Sodium in PDB 4fzx: Exonuclease X in Complex with 3' Overhanging Duplex Dna

The structure of Exonuclease X in Complex with 3' Overhanging Duplex Dna, PDB code: 4fzx 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 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.475, 107.927, 117.124, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23

The binding sites of Sodium atom in the Exonuclease X in Complex with 3' Overhanging Duplex Dna (pdb code 4fzx). 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 3' Overhanging Duplex Dna, PDB code: 4fzx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Exonuclease X in Complex with 3' Overhanging Duplex Dna


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 3' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:25.5 occ:1.00 O C:HOH376 2.2 19.3 1.0 O C:HOH308 2.3 16.9 1.0 OD1 C:ASP6 2.4 17.9 1.0 OP1 B:DG17 2.5 14.7 1.0 O C:HOH377 2.5 27.7 1.0 O3' B:DA16 2.9 9.3 1.0 P B:DG17 3.3 10.1 1.0 CG C:ASP6 3.6 15.6 1.0 NA C:NA201 3.6 24.1 1.0 O C:HOH303 3.6 15.2 1.0 O C:HOH321 4.1 20.2 1.0 OD2 C:ASP85 4.1 21.9 1.0 C3' B:DA16 4.2 12.8 1.0 OD2 C:ASP6 4.2 17.2 1.0 C5' B:DG17 4.3 11.4 1.0 O C:THR7 4.3 13.3 1.0 OD1 C:ASP85 4.3 18.5 1.0 O5' B:DG17 4.3 12.5 1.0 OP2 B:DG17 4.3 11.9 1.0 C4' B:DA16 4.4 9.4 1.0 O C:HIS80 4.4 12.4 1.0 O B:HOH202 4.6 16.5 1.0 CG C:ASP85 4.7 19.0 1.0 CB C:ASP6 4.7 14.1 1.0 N C:THR7 4.7 14.3 1.0 CA C:ASP6 4.9 14.5 1.0 C5' B:DA16 5.0 9.3 1.0

Sodium binding site 2 out of 4 in the Exonuclease X in Complex with 3' Overhanging Duplex Dna


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 3' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:30.8 occ:1.00 O D:HOH360 2.1 20.0 1.0 O D:HOH307 2.3 16.6 1.0 OP1 A:DT17 2.4 17.0 1.0 O A:HOH204 2.5 22.8 1.0 O3' A:DC16 2.7 15.3 1.0 OD1 D:ASP6 2.8 24.4 1.0 P A:DT17 3.2 13.6 1.0 O D:HOH305 3.7 17.7 1.0 NA D:NA201 3.7 30.6 1.0 CG D:ASP6 3.7 18.9 1.0 C3' A:DC16 4.0 12.0 1.0 OD1 D:ASP85 4.1 30.1 1.0 O D:HOH336 4.1 21.4 1.0 C5' A:DT17 4.1 10.2 1.0 OD2 D:ASP6 4.1 26.6 1.0 O5' A:DT17 4.2 13.4 1.0 C4' A:DC16 4.2 13.5 1.0 OD2 D:ASP85 4.2 26.6 1.0 OP2 A:DT17 4.2 16.6 1.0 O D:THR7 4.3 15.2 1.0 O D:HIS80 4.3 15.4 1.0 O A:HOH201 4.5 26.8 1.0 CG D:ASP85 4.6 23.5 1.0 C5' A:DC16 4.7 10.6 1.0 N D:THR7 4.7 13.6 1.0 C2' A:DC16 4.7 12.9 1.0 CB D:ASP6 4.8 14.5 1.0 CA D:ASP6 4.9 14.1 1.0 CD2 D:PHE84 4.9 13.8 1.0

Sodium binding site 3 out of 4 in the Exonuclease X in Complex with 3' Overhanging Duplex Dna


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 3' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:24.1 occ:1.00 OD2 C:ASP139 2.2 16.5 1.0 OE2 C:GLU8 2.2 18.7 1.0 OP1 B:DG17 2.3 14.7 1.0 O C:HOH378 2.6 34.9 1.0 OD2 C:ASP6 2.9 17.2 1.0 OD1 C:ASP6 3.0 17.9 1.0 CG C:ASP139 3.2 13.2 1.0 CD C:GLU8 3.3 16.7 1.0 CG C:ASP6 3.3 15.6 1.0 O C:HOH377 3.4 27.7 1.0 OE1 C:GLU8 3.6 15.4 1.0 NA B:NA101 3.6 25.5 1.0 CB C:ASP139 3.6 9.2 1.0 P B:DG17 3.6 10.1 1.0 O C:HOH340 4.1 24.3 1.0 OP2 B:DG17 4.2 11.9 1.0 CA C:HIS134 4.3 15.7 1.0 OD1 C:ASP139 4.3 14.9 1.0 O5' B:DG17 4.5 12.5 1.0 O B:HOH202 4.6 16.5 1.0 ND1 C:HIS134 4.6 23.9 1.0 CG C:GLU8 4.6 11.9 1.0 O C:HOH376 4.6 19.3 1.0 O C:HOH321 4.6 20.2 1.0 O C:THR7 4.7 13.3 1.0 O3' B:DA16 4.7 9.3 1.0 C C:HIS134 4.8 14.7 1.0 CB C:ASP6 4.8 14.1 1.0 C5' B:DG17 4.8 11.4 1.0 O C:HIS134 4.9 14.6 1.0 N C:HIS134 5.0 15.0 1.0

Sodium binding site 4 out of 4 in the Exonuclease X in Complex with 3' Overhanging Duplex Dna


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 3' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:30.6 occ:1.00 OD2 D:ASP139 2.3 28.7 1.0 OP1 A:DT17 2.3 17.0 1.0 OE2 D:GLU8 2.5 20.9 1.0 OD1 D:ASP6 2.9 24.4 1.0 OD2 D:ASP6 3.0 26.6 1.0 O D:HOH363 3.1 37.4 1.0 CG D:ASP139 3.3 24.8 1.0 CG D:ASP6 3.3 18.9 1.0 CD D:GLU8 3.5 22.3 1.0 CB D:ASP139 3.5 17.8 1.0 P A:DT17 3.7 13.6 1.0 NA A:NA101 3.7 30.8 1.0 OE1 D:GLU8 3.8 23.4 1.0 O A:HOH204 3.8 22.8 1.0 O D:HOH358 4.0 35.5 1.0 OP2 A:DT17 4.2 16.6 1.0 CA D:HIS134 4.3 20.4 1.0 O5' A:DT17 4.4 13.4 1.0 OD1 D:ASP139 4.4 31.9 1.0 O A:HOH201 4.5 26.8 1.0 O D:HOH336 4.6 21.4 1.0 O D:THR7 4.6 15.2 1.0 C D:HIS134 4.7 19.1 1.0 ND1 D:HIS134 4.7 27.6 1.0 O3' A:DC16 4.8 15.3 1.0 C5' A:DT17 4.8 10.2 1.0 CB D:ASP6 4.8 14.5 1.0 CG D:GLU8 4.9 17.1 1.0 O D:HOH307 4.9 16.6 1.0 O D:HIS134 4.9 19.6 1.0 N D:HIS134 4.9 21.7 1.0 O D:ARG135 4.9 13.4 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