Iron in PDB 3dhz: Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein

The structure of Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein, PDB code: 3dhz was solved by M.Hogbom, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.908, 86.537, 70.610, 90.00, 105.48, 90.00
R / Rfree (%)	16.5 / 22.2

The binding sites of Iron atom in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein (pdb code 3dhz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein, PDB code: 3dhz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:13.2 occ:0.14 OD1 A:ASP77 1.9 25.0 1.0 ND1 A:HIS111 2.1 16.9 1.0 OE2 A:GLU202 2.2 35.9 1.0 OE1 A:GLU108 2.3 26.8 1.0 OE2 A:GLU108 2.5 26.9 1.0 CD A:GLU108 2.7 26.4 1.0 CE1 A:HIS111 3.0 19.0 1.0 CG A:ASP77 3.0 20.2 1.0 CG A:HIS111 3.1 13.4 1.0 CD A:GLU202 3.2 21.9 1.0 CB A:HIS111 3.4 14.6 1.0 FE A:FE2902 3.7 17.5 0.3 OD2 A:ASP77 3.7 23.4 1.0 CZ A:PHE172 3.8 24.1 1.0 CG A:GLU202 4.0 24.8 1.0 OE1 A:GLU202 4.0 26.9 1.0 CG A:GLU108 4.1 13.1 1.0 CB A:ASP77 4.1 12.4 1.0 CA A:GLU108 4.1 15.4 1.0 NE2 A:HIS111 4.2 12.7 1.0 O A:HOH930 4.2 25.4 1.0 CD2 A:HIS111 4.2 12.9 1.0 CE1 A:PHE172 4.3 21.2 1.0 CE2 A:PHE172 4.4 28.9 1.0 CG2 A:ILE198 4.4 21.0 1.0 CB A:GLU108 4.4 10.8 1.0 CA A:ASP77 4.5 14.0 1.0 O A:GLU108 4.7 11.9 1.0 C A:GLU108 4.9 16.8 1.0 CA A:HIS111 5.0 9.2 1.0 OE1 A:GLU168 5.0 43.1 1.0 O A:MET107 5.0 12.7 1.0 N A:GLU108 5.0 12.4 1.0

Iron binding site 2 out of 4 in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:17.5 occ:0.30 OE1 A:GLU168 1.7 43.1 1.0 OE1 A:GLU202 1.9 26.9 1.0 OE2 A:GLU202 2.1 35.9 1.0 OE2 A:GLU108 2.2 26.9 1.0 ND1 A:HIS205 2.2 14.9 1.0 CD A:GLU202 2.2 21.9 1.0 CD A:GLU168 2.9 43.0 1.0 CE1 A:HIS205 3.0 13.6 1.0 CD A:GLU108 3.0 26.4 1.0 CG A:HIS205 3.3 14.8 1.0 OE2 A:GLU168 3.6 30.6 1.0 OE1 A:GLU108 3.6 26.8 1.0 CG A:GLU202 3.7 24.8 1.0 FE A:FE2901 3.7 13.2 0.1 CB A:HIS205 3.7 13.2 1.0 CA A:GLU202 4.0 16.7 1.0 CG A:GLU168 4.0 24.5 1.0 CG A:GLU108 4.0 13.1 1.0 NE2 A:HIS205 4.2 14.7 1.0 CB A:GLU202 4.2 18.4 1.0 CD2 A:HIS205 4.4 12.9 1.0 CB A:GLU168 4.5 21.4 1.0 CE1 A:HIS111 4.5 19.0 1.0 CG A:GLN80 4.6 14.4 1.0 CE2 A:PHE172 4.6 28.9 1.0 N A:GLU202 4.6 18.2 1.0 CG2 A:ILE104 4.7 12.9 1.0 ND1 A:HIS111 4.7 16.9 1.0 CZ A:PHE172 4.9 24.1 1.0

