Iron in PDB 3bj3: Met-Perch Hemoglobin at pH 8.0

The structure of Met-Perch Hemoglobin at pH 8.0, PDB code: 3bj3 was solved by R.Aranda Iv, H.Cai, E.J.Levin, M.P.Richards, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.50 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.730, 84.897, 121.475, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.2

The binding sites of Iron atom in the Met-Perch Hemoglobin at pH 8.0 (pdb code 3bj3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Met-Perch Hemoglobin at pH 8.0, PDB code: 3bj3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Met-Perch Hemoglobin at pH 8.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Met-Perch Hemoglobin at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe143 b:47.3 occ:1.00 FE A:HEM143 0.0 47.3 1.0 NB A:HEM143 2.0 43.8 1.0 NC A:HEM143 2.1 45.2 1.0 NA A:HEM143 2.1 48.4 1.0 ND A:HEM143 2.1 48.6 1.0 NE2 A:HIS88 2.2 33.6 1.0 O A:HOH150 2.3 43.1 1.0 C4B A:HEM143 2.9 45.4 1.0 C1C A:HEM143 3.0 43.0 1.0 C4D A:HEM143 3.1 49.8 1.0 C1A A:HEM143 3.1 48.6 1.0 C1B A:HEM143 3.1 46.2 1.0 CD2 A:HIS88 3.1 34.1 1.0 C4A A:HEM143 3.1 47.6 1.0 CE1 A:HIS88 3.2 34.1 1.0 C4C A:HEM143 3.2 45.0 1.0 C1D A:HEM143 3.2 49.4 1.0 CHC A:HEM143 3.3 44.3 1.0 CHA A:HEM143 3.4 49.0 1.0 CHB A:HEM143 3.5 46.9 1.0 CHD A:HEM143 3.6 48.1 1.0 CD1 A:ILE63 3.8 42.9 1.0 C3B A:HEM143 4.2 43.6 1.0 C2B A:HEM143 4.2 44.1 1.0 ND1 A:HIS88 4.3 34.9 1.0 C2C A:HEM143 4.3 43.6 1.0 CG A:HIS88 4.3 36.0 1.0 C2A A:HEM143 4.3 51.0 1.0 C3D A:HEM143 4.3 50.4 1.0 C3A A:HEM143 4.3 49.2 1.0 C3C A:HEM143 4.3 43.9 1.0 C2D A:HEM143 4.4 49.5 1.0 NE2 A:HIS59 4.5 39.3 1.0 CE1 A:HIS59 4.5 39.2 1.0

Iron binding site 2 out of 4 in the Met-Perch Hemoglobin at pH 8.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Met-Perch Hemoglobin at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe148 b:35.4 occ:1.00 FE B:HEM148 0.0 35.4 1.0 ND B:HEM148 2.0 35.6 1.0 NA B:HEM148 2.0 35.5 1.0 NC B:HEM148 2.0 32.5 1.0 NB B:HEM148 2.1 32.6 1.0 NE2 B:HIS92 2.1 21.6 1.0 O B:HOH153 2.1 52.1 1.0 CE1 B:HIS92 3.0 22.0 1.0 C1D B:HEM148 3.0 35.9 1.0 C4D B:HEM148 3.0 35.8 1.0 C4C B:HEM148 3.0 34.0 1.0 C1A B:HEM148 3.1 36.0 1.0 CD2 B:HIS92 3.1 21.6 1.0 C4A B:HEM148 3.1 35.8 1.0 C1C B:HEM148 3.1 34.7 1.0 C4B B:HEM148 3.1 33.4 1.0 C1B B:HEM148 3.1 34.5 1.0 CHD B:HEM148 3.4 34.3 1.0 CHA B:HEM148 3.4 35.1 1.0 CHC B:HEM148 3.5 32.6 1.0 CHB B:HEM148 3.5 35.0 1.0 NE2 B:HIS63 4.0 26.7 1.0 ND1 B:HIS92 4.1 24.2 1.0 CG B:HIS92 4.2 23.5 1.0 C2A B:HEM148 4.3 35.1 1.0 C2D B:HEM148 4.3 37.2 1.0 C3D B:HEM148 4.3 38.4 1.0 C3C B:HEM148 4.3 34.0 1.0 C3A B:HEM148 4.3 35.7 1.0 C2C B:HEM148 4.3 35.5 1.0 C3B B:HEM148 4.3 33.9 1.0 C2B B:HEM148 4.3 34.7 1.0 CE1 B:HIS63 4.5 29.6 1.0 CG1 B:ILE67 4.7 26.2 1.0

