Sodium in PDB 1p59: Structure of A Non-Covalent Endonuclease III-Dna Complex

The structure of Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59 was solved by J.C.Fromme, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.31 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.321, 105.896, 41.518, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.9

The structure of Structure of A Non-Covalent Endonuclease III-Dna Complex also contains other interesting chemical elements:

Iodine	(I)	3 atoms
Iron	(Fe)	4 atoms

The binding sites of Sodium atom in the Structure of A Non-Covalent Endonuclease III-Dna Complex (pdb code 1p59). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59:

Sodium binding site 1 out of 1 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na224 b:28.1 occ:1.00 O A:MET113 2.3 24.3 1.0 OP1 C:DC21 2.4 32.5 1.0 O A:LEU115 2.4 30.2 1.0 O A:VAL118 2.6 24.2 1.0 O C:HOH26 3.2 43.6 1.0 C A:LEU115 3.2 28.3 1.0 C A:MET113 3.3 25.2 1.0 P C:DC21 3.5 31.4 1.0 C A:VAL118 3.6 22.7 1.0 N A:LEU115 3.8 26.0 1.0 C A:LYS114 3.8 25.4 1.0 OP2 C:DC21 3.8 33.5 1.0 N A:VAL118 3.9 20.6 1.0 N A:PRO116 3.9 27.4 1.0 CA A:MET113 4.0 25.6 1.0 O A:LYS114 4.0 24.8 1.0 CA A:PRO116 4.1 28.0 1.0 CA A:LEU115 4.1 28.3 1.0 CA A:VAL118 4.1 21.5 1.0 N A:LYS114 4.2 24.3 1.0 N A:GLY117 4.3 24.6 1.0 CA A:LYS114 4.4 25.3 1.0 CB A:VAL118 4.4 19.9 1.0 C A:PRO116 4.5 26.9 1.0 O3' C:5IU20 4.6 31.6 1.0 N A:GLY119 4.6 23.5 1.0 O5' C:DC21 4.7 31.4 1.0 O A:LEU112 4.7 26.3 1.0 CB A:MET113 4.8 26.7 1.0 C A:GLY117 5.0 22.9 1.0

J.C.Fromme, G.L.Verdine. Structure of A Trapped Endonuclease III-Dna Covalent Intermediate Embo J. V. 22 3461 2003.
ISSN: ISSN 0261-4189
PubMed: 12840008
DOI: 10.1093/EMBOJ/CDG311