Iron in PDB 1oqu: A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes

The structure of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes, PDB code: 1oqu 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 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.319, 91.237, 136.956, 90.00, 91.46, 90.00
R / Rfree (%)	18.1 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes (pdb code 1oqu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes, PDB code: 1oqu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:31.4 occ:1.00 OD1 A:ASP77 1.9 34.5 1.0 ND1 A:HIS111 2.1 11.0 1.0 OE1 A:GLU108 2.3 40.7 1.0 OE2 A:GLU202 2.5 29.9 1.0 CE1 A:HIS111 3.0 13.0 1.0 CD A:GLU108 3.0 33.6 1.0 CG A:ASP77 3.0 38.1 1.0 CD A:GLU202 3.1 40.1 1.0 CG A:HIS111 3.1 9.9 1.0 OE2 A:GLU108 3.1 34.5 1.0 OE1 A:GLU202 3.5 64.0 1.0 CB A:HIS111 3.5 10.8 1.0 CZ A:PHE172 3.6 24.2 1.0 OD2 A:ASP77 3.6 34.9 1.0 FE A:FE1002 3.8 26.6 1.0 O A:HOH2061 4.0 36.0 1.0 CG A:GLU202 4.0 25.9 1.0 NE2 A:HIS111 4.2 12.3 1.0 CB A:ASP77 4.2 23.0 1.0 CE2 A:PHE172 4.2 33.3 1.0 CD2 A:HIS111 4.2 10.8 1.0 CE1 A:PHE172 4.3 30.0 1.0 CA A:GLU108 4.3 15.4 1.0 CG2 A:ILE198 4.3 13.5 1.0 CG A:GLU108 4.4 25.1 1.0 CB A:GLU108 4.6 15.8 1.0 CA A:ASP77 4.7 24.6 1.0 O A:GLU108 5.0 17.5 1.0

Iron binding site 2 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:26.6 occ:1.00 OE2 A:GLU108 1.9 34.5 1.0 OE2 A:GLU202 2.2 29.9 1.0 OE1 A:GLU168 2.2 27.8 1.0 ND1 A:HIS205 2.2 16.9 1.0 OE2 A:GLU168 2.4 28.5 1.0 OE1 A:GLU202 2.6 64.0 1.0 CD A:GLU168 2.6 34.3 1.0 CD A:GLU202 2.7 40.1 1.0 CD A:GLU108 3.0 33.6 1.0 CE1 A:HIS205 3.1 13.5 1.0 CG A:HIS205 3.3 13.0 1.0 OE1 A:GLU108 3.5 40.7 1.0 CB A:HIS205 3.6 14.4 1.0 FE A:FE1001 3.8 31.4 1.0 CG A:GLU202 4.0 25.9 1.0 CG A:GLU168 4.1 22.2 1.0 CA A:GLU202 4.1 18.2 1.0 CG A:GLU108 4.2 25.1 1.0 NE2 A:HIS205 4.3 13.0 1.0 CG A:GLN80 4.4 28.0 1.0 CD2 A:HIS205 4.4 15.2 1.0 CB A:GLU202 4.4 16.3 1.0 CE2 A:PHE172 4.5 33.3 1.0 CE1 A:HIS111 4.6 13.0 1.0 CG2 A:ILE104 4.6 12.6 1.0 N A:GLU202 4.7 19.0 1.0 ND1 A:HIS111 4.7 11.0 1.0 CB A:GLU168 4.8 18.9 1.0 CZ A:PHE172 4.9 24.2 1.0 NE2 A:GLN80 4.9 35.4 1.0