Iron binding site 3 out of 4 in the Met-Perch Hemoglobin at pH 8.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Met-Perch Hemoglobin at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe143 b:40.4 occ:1.00 FE C:HEM143 0.0 40.4 1.0 O C:HOH145 1.9 41.6 1.0 NB C:HEM143 1.9 39.6 1.0 NC C:HEM143 2.1 38.3 1.0 ND C:HEM143 2.1 38.6 1.0 NE2 C:HIS88 2.1 23.7 1.0 NA C:HEM143 2.2 42.1 1.0 C4B C:HEM143 2.9 39.0 1.0 C1B C:HEM143 3.0 39.8 1.0 CD2 C:HIS88 3.0 22.7 1.0 C1C C:HEM143 3.0 37.2 1.0 C4D C:HEM143 3.1 42.3 1.0 C4A C:HEM143 3.1 42.6 1.0 C1D C:HEM143 3.2 40.6 1.0 C1A C:HEM143 3.2 42.1 1.0 C4C C:HEM143 3.2 36.6 1.0 CE1 C:HIS88 3.2 25.3 1.0 CHC C:HEM143 3.3 38.8 1.0 CHB C:HEM143 3.4 41.8 1.0 CHA C:HEM143 3.5 40.6 1.0 CHD C:HEM143 3.6 41.0 1.0 C3B C:HEM143 4.1 38.7 1.0 C2B C:HEM143 4.1 39.8 1.0 CG C:HIS88 4.2 23.8 1.0 ND1 C:HIS88 4.2 22.6 1.0 C2C C:HEM143 4.3 38.3 1.0 C3D C:HEM143 4.3 43.9 1.0 C3A C:HEM143 4.4 43.3 1.0 C3C C:HEM143 4.4 38.3 1.0 NE2 C:HIS59 4.4 31.6 1.0 C2D C:HEM143 4.4 41.8 1.0 C2A C:HEM143 4.4 44.7 1.0 CE1 C:HIS59 4.6 31.4 1.0 CG1 C:ILE63 4.7 30.1 1.0

Iron binding site 4 out of 4 in the Met-Perch Hemoglobin at pH 8.0


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Met-Perch Hemoglobin at pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe148 b:34.6 occ:1.00 FE D:HEM148 0.0 34.6 1.0 O D:HOH158 2.0 36.9 1.0 NC D:HEM148 2.0 35.1 1.0 NB D:HEM148 2.0 32.3 1.0 ND D:HEM148 2.1 35.3 1.0 NA D:HEM148 2.2 33.5 1.0 NE2 D:HIS92 2.2 21.9 1.0 C4B D:HEM148 2.9 31.3 1.0 C1C D:HEM148 2.9 34.1 1.0 C4C D:HEM148 3.0 34.9 1.0 C4D D:HEM148 3.1 36.3 1.0 C1D D:HEM148 3.1 37.8 1.0 C1B D:HEM148 3.1 31.4 1.0 CD2 D:HIS92 3.1 20.1 1.0 C1A D:HEM148 3.1 35.2 1.0 CE1 D:HIS92 3.2 22.9 1.0 C4A D:HEM148 3.2 32.4 1.0 CHC D:HEM148 3.3 34.8 1.0 CHA D:HEM148 3.5 35.7 1.0 CHD D:HEM148 3.5 36.5 1.0 CHB D:HEM148 3.6 33.6 1.0 NE2 D:HIS63 4.1 28.4 1.0 C3B D:HEM148 4.2 32.6 1.0 C2C D:HEM148 4.2 36.7 1.0 C3C D:HEM148 4.2 35.1 1.0 C2B D:HEM148 4.3 32.5 1.0 CG D:HIS92 4.3 20.9 1.0 ND1 D:HIS92 4.3 20.1 1.0 C3D D:HEM148 4.3 38.8 1.0 C2D D:HEM148 4.3 37.5 1.0 C2A D:HEM148 4.4 34.2 1.0 C3A D:HEM148 4.4 34.0 1.0 CG1 D:ILE67 4.5 20.4 1.0 CD1 D:ILE67 4.9 20.6 1.0 CE1 D:HIS63 4.9 29.4 1.0

R.Aranda, H.Cai, C.E.Worley, E.J.Levin, R.Li, J.S.Olson, G.N.Phillips, M.P.Richards. Structural Analysis of Fish Versus Mammalian Hemoglobins: Effect of the Heme Pocket Environment on Autooxidation and Hemin Loss. Proteins V. 75 217 2008.
ISSN: ISSN 0887-3585
PubMed: 18831041
DOI: 10.1002/PROT.22236