25.2 1.0 O5' D:DA12 4.1 12.9 1.0 OD1 B:ASP85 4.2 21.6 1.0 C4' D:DC11 4.3 15.5 1.0 N B:THR7 4.4 14.3 1.0 OP2 D:DA12 4.5 13.2 1.0 CG B:ASP85 4.5 24.0 1.0 CB B:ASP6 4.6 14.9 1.0 C2' D:DC11 4.7 17.3 1.0 O B:HIS80 4.7 20.0 1.0 CA B:ASP6 4.9 15.4 1.0 C5' D:DC11 4.9 13.8 1.0 CD2 B:PHE84 4.9 20.7 1.0 C B:THR7 5.0 15.4 1.0

Sodium binding site 4 out of 4 in the Exonuclease X in Complex with 12BP Blunt-Ended Dsdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Exonuclease X in Complex with 12BP Blunt-Ended Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:24.7 occ:1.00 OP1 D:DA12 2.3 12.4 1.0 OD2 B:ASP139 2.3 32.9 1.0 OE2 B:GLU8 2.7 17.0 1.0 OD2 B:ASP6 2.8 20.0 1.0 CG B:ASP139 3.3 28.6 1.0 CD B:GLU8 3.4 14.9 1.0 OE1 B:GLU8 3.4 13.4 1.0 CG B:ASP6 3.6 19.8 1.0 CB B:ASP139 3.6 20.4 1.0 OD1 B:ASP6 3.6 20.7 1.0 P D:DA12 3.7 11.9 1.0 ND1 B:HIS134 3.7 57.6 1.0 NA D:NA101 3.7 27.0 1.0 O D:HOH202 4.0 24.9 1.0 CA B:HIS134 4.1 50.3 1.0 O5' D:DA12 4.3 12.9 1.0 OP2 D:DA12 4.4 13.2 1.0 C B:HIS134 4.4 45.9 1.0 OD1 B:ASP139 4.5 29.6 1.0 CE1 B:HIS134 4.5 58.8 1.0 O B:ARG135 4.6 33.6 1.0 O B:THR7 4.6 17.3 1.0 O B:HOH301 4.7 25.2 1.0 CG B:HIS134 4.7 57.1 1.0 O3' D:DC11 4.7 16.7 1.0 O B:HIS134 4.7 44.4 1.0 C5' D:DA12 4.8 16.9 1.0 CG B:GLU8 4.8 13.0 1.0 C B:ARG135 4.8 33.6 1.0 CB B:HIS134 4.9 51.9 1.0 N B:ARG135 4.9 40.9 1.0 N B:HIS134 4.9 53.6 1.0

T.Wang, H.L.Sun, F.Cheng, X.E.Zhang, L.Bi, T.Jiang. Recognition and Processing of Double-Stranded Dna By Exox, A Distributive 3'-5' Exonuclease Nucleic Acids Res. V. 41 7556 2013.
ISSN: ISSN 0305-1048
PubMed: 23771145
DOI: 10.1093/NAR/GKT495