Iron in PDB 3bj1: Met-Perch Hemoglobin at pH 5.7

The structure of Met-Perch Hemoglobin at pH 5.7, PDB code: 3bj1 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)	69.67 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.225, 84.780, 121.905, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The binding sites of Iron atom in the Met-Perch Hemoglobin at pH 5.7 (pdb code 3bj1). 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 5.7, PDB code: 3bj1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Met-Perch Hemoglobin at pH 5.7


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 5.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe143 b:31.8 occ:1.00 FE A:HEM143 0.0 31.8 1.0 NB A:HEM143 2.0 28.8 1.0 NC A:HEM143 2.0 28.9 1.0 ND A:HEM143 2.0 32.7 1.0 NA A:HEM143 2.1 31.3 1.0 O A:HOH173 2.1 34.1 1.0 NE2 A:HIS88 2.2 12.9 1.0 C4B A:HEM143 3.0 27.8 1.0 C1C A:HEM143 3.0 30.5 1.0 C1A A:HEM143 3.0 32.1 1.0 C4D A:HEM143 3.0 34.6 1.0 C1B A:HEM143 3.1 29.2 1.0 C4C A:HEM143 3.1 31.4 1.0 C1D A:HEM143 3.1 33.8 1.0 CE1 A:HIS88 3.1 13.6 1.0 C4A A:HEM143 3.1 29.8 1.0 CD2 A:HIS88 3.2 15.2 1.0 CHC A:HEM143 3.3 29.2 1.0 CHA A:HEM143 3.4 33.2 1.0 CHD A:HEM143 3.5 32.5 1.0 CHB A:HEM143 3.5 31.1 1.0 CD1 A:ILE63 3.9 19.3 1.0 ND1 A:HIS88 4.2 10.4 1.0 C3B A:HEM143 4.2 27.2 1.0 C2C A:HEM143 4.3 30.1 1.0 C2B A:HEM143 4.3 28.4 1.0 C2A A:HEM143 4.3 34.8 1.0 C3D A:HEM143 4.3 37.3 1.0 CG A:HIS88 4.3 13.2 1.0 C3C A:HEM143 4.3 28.9 1.0 C2D A:HEM143 4.3 35.2 1.0 C3A A:HEM143 4.3 30.5 1.0 NE2 A:HIS59 4.4 14.3 1.0 CE1 A:HIS59 4.4 14.4 1.0 CD1 A:LEU92 5.0 29.5 1.0

Iron binding site 2 out of 4 in the Met-Perch Hemoglobin at pH 5.7


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 5.7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe148 b:28.0 occ:1.00 FE B:HEM148 0.0 28.0 1.0 NA B:HEM148 2.0 28.4 1.0 ND B:HEM148 2.0 28.0 1.0 NC B:HEM148 2.0 25.2 1.0 NB B:HEM148 2.0 26.1 1.0 NE2 B:HIS92 2.1 6.2 1.0 O B:HOH199 2.1 34.9 1.0 C1D B:HEM148 3.0 25.5 1.0 C1A B:HEM148 3.0 29.6 1.0 CD2 B:HIS92 3.0 9.1 1.0 C4C B:HEM148 3.0 25.5 1.0 C4D B:HEM148 3.0 30.7 1.0 C4B B:HEM148 3.0 27.1 1.0 C1C B:HEM148 3.1 26.7 1.0 C4A B:HEM148 3.1 27.6 1.0 CE1 B:HIS92 3.1 8.6 1.0 C1B B:HEM148 3.1 26.4 1.0 CHD B:HEM148 3.4 27.5 1.0 CHC B:HEM148 3.4 27.1 1.0 CHA B:HEM148 3.4 28.3 1.0 CHB B:HEM148 3.5 27.7 1.0 NE2 B:HIS63 4.0 22.3 1.0 ND1 B:HIS92 4.2 8.9 1.0 CG B:HIS92 4.2 6.5 1.0 C2A B:HEM148 4.2 29.1 1.0 C2D B:HEM148 4.3 30.1 1.0 C3C B:HEM148 4.3 26.8 1.0 C3A B:HEM148 4.3 29.2 1.0 C3D B:HEM148 4.3 30.8 1.0 C2C B:HEM148 4.3 26.7 1.0 C3B B:HEM148 4.3 27.9 1.0 C2B B:HEM148 4.4 25.2 1.0 CE1 B:HIS63 4.4 22.8 1.0 CG1 B:ILE67 4.8 13.5 1.0