Iron binding site 3 out of 4 in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe903 b:13.0 occ:0.16 OD1 B:ASP77 1.7 19.1 1.0 OE2 B:GLU202 2.1 30.2 1.0 ND1 B:HIS111 2.2 13.2 1.0 OE1 B:GLU108 2.2 23.1 1.0 OE2 B:GLU108 2.6 29.4 1.0 CD B:GLU108 2.7 20.1 1.0 CG B:ASP77 2.9 21.2 1.0 CE1 B:HIS111 3.1 14.1 1.0 CD B:GLU202 3.1 26.3 1.0 CG B:HIS111 3.2 11.5 1.0 CB B:HIS111 3.5 10.3 1.0 CZ B:PHE172 3.5 20.9 1.0 OD2 B:ASP77 3.6 19.1 1.0 FE B:FE2904 3.9 14.2 0.2 OE1 B:GLU202 3.9 27.6 1.0 CB B:ASP77 4.0 11.4 1.0 CG B:GLU202 4.0 17.5 1.0 O B:HOH1036 4.1 21.4 1.0 CG B:GLU108 4.1 10.8 1.0 CE2 B:PHE172 4.1 20.9 1.0 CA B:GLU108 4.2 11.8 1.0 CE1 B:PHE172 4.2 19.5 1.0 NE2 B:HIS111 4.2 13.0 1.0 CD2 B:HIS111 4.3 11.7 1.0 CG2 B:ILE198 4.4 15.9 1.0 CB B:GLU108 4.4 11.1 1.0 CA B:ASP77 4.5 11.0 1.0 O B:GLU108 4.7 10.6 1.0 C B:GLU108 5.0 9.7 1.0 CA B:HIS111 5.0 9.2 1.0

Iron binding site 4 out of 4 in the Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Apo (Iron Free) Structure of C. Ammoniagenes R2 Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe904 b:14.2 occ:0.25 O B:HOH1439 1.7 27.5 1.0 OE1 B:GLU202 1.9 27.6 1.0 ND1 B:HIS205 2.2 13.0 1.0 OE2 B:GLU108 2.3 29.4 1.0 CD B:GLU202 2.4 26.3 1.0 OE2 B:GLU202 2.4 30.2 1.0 CE1 B:HIS205 3.0 11.7 1.0 CD B:GLU108 3.0 20.1 1.0 CG B:HIS205 3.3 12.0 1.0 OE2 B:GLU168 3.6 27.7 1.0 OE1 B:GLU108 3.6 23.1 1.0 CB B:HIS205 3.7 13.6 1.0 CG B:GLU168 3.8 21.1 1.0 CG B:GLU202 3.8 17.5 1.0 FE B:FE2903 3.9 13.0 0.2 CG B:GLU108 4.0 10.8 1.0 CA B:GLU202 4.0 13.5 1.0 CD B:GLU168 4.1 39.8 1.0 NE2 B:HIS205 4.2 12.1 1.0 CB B:GLU202 4.3 18.0 1.0 CD2 B:HIS205 4.4 12.6 1.0 CE2 B:PHE172 4.5 20.9 1.0 CB B:GLU168 4.5 15.6 1.0 CG B:GLN80 4.6 13.9 1.0 CG2 B:ILE104 4.6 9.5 1.0 CE1 B:HIS111 4.7 14.1 1.0 N B:GLU202 4.7 13.3 1.0 ND1 B:HIS111 4.8 13.2 1.0 CZ B:PHE172 4.9 20.9 1.0

M.E.Andersson, M.Hogbom, A.Rinaldo-Matthis, W.Blodig, Y.Liang, B.O.Persson, B.M.Sjoberg, X.D.Su, P.Nordlund. Structural and Mutational Studies of the Carboxylate Cluster in Iron-Free Ribonucleotide Reductase R2. Biochemistry V. 43 7966 2004.
ISSN: ISSN 0006-2960
PubMed: 15196041
DOI: 10.1021/BI036088L