Iron in PDB 1iqc: Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc was solved by H.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.134, 55.111, 144.000, 90.00, 103.60, 90.00
R / Rfree (%)	22.2 / 25.7

The structure of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	5 atoms

The binding sites of Iron atom in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea (pdb code 1iqc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea, PDB code: 1iqc:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.0 occ:1.00 FE A:HEC401 0.0 13.0 1.0 NC A:HEC401 2.0 13.7 1.0 NA A:HEC401 2.0 15.8 1.0 NB A:HEC401 2.0 11.4 1.0 ND A:HEC401 2.0 14.4 1.0 NE2 A:HIS43 2.1 11.6 1.0 O A:HOH1680 2.3 18.6 1.0 C1C A:HEC401 3.0 10.5 1.0 C4B A:HEC401 3.0 12.0 1.0 C4D A:HEC401 3.0 14.2 1.0 C4C A:HEC401 3.0 12.8 1.0 C1A A:HEC401 3.0 12.2 1.0 C1D A:HEC401 3.0 12.5 1.0 C4A A:HEC401 3.1 12.9 1.0 CD2 A:HIS43 3.1 14.5 1.0 C1B A:HEC401 3.1 11.0 1.0 CE1 A:HIS43 3.1 11.4 1.0 CHC A:HEC401 3.4 13.8 1.0 CHA A:HEC401 3.4 10.9 1.0 CHD A:HEC401 3.4 11.0 1.0 CHB A:HEC401 3.4 11.1 1.0 NE2 A:GLN92 4.1 15.8 1.0 ND1 A:HIS43 4.2 9.4 1.0 CG A:HIS43 4.2 10.9 1.0 C2C A:HEC401 4.2 11.7 1.0 C3C A:HEC401 4.3 12.8 1.0 C3B A:HEC401 4.3 12.5 1.0 C3D A:HEC401 4.3 12.6 1.0 C2A A:HEC401 4.3 13.8 1.0 C3A A:HEC401 4.3 13.9 1.0 C2B A:HEC401 4.3 10.9 1.0 C2D A:HEC401 4.3 16.6 1.0 O A:HOH1479 4.7 41.3 1.0 CB A:PRO96 4.9 21.4 1.0 CG A:PRO96 5.0 25.3 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:15.7 occ:1.00 FE A:HEC402 0.0 15.7 1.0 ND A:HEC402 2.0 15.5 1.0 NB A:HEC402 2.0 17.9 1.0 NC A:HEC402 2.0 19.1 1.0 NA A:HEC402 2.0 15.2 1.0 NE2 A:HIS187 2.1 12.1 1.0 SD A:MET258 2.3 20.6 1.0 C1D A:HEC402 3.0 16.8 1.0 C4B A:HEC402 3.0 16.9 1.0 C4D A:HEC402 3.0 13.3 1.0 C1C A:HEC402 3.0 17.4 1.0 C4C A:HEC402 3.0 18.1 1.0 C1A A:HEC402 3.0 14.3 1.0 C1B A:HEC402 3.0 16.7 1.0 C4A A:HEC402 3.1 18.1 1.0 CD2 A:HIS187 3.1 10.7 1.0 CE1 A:HIS187 3.1 13.2 1.0 CHC A:HEC402 3.4 17.1 1.0 CHD A:HEC402 3.4 17.4 1.0 CHA A:HEC402 3.4 14.7 1.0 CG A:MET258 3.4 17.5 1.0 CHB A:HEC402 3.5 16.8 1.0 CE A:MET258 3.6 16.2 1.0 ND1 A:HIS187 4.2 15.6 1.0 CG A:HIS187 