Iodine 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:

Iron	(Fe)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 B:I7 b:58.6 occ:1.00 I5 B:5IU7 0.0 58.6 1.0 C5 B:5IU7 1.6 53.0 1.0 C6 B:5IU7 2.6 51.3 1.0 C4 B:5IU7 2.7 52.1 1.0 O4 B:5IU7 3.0 51.8 1.0 O B:HOH14 3.8 49.5 1.0 C2' B:DG6 3.9 49.4 1.0 N1 B:5IU7 3.9 50.0 1.0 N3 B:5IU7 3.9 48.1 1.0 N9 B:DG6 3.9 47.8 1.0 C8 B:DG6 4.0 47.4 1.0 O B:HOH12 4.0 46.6 1.0 C1' B:DG6 4.2 48.4 1.0 C4 B:DG6 4.4 47.4 1.0 N7 B:DG6 4.4 47.5 1.0 C2 B:5IU7 4.5 48.4 1.0 C5 B:DG6 4.7 47.4 1.0 OP2 B:5IU7 4.9 53.1 1.0

Iodine binding site 2 out of 3 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I14 b:63.3 occ:1.00 I5 C:5IU14 0.0 63.3 1.0 C5 C:5IU14 1.6 59.1 1.0 C6 C:5IU14 2.6 58.9 1.0 C4 C:5IU14 2.7 58.5 1.0 O4 C:5IU14 3.0 56.2 1.0 C2' C:DG13 3.6 58.1 1.0 N1 C:5IU14 3.9 59.3 1.0 N3 C:5IU14 3.9 57.1 1.0 N9 C:DG13 4.0 52.7 1.0 C8 C:DG13 4.1 52.4 1.0 C1' C:DG13 4.3 56.3 1.0 C4 C:DG13 4.4 50.3 1.0 OP2 C:5IU14 4.4 64.3 1.0 C2 C:5IU14 4.4 58.5 1.0 N7 C:DG13 4.5 52.0 1.0 N4 C:DC15 4.5 46.9 1.0 C5 C:DG13 4.6 50.2 1.0 C3' C:DG13 5.0 60.8 1.0 N3 C:DG13 5.0 49.8 1.0

Iodine binding site 3 out of 3 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I20 b:42.3 occ:1.00 I5 C:5IU20 0.0 42.3 1.0 C5 C:5IU20 1.7 35.4 1.0 C6 C:5IU20 2.7 34.0 1.0 C4 C:5IU20 2.7 34.0 1.0 O4 C:5IU20 3.1 34.7 1.0 O C:HOH23 3.6 22.9 1.0 C8 C:DG19 3.7 30.3 1.0 N9 C:DG19 3.9 29.9 1.0 C2' C:DG19 3.9 30.5 1.0 N3 C:5IU20 4.0 31.9 1.0 N1 C:5IU20 4.0 32.8 1.0 N7 C:DG19 4.0 28.0 1.0 C4 C:DG19 4.3 28.2 1.0 C5 C:DG19 4.3 28.2 1.0 C1' C:DG19 4.4 29.9 1.0 N4 C:DC21 4.5 25.9 1.0 C2 C:5IU20 4.5 31.3 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