Iron in PDB 1dke: Ni Beta Heme Human Hemoglobin

The structure of Ni Beta Heme Human Hemoglobin, PDB code: 1dke was solved by S.Bruno, S.Bettatti, A.Mozzarelli, M.Bolognesi, D.Deriu, C.Rosano, A.Tsuneshige, T.Yonetani, E.R.Henry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.720, 81.400, 63.150, 90.00, 97.81, 90.00
R / Rfree (%)	20 / 28

The binding sites of Iron atom in the Ni Beta Heme Human Hemoglobin (pdb code 1dke). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ni Beta Heme Human Hemoglobin, PDB code: 1dke:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ni Beta Heme Human Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ni Beta Heme Human Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:22.2 occ:1.00 FE A:HEM142 0.0 22.2 1.0 NA A:HEM142 2.0 23.6 1.0 NC A:HEM142 2.0 22.5 1.0 ND A:HEM142 2.0 27.6 1.0 NB A:HEM142 2.1 23.8 1.0 NE2 A:HIS87 2.1 13.3 1.0 CE1 A:HIS87 3.0 13.6 1.0 C1A A:HEM142 3.0 25.4 1.0 C4A A:HEM142 3.0 23.1 1.0 C1D A:HEM142 3.1 27.3 1.0 C4C A:HEM142 3.1 23.5 1.0 C1C A:HEM142 3.1 22.6 1.0 C4D A:HEM142 3.1 28.6 1.0 C4B A:HEM142 3.1 24.3 1.0 C1B A:HEM142 3.2 23.6 1.0 O A:HOH186 3.2 19.1 1.0 CD2 A:HIS87 3.3 14.5 1.0 CHD A:HEM142 3.4 23.2 1.0 CHB A:HEM142 3.5 23.2 1.0 CHC A:HEM142 3.5 23.7 1.0 CHA A:HEM142 3.5 26.4 1.0 ND1 A:HIS87 4.2 14.5 1.0 C2A A:HEM142 4.3 25.7 1.0 C3A A:HEM142 4.3 23.4 1.0 C2D A:HEM142 4.3 28.6 1.0 C2C A:HEM142 4.3 24.9 1.0 C3D A:HEM142 4.3 29.8 1.0 C3C A:HEM142 4.3 23.9 1.0 CG A:HIS87 4.4 16.2 1.0 C3B A:HEM142 4.4 24.0 1.0 C2B A:HEM142 4.4 23.1 1.0 NE2 A:HIS58 4.4 17.9 1.0 CD1 A:LEU91 4.6 20.6 1.0 CE1 A:HIS58 4.6 20.9 1.0

Iron binding site 2 out of 4 in the Ni Beta Heme Human Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ni Beta Heme Human Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:25.0 occ:1.00 FE B:HEM147 0.0 25.0 1.0 NC B:HEM147 2.0 22.7 1.0 NB B:HEM147 2.0 26.7 1.0 NA B:HEM147 2.0 27.8 1.0 ND B:HEM147 2.1 26.5 1.0 NE2 B:HIS92 2.2 26.4 1.0 C4A B:HEM147 3.0 28.5 1.0 CD2 B:HIS92 3.0 21.1 1.0 C4C B:HEM147 3.0 23.8 1.0 C1C B:HEM147 3.0 23.2 1.0 C1B B:HEM147 3.1 25.8 1.0 C4B B:HEM147 3.1 23.7 1.0 C1D B:HEM147 3.1 25.1 1.0 C1A B:HEM147 3.1 28.3 1.0 C4D B:HEM147 3.1 27.0 1.0 CHB B:HEM147 3.3 25.7 1.0 CE1 B:HIS92 3.3 24.4 1.0 CHD B:HEM147 3.4 24.3 1.0 CHC B:HEM147 3.4 22.8 1.0 CHA B:HEM147 3.6 25.4 1.0 CG B:HIS92 4.2 27.0 1.0 C2B B:HEM147 4.2 26.1 1.0 C3A B:HEM147 4.2 29.6 1.0 C3B B:HEM147 4.2 24.2 1.0 CG2 B:VAL67 4.3 14.2 1.0 C3C B:HEM147 4.3 23.7 1.0 C2C B:HEM147 4.3 23.9 1.0 C2D B:HEM147 4.3 26.1 1.0 C2A B:HEM147 4.3 31.9 1.0 C3D B:HEM147 4.3 28.3 1.0 ND1 B:HIS92 4.3 24.8 1.0 NE2 B:HIS63 4.4 34.1 1.0 CE1 B:HIS63 4.6 39.4 1.0 CD1 B:LEU96 4.9 15.3 1.0

