Iron in PDB 3eee: Probing the Function of Heme Distortion in the H-Nox Family

The structure of Probing the Function of Heme Distortion in the H-Nox Family, PDB code: 3eee was solved by C.Olea Jr, E.M.Boon, P.Pellicena, J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.67 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.253, 124.686, 83.555, 90.00, 126.58, 90.00
R / Rfree (%)	20.5 / 25.2

The structure of Probing the Function of Heme Distortion in the H-Nox Family also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Probing the Function of Heme Distortion in the H-Nox Family (pdb code 3eee). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Probing the Function of Heme Distortion in the H-Nox Family, PDB code: 3eee:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Probing the Function of Heme Distortion in the H-Nox Family


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Probing the Function of Heme Distortion in the H-Nox Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:39.5 occ:1.00 FE A:HEM200 0.0 39.5 1.0 O1 A:OXY493 1.8 49.7 1.0 NB A:HEM200 2.0 39.5 1.0 NA A:HEM200 2.0 48.9 1.0 NE2 A:HIS102 2.1 39.7 1.0 NC A:HEM200 2.1 36.4 1.0 ND A:HEM200 2.1 41.1 1.0 O2 A:OXY493 2.8 56.1 1.0 CE1 A:HIS102 2.9 40.7 1.0 C1B A:HEM200 3.0 45.2 1.0 C4B A:HEM200 3.0 39.1 1.0 C4A A:HEM200 3.0 44.6 1.0 C1A A:HEM200 3.1 42.8 1.0 C4D A:HEM200 3.1 43.2 1.0 C1C A:HEM200 3.1 36.4 1.0 C1D A:HEM200 3.1 46.1 1.0 C4C A:HEM200 3.1 40.0 1.0 CD2 A:HIS102 3.2 42.9 1.0 CHB A:HEM200 3.4 48.4 1.0 CHA A:HEM200 3.4 41.8 1.0 CHC A:HEM200 3.4 40.0 1.0 CHD A:HEM200 3.5 37.1 1.0 ND1 A:HIS102 4.1 41.0 1.0 C3B A:HEM200 4.2 43.8 1.0 C2B A:HEM200 4.2 43.7 1.0 C3A A:HEM200 4.2 50.9 1.0 CG A:HIS102 4.3 43.9 1.0 C2A A:HEM200 4.3 47.5 1.0 C2C A:HEM200 4.3 41.5 1.0 C3C A:HEM200 4.3 43.6 1.0 C3D A:HEM200 4.3 43.5 1.0 C2D A:HEM200 4.3 42.5 1.0 CD1 A:LEU144 4.6 40.6 1.0 OH A:TYR140 5.0 37.7 1.0

Iron binding site 2 out of 4 in the Probing the Function of Heme Distortion in the H-Nox Family


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Probing the Function of Heme Distortion in the H-Nox Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:39.9 occ:1.00 FE B:HEM200 0.0 39.9 1.0 O1 B:OXY494 1.7 46.2 1.0 NE2 B:HIS102 2.0 38.4 1.0 NB B:HEM200 2.0 43.0 1.0 NA B:HEM200 2.1 42.4 1.0 NC B:HEM200 2.1 40.9 1.0 ND B:HEM200 2.1 42.8 1.0 CE1 B:HIS102 2.7 40.6 1.0 O2 B:OXY494 2.7 63.6 1.0 C4B B:HEM200 3.0 39.5 1.0 C1A B:HEM200 3.1 46.7 1.0 C1C B:HEM200 3.1 42.1 1.0 C1B B:HEM200 3.1 45.4 1.0 C4A B:HEM200 3.1 46.7 1.0 C4D B:HEM200 3.1 42.0 1.0 C4C B:HEM200 3.1 44.6 1.0 C1D B:HEM200 3.1 44.4 1.0 CD2 B:HIS102 3.2 48.6 1.0 CHC B:HEM200 3.4 34.4 1.0 CHA B:HEM200 3.4 41.4 1.0 CHD B:HEM200 3.5 36.6 1.0 CHB B:HEM200 3.5 47.4 1.0 ND1 B:HIS102 4.0 39.5 1.0 CG B:HIS102 4.2 45.3 1.0 C3B B:HEM200 4.3 45.6 1.0 C2B B:HEM200 4.3 47.1 1.0 C2A B:HEM200 4.3 46.5 1.0 C2C B:HEM200 4.3 44.9 1.0 C3A B:HEM200 4.3 51.9 1.0 C3C B:HEM200 4.3 42.9 1.0 C3D B:HEM200 4.3 42.2 1.0 C2D B:HEM200 4.3 41.1 1.0 CD1 B:LEU144 4.7 37.0 1.0 OH B:TYR140 5.0 40.2 1.0