Iron binding site 3 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2001 b:26.2 occ:0.60 OE1 A:GLU245 2.1 34.2 1.0 OE1 A:GLU248 2.1 35.5 1.0 O1 A:OXY2004 2.3 26.2 1.0 O A:HOH2200 2.4 47.0 1.0 O A:HOH2063 2.8 40.4 1.0 CD A:GLU245 3.2 34.0 1.0 CD A:GLU248 3.2 28.9 1.0 FE A:FE2002 3.3 28.2 0.6 FE A:FE2003 3.5 30.9 0.6 OE2 A:GLU245 3.6 39.5 1.0 OE2 A:GLU248 3.6 38.8 1.0 CG A:GLU248 4.4 28.6 1.0 CG A:GLU245 4.5 34.5 1.0 CB A:GLU248 4.6 22.6 1.0 O A:HOH2121 4.6 44.4 1.0 O A:HOH2201 4.6 36.2 1.0 CB A:GLU245 4.7 25.8 1.0 CA A:GLU245 4.8 23.3 1.0 O A:HOH2192 4.9 50.2 1.0

Iron binding site 4 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2002 b:28.2 occ:0.60 O A:HOH2192 1.9 50.2 1.0 O1 A:OXY2004 2.2 26.2 1.0 OE2 A:GLU248 2.2 38.8 1.0 O A:HOH2121 2.4 44.4 1.0 O A:HOH2201 2.6 36.2 1.0 CD A:GLU248 3.0 28.9 1.0 OE1 A:GLU248 3.1 35.5 1.0 FE A:FE2001 3.3 26.2 0.6 FE A:FE2003 3.4 30.9 0.6 O A:HOH2200 3.5 47.0 1.0 CG A:GLU248 4.4 28.6 1.0 OE2 A:GLU245 4.4 39.5 1.0 OE1 A:GLU245 4.5 34.2 1.0 O A:HOH2063 4.6 40.4 1.0 NZ A:LYS261 4.8 41.0 1.0 CD A:GLU245 4.9 34.0 1.0 O A:HOH2161 5.0 56.5 1.0

Iron binding site 5 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2003 b:30.9 occ:0.60 O1 A:OXY2004 1.6 26.2 1.0 OE2 A:GLU245 2.2 39.5 1.0 O A:HOH2063 2.6 40.4 1.0 O A:HOH2201 2.7 36.2 1.0 CD A:GLU245 3.1 34.0 1.0 OE1 A:GLU245 3.3 34.2 1.0 O A:HOH2121 3.4 44.4 1.0 FE A:FE2002 3.4 28.2 0.6 FE A:FE2001 3.5 26.2 0.6 O A:HOH2030 4.0 28.3 1.0 O A:HOH2161 4.2 56.5 1.0 CG A:GLU245 4.5 34.5 1.0 OE2 A:GLU248 4.6 38.8 1.0 OE1 A:GLU248 4.7 35.5 1.0

Iron binding site 6 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1003 b:27.4 occ:1.00 OD1 B:ASP77 1.9 38.5 1.0 OE1 B:GLU202 2.0 60.0 1.0 ND1 B:HIS111 2.1 14.9 1.0 OE1 B:GLU108 2.1 30.9 1.0 CD B:GLU202 2.6 46.3 1.0 OE2 B:GLU202 2.7 30.6 1.0 CG B:ASP77 2.8 38.0 1.0 CE1 B:HIS111 3.0 15.0 1.0 CD B:GLU108 3.2 24.7 1.0 CG B:HIS111 3.2 12.5 1.0 OD2 B:ASP77 3.2 40.5 1.0 OE2 B:GLU108 3.5 29.9 1.0 CB B:HIS111 3.6 14.8 1.0 FE B:FE1004 3.7 22.2 1.0 CZ B:PHE172 3.7 53.7 1.0 CG B:GLU202 4.0 45.7 1.0 CB B:ASP77 4.1 27.9 1.0 O B:HOH1076 4.1 32.6 1.0 NE2 B:HIS111 4.2 20.1 1.0 CE2 B:PHE172 4.2 52.1 1.0 CD2 B:HIS111 4.3 18.6 1.0 CE1 B:PHE172 4.3 51.7 1.0 CA B:GLU108 4.4 19.1 1.0 CG2 B:ILE198 4.5 19.3 1.0 CG B:GLU108 4.5 22.2 1.0 CB B:GLU108 4.7 15.3 1.0 CA B:ASP77 4.8 28.0 1.0 OE2 B:GLU168 4.9 36.4 1.0