4.2 14.4 1.0 C3D A:HEC402 4.2 15.6 1.0 C2D A:HEC402 4.2 19.5 1.0 C3B A:HEC402 4.3 16.3 1.0 C2B A:HEC402 4.3 18.6 1.0 C3C A:HEC402 4.3 15.8 1.0 C2C A:HEC402 4.3 15.7 1.0 C2A A:HEC402 4.3 12.4 1.0 C3A A:HEC402 4.3 15.8 1.0 CB A:MET258 4.4 20.3 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.1 occ:1.00 FE B:HEC401 0.0 19.1 1.0 ND B:HEC401 1.9 20.4 1.0 NB B:HEC401 2.0 18.6 1.0 NC B:HEC401 2.0 17.9 1.0 NA B:HEC401 2.0 18.0 1.0 O B:HOH1609 2.1 25.8 1.0 NE2 B:HIS43 2.1 21.2 1.0 C1D B:HEC401 3.0 19.8 1.0 C4C B:HEC401 3.0 22.5 1.0 C4D B:HEC401 3.0 15.2 1.0 C1B B:HEC401 3.0 19.6 1.0 C4A B:HEC401 3.0 17.2 1.0 C4B B:HEC401 3.0 16.2 1.0 C1A B:HEC401 3.1 17.6 1.0 C1C B:HEC401 3.1 20.5 1.0 CD2 B:HIS43 3.1 21.0 1.0 CE1 B:HIS43 3.2 20.8 1.0 CHD B:HEC401 3.4 19.7 1.0 CHB B:HEC401 3.4 16.7 1.0 CHA B:HEC401 3.4 14.6 1.0 CHC B:HEC401 3.5 17.3 1.0 NE2 B:GLN92 4.0 14.3 1.0 CG B:HIS43 4.2 23.6 1.0 C2D B:HEC401 4.2 18.6 1.0 C3D B:HEC401 4.2 19.0 1.0 ND1 B:HIS43 4.2 22.1 1.0 C3A B:HEC401 4.3 19.4 1.0 C2B B:HEC401 4.3 20.1 1.0 C3B B:HEC401 4.3 19.6 1.0 C2A B:HEC401 4.3 16.7 1.0 C2C B:HEC401 4.3 19.9 1.0 C3C B:HEC401 4.3 20.2 1.0 O B:HOH1413 4.3 26.4 1.0 CG B:PRO96 4.4 22.6 1.0 CD B:GLN92 4.9 17.7 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:28.3 occ:1.00 FE B:HEC402 0.0 28.3 1.0 NA B:HEC402 2.0 31.3 1.0 NB B:HEC402 2.0 32.3 1.0 ND B:HEC402 2.0 26.1 1.0 NC B:HEC402 2.0 29.6 1.0 NE2 B:HIS187 2.1 28.1 1.0 SD B:MET258 2.3 35.6 1.0 CD2 B:HIS187 3.0 29.3 1.0 C1A B:HEC402 3.0 31.8 1.0 C4D B:HEC402 3.0 26.1 1.0 C4A B:HEC402 3.0 32.8 1.0 C4B B:HEC402 3.0 33.9 1.0 C1B B:HEC402 3.1 35.4 1.0 C1C B:HEC402 3.1 29.2 1.0 C1D B:HEC402 3.1 26.8 1.0 C4C B:HEC402 3.1 30.9 1.0 CE1 B:HIS187 3.1 26.9 1.0 CHA B:HEC402 3.4 29.3 1.0 CHC B:HEC402 3.4 32.4 1.0 CHB B:HEC402 3.4 36.6 1.0 CG B:MET258 3.5 32.9 1.0 CHD B:HEC402 3.5 26.3 1.0 CE B:MET258 3.7 27.0 1.0 CG B:HIS187 4.2 30.3 1.0 ND1 B:HIS187 4.2 27.0 1.0 C3A B:HEC402 4.3 34.3 1.0 C2A B:HEC402 4.3 32.8 1.0 C3B B:HEC402 4.3 34.4 1.0 C2B B:HEC402 4.3 37.1 1.0 C3D B:HEC402 4.3 26.6 1.0 C2D B:HEC402 4.3 25.8 1.0 C2C B:HEC402 4.3 31.3 1.0 C3C B:HEC402 4.3 28.8 1.0 