Iron 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
Sodium	(Na)	1 atom

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Structure of A Non-Covalent Endonuclease III-Dna Complex, PDB code: 1p59:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe300 b:38.9 occ:1.00 FE1 A:SF4300 0.0 38.9 1.0 S2 A:SF4300 2.2 38.7 1.0 S4 A:SF4300 2.2 37.5 1.0 SG A:CYS199 2.3 36.0 1.0 S3 A:SF4300 2.4 37.2 1.0 FE3 A:SF4300 2.6 38.6 1.0 FE4 A:SF4300 2.7 37.3 1.0 FE2 A:SF4300 2.8 39.2 1.0 CB A:CYS199 2.9 39.0 1.0 S1 A:SF4300 3.9 37.5 1.0 CA A:CYS196 4.3 41.8 1.0 CZ A:PHE184 4.3 37.9 1.0 NE2 A:HIS188 4.3 42.4 1.0 CA A:CYS199 4.3 41.1 1.0 CD2 A:HIS188 4.5 41.4 1.0 N A:LEU202 4.7 38.5 1.0 CB A:LEU201 4.8 36.4 1.0 SG A:CYS205 4.8 32.8 1.0 CB A:CYS196 4.9 42.0 1.0 N A:CYS196 4.9 40.2 1.0 CE2 A:PHE184 4.9 37.9 1.0 SG A:CYS196 4.9 42.2 1.0 C A:LEU201 4.9 38.8 1.0 C A:CYS199 5.0 41.4 1.0 O A:GLN195 5.0 38.5 1.0

Iron binding site 2 out of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe300 b:39.2 occ:1.00 FE2 A:SF4300 0.0 39.2 1.0 S3 A:SF4300 2.2 37.2 1.0 S1 A:SF4300 2.2 37.5 1.0 S4 A:SF4300 2.3 37.5 1.0 FE4 A:SF4300 2.5 37.3 1.0 SG A:CYS189 2.6 36.2 1.0 FE3 A:SF4300 2.6 38.6 1.0 FE1 A:SF4300 2.8 38.9 1.0 CB A:CYS189 3.2 38.1 1.0 S2 A:SF4300 3.6 38.7 1.0 CA A:CYS189 3.9 38.8 1.0 CB A:PRO194 4.4 43.3 1.0 CE2 A:PHE184 4.5 37.9 1.0 CD A:ARG148 4.7 33.5 1.0 SG A:CYS196 4.7 42.2 1.0 NH1 A:ARG148 4.7 29.3 1.0 CZ A:PHE184 4.8 37.9 1.0 SG A:CYS205 4.8 32.8 1.0 C A:CYS189 4.9 38.4 1.0 SG A:CYS199 4.9 36.0 1.0 N A:CYS189 5.0 38.9 1.0

Iron binding site 3 out of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 A:Fe300 b:38.6 occ:1.00 FE3 A:SF4300 0.0 38.6 1.0 S4 A:SF4300 2.1 37.5 1.0 S2 A:SF4300 2.1 38.7 1.0 S1 A:SF4300 2.3 37.5 1.0 SG A:CYS196 2.5 42.2 1.0 FE1 A:SF4300 2.6 38.9 1.0 FE2 A:SF4300 2.6 39.2 1.0 FE4 A:SF4300 2.7 37.3 1.0 CB A:CYS196 3.1 42.0 1.0 CA A:CYS196 3.3 41.8 1.0 N A:CYS196 3.8 40.2 1.0 S3 A:SF4300 3.8 37.2 1.0 CA A:GLY208 4.0 44.5 1.0 CB A:PRO194 4.1 43.3 1.0 CB A:CYS199 4.5 39.0 1.0 N A:GLY208 4.5 42.1 1.0 C A:CYS196 4.6 43.0 1.0 C A:GLN195 4.6 39.8 1.0 CG A:PRO194 4.7 41.7 1.0 SG A:CYS199 4.8 36.0 1.0 SG A:CYS205 4.8 32.8 1.0 O A:CYS196 5.0 44.2 1.0

Iron binding site 4 out of 4 in the Structure of A Non-Covalent Endonuclease III-Dna Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of A Non-Covalent Endonuclease III-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:37.3 occ:1.00 FE4 A:SF4300 0.0 37.3 1.0 S2 A:SF4300 2.1 38.7 1.0 S3 A:SF4300 2.3 37.2 1.0 S1 A:SF4300 2.3 37.5 1.0 SG A:CYS205 2.4 32.8 1.0 FE2 A:SF4300 2.5 39.2 1.0 FE3 A:SF4300 2.7 38.6 1.0 FE1 A:SF4300 2.7 38.9 1.0 CB A:CYS205 3.5 37.8 1.0 S4 A:SF4300 3.8 37.5 1.0 N A:GLY208 3.8 42.1 1.0 CD1 A:LEU149 4.0 30.2 1.0 CA A:GLY208 4.0 44.5 1.0 CB A:GLU207 4.5 38.3 1.0 C A:GLU207 4.6 39.7 1.0 SG A:CYS199 4.8 36.0 1.0 SG A:CYS189 4.9 36.2 1.0 CA A:CYS205 4.9 38.1 1.0 CB A:ARG148 4.9 33.7 1.0 SG A:CYS196 4.9 42.2 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