Iron in PDB 1orp: Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex

The structure of Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex, PDB code: 1orp 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)	24.51 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.732, 106.516, 41.661, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 26.2

The structure of Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex (pdb code 1orp). 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 Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex, PDB code: 1orp:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine 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 Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:61.1 occ:1.00 FE1 A:SF4300 0.0 61.1 1.0 S2 A:SF4300 2.2 62.1 1.0 S4 A:SF4300 2.3 60.6 1.0 S3 A:SF4300 2.4 60.9 1.0 SG A:CYS199 2.4 63.5 1.0 FE3 A:SF4300 2.7 60.5 1.0 FE4 A:SF4300 2.8 60.4 1.0 FE2 A:SF4300 2.8 61.0 1.0 CB A:CYS199 3.1 68.1 1.0 S1 A:SF4300 4.0 61.4 1.0 CZ A:PHE184 4.1 44.0 1.0 NE2 A:HIS188 4.3 63.4 1.0 CD2 A:HIS188 4.4 62.0 1.0 CA A:CYS196 4.5 69.4 1.0 CB A:LEU201 4.5 68.5 1.0 CA A:CYS199 4.6 68.6 1.0 N A:LEU202 4.6 70.6 1.0 CE2 A:PHE184 4.8 44.4 1.0 SG A:CYS205 4.9 62.0 1.0 C A:LEU201 5.0 70.2 1.0 CB A:CYS196 5.0 68.9 1.0

Iron binding site 2 out of 4 in the Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine 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 Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:61.0 occ:1.00 FE2 A:SF4300 0.0 61.0 1.0 S3 A:SF4300 2.2 60.9 1.0 S4 A:SF4300 2.3 60.6 1.0 S1 A:SF4300 2.4 61.4 1.0 SG A:CYS189 2.6 55.3 1.0 FE4 A:SF4300 2.7 60.4 1.0 FE3 A:SF4300 2.8 60.5 1.0 FE1 A:SF4300 2.8 61.1 1.0 CB A:CYS189 3.1 56.4 1.0 CA A:CYS189 3.8 57.6 1.0 S2 A:SF4300 3.8 62.1 1.0 CE2 A:PHE184 4.2 44.4 1.0 CZ A:PHE184 4.5 44.0 1.0 CB A:PRO194 4.5 70.9 1.0 CD A:ARG148 4.5 50.9 1.0 NH1 A:ARG148 4.7 50.1 1.0 N A:CYS189 4.7 58.0 1.0 C A:CYS189 4.9 58.7 1.0 SG A:CYS205 5.0 62.0 1.0 SG A:CYS199 5.0 63.5 1.0 CB A:ARG148 5.0 52.3 1.0

Iron binding site 3 out of 4 in the Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine 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 Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:60.5 occ:1.00 FE3 A:SF4300 0.0 60.5 1.0 S2 A:SF4300 2.2 62.1 1.0 S4 A:SF4300 2.2 60.6 1.0 S1 A:SF4300 2.3 61.4 1.0 SG A:CYS196 2.7 68.9 1.0 FE4 A:SF4300 2.7 60.4 1.0 FE1 A:SF4300 2.7 61.1 1.0 FE2 A:SF4300 2.8 61.0 1.0 CB A:CYS196 3.1 68.9 1.0 CA A:CYS196 3.4 69.4 1.0 S3 A:SF4300 3.9 60.9 1.0 CA A:GLY208 3.9 72.9 1.0 N A:CYS196 3.9 68.8 1.0 CB A:PRO194 4.3 70.9 1.0 N A:GLY208 4.5 72.2 1.0 C A:CYS196 4.8 70.1 1.0 C A:GLN195 4.8 68.5 1.0 CB A:CYS199 4.8 68.1 1.0 CG A:PRO194 4.8 70.5 1.0 SG A:CYS205 4.9 62.0 1.0 SG A:CYS199 4.9 63.5 1.0

Iron binding site 4 out of 4 in the Structure of A Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine 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 Trapped Endonuclease III-Dna Covalent Intermediate: Estranged-Adenine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:60.4 occ:1.00 FE4 A:SF4300 0.0 60.4 1.0 S2 A:SF4300 2.1 62.1 1.0 S3 A:SF4300 2.3 60.9 1.0 S1 A:SF4300 2.4 61.4 1.0 SG A:CYS205 2.4 62.0 1.0 FE2 A:SF4300 2.7 61.0 1.0 FE3 A:SF4300 2.7 60.5 1.0 FE1 A:SF4300 2.8 61.1 1.0 CB A:CYS205 3.4 65.3 1.0 CD1 A:LEU149 3.8 58.2 1.0 N A:GLY208 3.8 72.2 1.0 S4 A:SF4300 3.8 60.6 1.0 CA A:GLY208 3.9 72.9 1.0 C A:GLU207 4.7 72.3 1.0 CB A:GLU207 4.8 71.3 1.0 CA A:CYS205 4.8 67.7 1.0 SG A:CYS199 4.9 63.5 1.0 SG A:CYS189 4.9 55.3 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