CB B:MET258 4.4 32.3 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:14.2 occ:1.00 FE C:HEC401 0.0 14.2 1.0 NB C:HEC401 1.9 11.1 1.0 ND C:HEC401 2.0 14.5 1.0 NA C:HEC401 2.0 12.3 1.0 NC C:HEC401 2.0 13.3 1.0 NE2 C:HIS43 2.1 12.9 1.0 O C:HOH689 2.3 20.5 1.0 C4B C:HEC401 3.0 10.5 1.0 C4D C:HEC401 3.0 11.3 1.0 C1D C:HEC401 3.0 13.5 1.0 C1B C:HEC401 3.0 11.1 1.0 C1A C:HEC401 3.0 12.6 1.0 C4A C:HEC401 3.0 11.6 1.0 C4C C:HEC401 3.0 13.5 1.0 CD2 C:HIS43 3.0 13.6 1.0 C1C C:HEC401 3.1 10.1 1.0 CE1 C:HIS43 3.1 16.1 1.0 CHD C:HEC401 3.4 14.4 1.0 CHA C:HEC401 3.4 16.2 1.0 CHC C:HEC401 3.4 14.7 1.0 CHB C:HEC401 3.4 12.4 1.0 NE2 C:GLN92 4.0 15.8 1.0 ND1 C:HIS43 4.2 11.1 1.0 CG C:HIS43 4.2 12.4 1.0 C3B C:HEC401 4.2 13.2 1.0 C2D C:HEC401 4.2 13.8 1.0 C3D C:HEC401 4.2 15.6 1.0 C2B C:HEC401 4.2 13.1 1.0 C3A C:HEC401 4.3 13.8 1.0 C3C C:HEC401 4.3 13.8 1.0 C2A C:HEC401 4.3 14.9 1.0 C2C C:HEC401 4.3 11.8 1.0 O C:HOH485 4.5 28.7 1.0 CB C:PRO96 4.9 18.6 1.0 CD C:GLN92 4.9 16.5 1.0 CG C:PRO96 5.0 19.4 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:14.2 occ:1.00 FE C:HEC402 0.0 14.2 1.0 NB C:HEC402 2.0 13.6 1.0 ND C:HEC402 2.0 16.9 1.0 NA C:HEC402 2.0 14.3 1.0 NC C:HEC402 2.0 13.6 1.0 NE2 C:HIS187 2.1 12.2 1.0 SD C:MET258 2.3 19.1 1.0 CD2 C:HIS187 3.0 19.0 1.0 C1B C:HEC402 3.0 15.4 1.0 C4B C:HEC402 3.0 16.9 1.0 C1D C:HEC402 3.0 14.3 1.0 C4A C:HEC402 3.0 12.9 1.0 C4D C:HEC402 3.0 11.4 1.0 C4C C:HEC402 3.0 16.0 1.0 C1C C:HEC402 3.0 16.2 1.0 C1A C:HEC402 3.1 14.2 1.0 CE1 C:HIS187 3.1 14.4 1.0 CHB C:HEC402 3.4 11.5 1.0 CHD C:HEC402 3.4 11.7 1.0 CHC C:HEC402 3.4 14.8 1.0 CHA C:HEC402 3.4 12.0 1.0 CG C:MET258 3.5 14.5 1.0 CE C:MET258 3.5 14.7 1.0 CG C:HIS187 4.2 12.5 1.0 ND1 C:HIS187 4.2 12.8 1.0 C2B C:HEC402 4.3 14.7 1.0 C3D C:HEC402 4.3 12.0 1.0 C3B C:HEC402 4.3 15.5 1.0 C2D C:HEC402 4.3 16.1 1.0 C3A C:HEC402 4.3 12.1 1.0 C2A C:HEC402 4.3 12.2 1.0 C2C C:HEC402 4.3 20.5 1.0 C3C C:HEC402 4.3 16.2 1.0 CB C:MET258 4.4 15.8 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:30.9 occ:1.00 FE D:HEC401 0.0 30.9 1.0 NC D:HEC401 2.0 37.4 1.0 ND D:HEC401 2.0 35.7 1.0 NB D:HEC401 2.0 36.1 1.0 NA