Sodium in PDB 4fzz: Exonuclease X in Complex with 5' Overhanging Duplex Dna

The structure of Exonuclease X in Complex with 5' Overhanging Duplex Dna, PDB code: 4fzz 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)	20.01 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.192, 79.009, 156.012, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26

The binding sites of Sodium atom in the Exonuclease X in Complex with 5' Overhanging Duplex Dna (pdb code 4fzz). 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 5' Overhanging Duplex Dna, PDB code: 4fzz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Exonuclease X in Complex with 5' 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 5' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:22.4 occ:1.00 O B:HOH317 2.1 30.2 1.0 OD2 B:ASP6 2.2 28.6 1.0 O B:HOH301 2.3 14.2 1.0 O B:HOH319 2.6 29.0 1.0 O3' D:DA11 2.6 35.6 1.0 OP1 D:DG12 2.7 36.3 1.0 P D:DG12 3.3 36.3 1.0 CG B:ASP6 3.3 29.1 1.0 OD1 B:ASP6 3.8 31.2 1.0 OD2 B:ASP85 3.9 39.1 1.0 C3' D:DA11 3.9 35.3 1.0 O B:THR7 3.9 27.1 1.0 NA B:NA201 4.0 26.1 1.0 C5' D:DG12 4.0 35.0 1.0 O B:HOH304 4.1 22.4 1.0 C4' D:DA11 4.1 33.9 1.0 O5' D:DG12 4.2 32.8 1.0 O B:HOH313 4.3 19.5 1.0 N B:THR7 4.3 27.5 1.0 OD1 B:ASP85 4.4 35.6 1.0 OP2 D:DG12 4.4 36.8 1.0 CG B:ASP85 4.5 36.2 1.0 C2' D:DA11 4.6 35.2 1.0 CB B:ASP6 4.6 28.5 1.0 C5' D:DA11 4.6 32.4 1.0 O B:HIS80 4.7 27.8 1.0 O D:HOH201 4.7 35.7 1.0 CA B:ASP6 4.8 28.5 1.0 C B:THR7 4.9 26.8 1.0

Sodium binding site 2 out of 4 in the Exonuclease X in Complex with 5' 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 5' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:29.4 occ:1.00 O A:HOH307 2.3 23.3 1.0 OD1 A:ASP6 2.4 24.8 1.0 OP1 C:DG12 2.4 20.6 1.0 O A:HOH301 2.4 19.4 1.0 O A:HOH303 2.4 38.3 1.0 O3' C:DA11 2.4 25.5 1.0 P C:DG12 3.0 23.1 1.0 CG A:ASP6 3.5 24.9 1.0 NA A:NA201 3.6 32.5 1.0 C3' C:DA11 3.7 26.6 1.0 O5' C:DG12 3.9 23.5 1.0 C5' C:DG12 3.9 24.8 1.0 OD2 A:ASP85 3.9 34.3 1.0 O A:THR7 3.9 28.1 1.0 OD2 A:ASP6 4.1 24.3 1.0 C4' C:DA11 4.1 27.4 1.0 OP2 C:DG12 4.2 21.7 1.0 OD1 A:ASP85 4.3 31.8 1.0 C2' C:DA11 4.3 27.2 1.0 N A:THR7 4.4 28.4 1.0 CG A:ASP85 4.5 32.5 1.0 O A:HOH306 4.7 21.6 1.0 O A:HIS80 4.7 25.1 1.0 CB A:ASP6 4.7 26.2 1.0 C5' C:DA11 4.8 24.1 1.0 CA A:ASP6 4.9 26.9 1.0 C A:THR7 5.0 28.2 1.0

Sodium binding site 3 out of 4 in the Exonuclease X in Complex with 5' 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 5' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:32.5 occ:1.00 OD2 A:ASP6 2.4 24.3 1.0 OP1 C:DG12 2.4 20.6 1.0 OD2 A:ASP139 2.4 21.3 1.0 OE2 A:GLU8 2.6 31.1 1.0 CG A:ASP6 3.2 24.9 1.0 OD1 A:ASP6 3.3 24.8 1.0 CG A:ASP139 3.3 23.1 1.0 CD A:GLU8 3.5 29.7 1.0 CB A:ASP139 3.6 23.7 1.0 NA C:NA101 3.6 29.4 1.0 OE1 A:GLU8 3.6 30.6 1.0 P C:DG12 3.8 23.1 1.0 ND1 A:HIS134 3.9 31.1 1.0 CA A:HIS134 4.0 28.5 1.0 O A:HOH307 4.1 23.3 1.0 O A:THR7 4.2 28.1 1.0 OD1 A:ASP139 4.5 25.1 1.0 OP2 C:DG12 4.5 21.7 1.0 N A:HIS134 4.6 29.2 1.0 C5' C:DG12 4.6 24.8 1.0 CE1 A:HIS134 4.6 30.8 1.0 N A:ALA136 4.6 21.7 1.0 CB A:ASP6 4.7 26.2 1.0 O5' C:DG12 4.7 23.5 1.0 CG A:HIS134 4.7 30.2 1.0 O3' C:DA11 4.8 25.5 1.0 O A:HOH306 4.8 21.6 1.0 C A:HIS134 4.8 27.5 1.0 CA A:ALA136 4.8 21.2 1.0 CB A:HIS134 4.8 28.6 1.0 CG A:GLU8 4.8 28.6 1.0 N A:ARG135 4.9 25.8 1.0 C A:THR7 4.9 28.2 1.0 O A:HOH303 5.0 38.3 1.0

Sodium binding site 4 out of 4 in the Exonuclease X in Complex with 5' 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 5' Overhanging Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:26.1 occ:1.00 OE2 B:GLU8 2.4 26.7 1.0 OP1 D:DG12 2.4 36.3 1.0 OD2 B:ASP139 2.5 25.4 1.0 OD1 B:ASP6 2.7 31.2 1.0 CD B:GLU8 3.3 26.8 1.0 ND1 B:HIS134 3.3 47.4 1.0 CG B:ASP139 3.4 27.2 1.0 OE1 B:GLU8 3.6 29.8 1.0 CG B:ASP6 3.6 29.1 1.0 CB B:ASP139 3.7 28.5 1.0 CA B:HIS134 3.7 43.9 1.0 OD2 B:ASP6 3.8 28.6 1.0 P D:DG12 3.8 36.3 1.0 NA D:NA101 4.0 22.4 1.0 CE1 B:HIS134 4.0 46.8 1.0 C B:HIS134 4.2 41.4 1.0 O B:HOH317 4.3 30.2 1.0 O B:THR7 4.3 27.1 1.0 CG B:HIS134 4.3 46.0 1.0 N B:ARG135 4.3 38.5 1.0 O5' D:DG12 4.5 32.8 1.0 C5' D:DG12 4.5 35.0 1.0 N B:HIS134 4.5 46.6 1.0 OD1 B:ASP139 4.5 25.8 1.0 O D:HOH201 4.6 35.7 1.0 OP2 D:DG12 4.6 36.8 1.0 CB B:HIS134 4.6 44.2 1.0 CG B:GLU8 4.7 26.2 1.0 O B:HOH313 4.9 19.5 1.0 O3' D:DA11 4.9 35.6 1.0 N B:ALA136 4.9 32.8 1.0 C B:ARG135 4.9 34.5 1.0 O B:HIS134 4.9 41.0 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