Iron binding site 3 out of 4 in the Ni Beta Heme Human Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ni Beta Heme Human Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:24.2 occ:1.00 FE C:HEM142 0.0 24.2 1.0 NA C:HEM142 2.0 28.6 1.0 ND C:HEM142 2.0 28.8 1.0 NC C:HEM142 2.1 23.5 1.0 NB C:HEM142 2.1 24.8 1.0 NE2 C:HIS87 2.2 17.0 1.0 CE1 C:HIS87 3.0 17.4 1.0 C4D C:HEM142 3.1 29.9 1.0 C1A C:HEM142 3.1 30.6 1.0 C4A C:HEM142 3.1 29.5 1.0 C1D C:HEM142 3.1 29.5 1.0 C1C C:HEM142 3.1 25.0 1.0 C1B C:HEM142 3.1 26.0 1.0 C4B C:HEM142 3.1 24.8 1.0 C4C C:HEM142 3.1 26.0 1.0 CHA C:HEM142 3.4 30.5 1.0 CHB C:HEM142 3.4 28.7 1.0 CD2 C:HIS87 3.4 19.4 1.0 CHC C:HEM142 3.5 24.6 1.0 CHD C:HEM142 3.5 27.0 1.0 O C:HOH168 3.6 17.9 1.0 ND1 C:HIS87 4.2 19.9 1.0 C3D C:HEM142 4.3 30.1 1.0 C3A C:HEM142 4.3 31.7 1.0 C2A C:HEM142 4.3 32.7 1.0 C2D C:HEM142 4.3 31.3 1.0 C2B C:HEM142 4.3 25.4 1.0 C3B C:HEM142 4.3 25.6 1.0 C2C C:HEM142 4.3 25.8 1.0 C3C C:HEM142 4.4 26.3 1.0 CD1 C:LEU91 4.5 15.8 1.0 CG C:HIS87 4.5 17.5 1.0 NE2 C:HIS58 4.7 35.0 1.0 CE1 C:HIS58 4.7 30.7 1.0

Iron binding site 4 out of 4 in the Ni Beta Heme Human Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ni Beta Heme Human Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:23.5 occ:1.00 FE D:HEM147 0.0 23.5 1.0 NA D:HEM147 2.0 28.0 1.0 ND D:HEM147 2.0 27.2 1.0 NB D:HEM147 2.1 25.0 1.0 NC D:HEM147 2.1 20.9 1.0 NE2 D:HIS92 2.1 17.9 1.0 C1A D:HEM147 3.0 30.6 1.0 C4A D:HEM147 3.1 28.8 1.0 C1B D:HEM147 3.1 26.8 1.0 C4C D:HEM147 3.1 21.6 1.0 CD2 D:HIS92 3.1 14.9 1.0 C1D D:HEM147 3.1 27.1 1.0 C4D D:HEM147 3.1 28.2 1.0 C1C D:HEM147 3.1 21.0 1.0 C4B D:HEM147 3.1 23.8 1.0 CE1 D:HIS92 3.1 22.1 1.0 CHB D:HEM147 3.4 27.3 1.0 CHD D:HEM147 3.4 21.6 1.0 CHA D:HEM147 3.4 27.9 1.0 CHC D:HEM147 3.5 20.3 1.0 CG2 D:VAL67 3.6 26.9 1.0 CG D:HIS92 4.2 16.7 1.0 C2A D:HEM147 4.3 32.8 1.0 ND1 D:HIS92 4.3 15.6 1.0 C3A D:HEM147 4.3 30.7 1.0 C2D D:HEM147 4.3 28.9 1.0 C3D D:HEM147 4.3 30.2 1.0 C2B D:HEM147 4.3 26.4 1.0 C2C D:HEM147 4.3 22.4 1.0 C3C D:HEM147 4.3 22.1 1.0 C3B D:HEM147 4.3 25.4 1.0 CE1 D:HIS63 4.5 47.2 1.0 NE2 D:HIS63 4.5 36.3 1.0 CB D:VAL67 4.8 34.3 1.0

S.Bruno, S.Bettati, M.Manfredini, A.Mozzarelli, M.Bolognesi, D.Deriu, C.Rosano, A.Tsuneshige, T.Yonetani, E.R.Henry. Oxygen Binding By Alpha(FE2+)2BETA(NI2+)2 Hemoglobin Crystals. Protein Sci. V. 9 683 2000.
ISSN: ISSN 0961-8368
PubMed: 10794410