D:HEC401 2.0 35.6 1.0 NE2 D:HIS43 2.1 28.7 1.0 O D:HOH2540 2.2 31.1 1.0 CD2 D:HIS43 3.0 31.2 1.0 C1C D:HEC401 3.0 38.6 1.0 C4B D:HEC401 3.0 39.4 1.0 C4D D:HEC401 3.0 37.1 1.0 C4C D:HEC401 3.0 37.4 1.0 C1A D:HEC401 3.0 36.6 1.0 C1D D:HEC401 3.1 37.5 1.0 C4A D:HEC401 3.1 37.0 1.0 C1B D:HEC401 3.1 38.0 1.0 CE1 D:HIS43 3.1 33.7 1.0 CHC D:HEC401 3.4 38.9 1.0 CHA D:HEC401 3.4 37.9 1.0 CHD D:HEC401 3.4 38.4 1.0 CHB D:HEC401 3.4 39.5 1.0 CG D:HIS43 4.1 34.0 1.0 ND1 D:HIS43 4.2 28.2 1.0 NE2 D:GLN92 4.2 41.6 1.0 C2C D:HEC401 4.3 40.5 1.0 C2D D:HEC401 4.3 36.9 1.0 C2B D:HEC401 4.3 38.1 1.0 C3D D:HEC401 4.3 37.4 1.0 C3C D:HEC401 4.3 37.7 1.0 C3B D:HEC401 4.3 39.8 1.0 C2A D:HEC401 4.3 39.1 1.0 C3A D:HEC401 4.3 38.4 1.0 CG D:PRO96 4.4 49.9 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Di-Heme Peroxidase From Nitrosomonas Europaea within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:27.0 occ:1.00 FE D:HEC402 0.0 27.0 1.0 ND D:HEC402 1.9 11.8 1.0 NB D:HEC402 2.0 30.9 1.0 NA D:HEC402 2.0 30.7 1.0 NC D:HEC402 2.0 25.2 1.0 NE2 D:HIS187 2.1 33.3 1.0 SD D:MET258 2.4 34.7 1.0 C4D D:HEC402 3.0 34.5 1.0 C4B D:HEC402 3.0 30.9 1.0 C1D D:HEC402 3.0 31.0 1.0 C1A D:HEC402 3.0 31.4 1.0 CD2 D:HIS187 3.0 39.5 1.0 C1B D:HEC402 3.0 32.5 1.0 C4A D:HEC402 3.1 28.7 1.0 C1C D:HEC402 3.1 31.0 1.0 C4C D:HEC402 3.1 28.3 1.0 CE1 D:HIS187 3.1 38.9 1.0 CG D:MET258 3.3 31.6 1.0 CHA D:HEC402 3.4 30.0 1.0 CHC D:HEC402 3.4 34.6 1.0 CHB D:HEC402 3.4 33.1 1.0 CHD D:HEC402 3.5 25.3 1.0 CE D:MET258 3.9 31.7 1.0 CB D:MET258 4.2 34.7 1.0 CG D:HIS187 4.2 41.2 1.0 ND1 D:HIS187 4.2 42.5 1.0 C3D D:HEC402 4.2 32.2 1.0 C2D D:HEC402 4.2 31.5 1.0 C3B D:HEC402 4.2 33.6 1.0 C2B D:HEC402 4.3 33.4 1.0 C2A D:HEC402 4.3 28.7 1.0 C3A D:HEC402 4.3 30.4 1.0 C2C D:HEC402 4.3 33.2 1.0 C3C D:HEC402 4.3 31.0 1.0

H.Shimizu, D.J.Schuller, W.N.Lanzilotta, M.Sundaramoorthy, D.M.Arciero, A.B.Hooper, T.L.Poulos. Crystal Structure of Nitrosomonas Europaea Cytochrome C Peroxidase and the Structural Basis For Ligand Switching in Bacterial Di-Heme Peroxidases Biochemistry V. 40 13483 2001.
ISSN: ISSN 0006-2960
PubMed: 11695895
DOI: 10.1021/BI011481H