Iron binding site 3 out of 4 in the Probing the Function of Heme Distortion in the H-Nox Family


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Probing the Function of Heme Distortion in the H-Nox Family within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:52.6 occ:1.00 FE C:HEM200 0.0 52.6 1.0 O1 C:OXY495 1.7 68.2 1.0 NA C:HEM200 2.0 60.7 1.0 NE2 C:HIS102 2.1 53.4 1.0 NB C:HEM200 2.1 59.2 1.0 NC C:HEM200 2.1 48.6 1.0 ND C:HEM200 2.1 58.0 1.0 O2 C:OXY495 2.7 80.0 1.0 CE1 C:HIS102 2.9 56.0 1.0 C4A C:HEM200 3.0 63.2 1.0 C1A C:HEM200 3.0 64.1 1.0 C1B C:HEM200 3.1 57.3 1.0 C4C C:HEM200 3.1 56.8 1.0 C1D C:HEM200 3.1 60.6 1.0 C4D C:HEM200 3.1 65.3 1.0 C4B C:HEM200 3.1 61.2 1.0 C1C C:HEM200 3.1 56.4 1.0 CD2 C:HIS102 3.1 54.9 1.0 CHB C:HEM200 3.4 51.6 1.0 CHA C:HEM200 3.4 62.4 1.0 CHD C:HEM200 3.4 61.7 1.0 CHC C:HEM200 3.5 60.1 1.0 ND1 C:HIS102 4.1 54.9 1.0 CG C:HIS102 4.2 54.9 1.0 C3A C:HEM200 4.2 72.4 1.0 C2A C:HEM200 4.2 67.5 1.0 C2B C:HEM200 4.3 61.9 1.0 C3B C:HEM200 4.3 61.2 1.0 C3C C:HEM200 4.3 55.8 1.0 C2D C:HEM200 4.3 65.6 1.0 C2C C:HEM200 4.3 52.6 1.0 C3D C:HEM200 4.3 66.2 1.0 CD1 C:LEU144 4.8 47.7 1.0 CE2 C:PHE78 4.9 61.0 1.0 OH C:TYR140 5.0 60.1 1.0

Iron binding site 4 out of 4 in the Probing the Function of Heme Distortion in the H-Nox Family


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Probing the Function of Heme Distortion in the H-Nox Family within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:44.6 occ:1.00 FE D:HEM200 0.0 44.6 1.0 O1 D:OXY496 1.7 55.0 1.0 NA D:HEM200 2.0 54.0 1.0 NC D:HEM200 2.0 43.8 1.0 NE2 D:HIS102 2.1 46.2 1.0 NB D:HEM200 2.1 46.4 1.0 ND D:HEM200 2.1 45.9 1.0 O2 D:OXY496 2.6 60.7 1.0 CD2 D:HIS102 3.0 45.5 1.0 CE1 D:HIS102 3.0 47.3 1.0 C4A D:HEM200 3.0 55.7 1.0 C4C D:HEM200 3.0 50.1 1.0 C1A D:HEM200 3.1 55.7 1.0 C1B D:HEM200 3.1 41.5 1.0 C1C D:HEM200 3.1 44.0 1.0 C1D D:HEM200 3.1 44.3 1.0 C4B D:HEM200 3.1 48.7 1.0 C4D D:HEM200 3.1 48.3 1.0 CHD D:HEM200 3.4 45.6 1.0 CHB D:HEM200 3.4 45.7 1.0 CHA D:HEM200 3.4 50.1 1.0 CHC D:HEM200 3.5 43.0 1.0 CG D:HIS102 4.2 47.9 1.0 ND1 D:HIS102 4.2 49.9 1.0 C3A D:HEM200 4.3 56.8 1.0 C2A D:HEM200 4.3 48.7 1.0 C3C D:HEM200 4.3 46.4 1.0 C2C D:HEM200 4.3 43.4 1.0 C2B D:HEM200 4.3 56.8 1.0 C3B D:HEM200 4.3 51.7 1.0 C2D D:HEM200 4.3 46.0 1.0 C3D D:HEM200 4.3 48.3 1.0 CD1 D:LEU144 4.7 40.3 1.0 CE2 D:PHE78 4.9 52.4 1.0 CZ D:PHE78 5.0 49.4 1.0

C.Olea, E.M.Boon, P.Pellicena, J.Kuriyan, M.A.Marletta. Probing the Function of Heme Distortion in the H-Nox Family. Acs Chem.Biol. V. 3 703 2008.
ISSN: ISSN 1554-8929
PubMed: 19032091
DOI: 10.1021/CB800185H