Iron binding site 7 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1004 b:22.2 occ:1.00 OE2 B:GLU202 1.9 30.6 1.0 OE2 B:GLU108 1.9 29.9 1.0 OE2 B:GLU168 2.0 36.4 1.0 OE1 B:GLU168 2.1 34.9 1.0 ND1 B:HIS205 2.1 17.8 1.0 CD B:GLU168 2.3 32.4 1.0 CD B:GLU108 3.0 24.7 1.0 CE1 B:HIS205 3.0 18.9 1.0 CD B:GLU202 3.0 46.3 1.0 CG B:HIS205 3.2 20.4 1.0 OE1 B:GLU108 3.4 30.9 1.0 CB B:HIS205 3.6 16.2 1.0 FE B:FE1003 3.7 27.4 1.0 OE1 B:GLU202 3.7 60.0 1.0 CG B:GLU168 3.9 34.4 1.0 CA B:GLU202 4.1 25.2 1.0 NE2 B:HIS205 4.2 15.6 1.0 CG B:GLU202 4.2 45.7 1.0 CD2 B:HIS205 4.3 19.2 1.0 CG B:GLU108 4.3 22.2 1.0 CB B:GLU202 4.3 35.3 1.0 CG B:GLN80 4.5 35.5 1.0 NE2 B:GLN80 4.5 50.0 1.0 CE1 B:HIS111 4.7 15.0 1.0 CB B:GLU168 4.7 27.2 1.0 N B:GLU202 4.7 19.7 1.0 CE2 B:PHE172 4.7 52.1 1.0 OD1 B:ASP77 4.7 38.5 1.0 CG2 B:ILE104 4.7 17.8 1.0 ND1 B:HIS111 4.8 14.9 1.0

Iron binding site 8 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1005 b:26.1 occ:0.30 OE1 B:GLU248 1.8 56.1 1.0 CD B:GLU248 2.8 57.8 1.0 OE2 B:GLU248 3.1 62.5 1.0 FE B:FE1006 3.5 36.3 0.3 FE B:FE1007 3.5 32.7 0.3 CG B:GLU245 4.1 62.5 1.0 CG B:GLU248 4.2 50.0 1.0 CB B:GLU248 4.6 49.6 1.0 CA B:GLU245 4.7 35.6 1.0 CB B:GLU245 4.9 38.9 1.0

Iron binding site 9 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1006 b:36.3 occ:0.30 OE2 B:GLU248 2.2 62.5 1.0 CD B:GLU248 3.3 57.8 1.0 FE B:FE1005 3.5 26.1 0.3 OE1 B:GLU248 3.7 56.1 1.0 FE B:FE1007 3.9 32.7 0.3 NZ B:LYS261 4.0 40.0 1.0 CG B:GLU248 4.5 50.0 1.0 CG2 B:ILE244 4.7 41.2 1.0

Iron binding site 10 out of 20 in the A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of A Protein Coordinated Tri-Nuclear Fe Complex Formed During Soaking of Crystals of the Ribonucleotide Reductase R2F Protein From Corynebacterium Ammoniagenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1007 b:32.7 occ:0.30 FE B:FE1005 3.5 26.1 0.3 FE B:FE1006 3.9 36.3 0.3 OE2 B:GLU248 4.8 62.5 1.0 OE1 B:GLU248 4.9 56.1 1.0

M.Hogbom, P.Nordlund. A Protein Carboxylate Coordinated Oxo-Centered Tri-Nuclear Iron Complex with Possible Implications For Ferritin Mineralization Febs Lett. V. 567 179 2004.
ISSN: ISSN 0014-5793
PubMed: 15178319
DOI: 10.1016/J.FEBSLET.2004.04.068