Iron binding site 3 out of 4 in the Met-Perch Hemoglobin at pH 5.7


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 5.7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe143 b:28.0 occ:1.00 FE C:HEM143 0.0 28.0 1.0 NB C:HEM143 2.0 27.4 1.0 ND C:HEM143 2.0 30.4 1.0 NC C:HEM143 2.1 24.2 1.0 NA C:HEM143 2.1 30.2 1.0 NE2 C:HIS88 2.1 13.0 1.0 O C:HOH178 2.1 28.8 1.0 C4B C:HEM143 3.0 29.1 1.0 C4D C:HEM143 3.0 32.2 1.0 C1C C:HEM143 3.0 25.9 1.0 CE1 C:HIS88 3.0 12.3 1.0 C1A C:HEM143 3.1 30.1 1.0 C1B C:HEM143 3.1 29.5 1.0 C4A C:HEM143 3.1 28.4 1.0 C1D C:HEM143 3.1 30.5 1.0 C4C C:HEM143 3.1 25.3 1.0 CD2 C:HIS88 3.1 12.8 1.0 CHC C:HEM143 3.3 27.9 1.0 CHA C:HEM143 3.4 31.1 1.0 CHB C:HEM143 3.5 29.6 1.0 CHD C:HEM143 3.5 28.2 1.0 CD1 C:ILE63 4.0 19.8 1.0 ND1 C:HIS88 4.2 9.7 1.0 C3B C:HEM143 4.2 29.8 1.0 NE2 C:HIS59 4.2 10.7 1.0 CG C:HIS88 4.3 11.3 1.0 C2B C:HEM143 4.3 30.0 1.0 C3D C:HEM143 4.3 33.1 1.0 C3A C:HEM143 4.3 30.4 1.0 C2C C:HEM143 4.3 24.4 1.0 C2A C:HEM143 4.3 31.2 1.0 C2D C:HEM143 4.3 30.9 1.0 C3C C:HEM143 4.3 24.1 1.0 CE1 C:HIS59 4.5 16.1 1.0

Iron binding site 4 out of 4 in the Met-Perch Hemoglobin at pH 5.7


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 5.7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe148 b:28.9 occ:1.00 FE D:HEM148 0.0 28.9 1.0 NC D:HEM148 2.0 29.6 1.0 NA D:HEM148 2.1 29.0 1.0 ND D:HEM148 2.1 27.2 1.0 NB D:HEM148 2.1 25.9 1.0 NE2 D:HIS92 2.1 9.6 1.0 O D:HOH236 2.1 40.6 1.0 C4B D:HEM148 3.0 28.1 1.0 C1C D:HEM148 3.0 29.5 1.0 C4C D:HEM148 3.1 29.3 1.0 C1D D:HEM148 3.1 28.4 1.0 C1A D:HEM148 3.1 30.5 1.0 C4D D:HEM148 3.1 30.3 1.0 CD2 D:HIS92 3.1 9.6 1.0 CE1 D:HIS92 3.1 13.1 1.0 C4A D:HEM148 3.1 29.2 1.0 C1B D:HEM148 3.1 28.9 1.0 CHC D:HEM148 3.4 29.7 1.0 CHD D:HEM148 3.4 28.8 1.0 CHA D:HEM148 3.4 29.7 1.0 CHB D:HEM148 3.5 29.6 1.0 NE2 D:HIS63 4.2 22.0 1.0 ND1 D:HIS92 4.2 10.8 1.0 CG D:HIS92 4.2 10.1 1.0 C2C D:HEM148 4.2 31.5 1.0 C3C D:HEM148 4.3 28.9 1.0 C3B D:HEM148 4.3 29.2 1.0 C2A D:HEM148 4.3 31.9 1.0 C2D D:HEM148 4.3 30.2 1.0 C3D D:HEM148 4.3 29.8 1.0 C3A D:HEM148 4.3 31.1 1.0 C2B D:HEM148 4.3 27.3 1.0 CG1 D:ILE67 4.7 13.3 1.0 CE1 D:HIS63 4.7 22.6 1.0 CD1 D:ILE67 4.9 13.8 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