Iron in PDB 2dn2: 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form

The structure of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form, PDB code: 2dn2 was solved by S.-Y.Park, T.Yokoyama, N.Shibayama, Y.Shiro, J.R.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.105, 82.914, 53.650, 90.00, 99.29, 90.00
R / Rfree (%)	17.9 / n/a

The binding sites of Iron atom in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form (pdb code 2dn2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form, PDB code: 2dn2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:14.1 occ:1.00 FE A:HEM142 0.0 14.1 1.0 ND A:HEM142 2.1 13.5 1.0 NA A:HEM142 2.1 15.0 1.0 NC A:HEM142 2.1 13.4 1.0 NB A:HEM142 2.1 14.6 1.0 NE2 A:HIS87 2.2 15.4 1.0 CE1 A:HIS87 3.1 16.0 1.0 C4A A:HEM142 3.1 16.1 1.0 C4C A:HEM142 3.1 14.1 1.0 C1D A:HEM142 3.1 13.9 1.0 C4D A:HEM142 3.1 15.7 1.0 C1B A:HEM142 3.2 14.7 1.0 C1C A:HEM142 3.2 12.9 1.0 C1A A:HEM142 3.2 14.7 1.0 C4B A:HEM142 3.2 15.1 1.0 O A:HOH156 3.3 29.4 1.0 CD2 A:HIS87 3.3 14.3 1.0 CHA A:HEM142 3.4 15.7 1.0 CHC A:HEM142 3.5 15.1 1.0 CHD A:HEM142 3.5 14.5 1.0 CHB A:HEM142 3.5 14.9 1.0 ND1 A:HIS87 4.3 15.6 1.0 C2A A:HEM142 4.3 18.3 1.0 C2C A:HEM142 4.4 12.8 1.0 C3C A:HEM142 4.4 13.4 1.0 C2D A:HEM142 4.4 14.3 1.0 C2B A:HEM142 4.4 15.3 1.0 C3B A:HEM142 4.4 15.4 1.0 C3D A:HEM142 4.4 14.1 1.0 C3A A:HEM142 4.4 17.0 1.0 CG A:HIS87 4.4 15.5 1.0 CD1 A:LEU91 4.5 19.9 1.0 NE2 A:HIS58 4.5 21.1 1.0 CE1 A:HIS58 4.6 21.9 1.0

Iron binding site 2 out of 4 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:12.8 occ:1.00 FE B:HEM147 0.0 12.8 1.0 ND B:HEM147 2.1 15.1 1.0 NC B:HEM147 2.1 13.8 1.0 NA B:HEM147 2.1 14.1 1.0 NB B:HEM147 2.1 13.0 1.0 NE2 B:HIS92 2.2 14.2 1.0 CE1 B:HIS92 3.1 16.5 1.0 C4A B:HEM147 3.1 13.9 1.0 C1D B:HEM147 3.1 14.4 1.0 C1A B:HEM147 3.1 15.0 1.0 C1B B:HEM147 3.1 13.0 1.0 C1C B:HEM147 3.1 14.1 1.0 C4C B:HEM147 3.1 13.2 1.0 C4D B:HEM147 3.2 16.0 1.0 C4B B:HEM147 3.2 13.5 1.0 CD2 B:HIS92 3.3 12.8 1.0 CHA B:HEM147 3.4 15.5 1.0 CHD B:HEM147 3.4 13.9 1.0 CHC B:HEM147 3.5 14.8 1.0 CHB B:HEM147 3.5 14.4 1.0 CG2 B:VAL67 4.2 20.5 1.0 NE2 B:HIS63 4.2 23.6 1.0 ND1 B:HIS92 4.2 14.8 1.0 C2C B:HEM147 4.3 14.2 1.0 C3D B:HEM147 4.3 16.4 1.0 C2A B:HEM147 4.3 16.2 1.0 C2D B:HEM147 4.3 15.9 1.0 C3C B:HEM147 4.3 13.6 1.0 C3B B:HEM147 4.3 14.1 1.0 C3A B:HEM147 4.4 16.1 1.0 CG B:HIS92 4.4 12.6 1.0 C2B B:HEM147 4.4 13.7 1.0 CE1 B:HIS63 4.5 26.1 1.0 CD1 B:LEU96 5.0 17.2 1.0

Iron binding site 3 out of 4 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:13.4 occ:1.00 FE C:HEM142 0.0 13.4 1.0 ND C:HEM142 2.0 13.9 1.0 NA C:HEM142 2.1 14.8 1.0 NB C:HEM142 2.1 13.7 1.0 NC C:HEM142 2.1 13.4 1.0 NE2 C:HIS87 2.2 13.4 1.0 CE1 C:HIS87 3.1 14.1 1.0 C1A C:HEM142 3.1 16.7 1.0 C1C C:HEM142 3.1 13.7 1.0 C4A C:HEM142 3.1 15.7 1.0 C4C C:HEM142 3.1 13.6 1.0 C4D C:HEM142 3.1 15.0 1.0 C1D C:HEM142 3.1 13.6 1.0 C1B C:HEM142 3.2 15.2 1.0 C4B C:HEM142 3.2 13.4 1.0 CD2 C:HIS87 3.3 12.4 1.0 CHD C:HEM142 3.4 14.2 1.0 CHB C:HEM142 3.4 15.6 1.0 CHA C:HEM142 3.5 15.8 1.0 O C:HOH174 3.5 32.6 1.0 CHC C:HEM142 3.5 13.2 1.0 ND1 C:HIS87 4.3 14.4 1.0 C2C C:HEM142 4.3 13.7 1.0 C3C C:HEM142 4.3 12.8 1.0 C3D C:HEM142 4.3 15.1 1.0 C3B C:HEM142 4.3 14.3 1.0 C3A C:HEM142 4.3 16.6 1.0 C2A C:HEM142 4.3 15.8 1.0 C2D C:HEM142 4.3 15.1 1.0 C2B C:HEM142 4.4 13.7 1.0 CG C:HIS87 4.4 13.0 1.0 NE2 C:HIS58 4.4 21.9 1.0 CE1 C:HIS58 4.6 26.2 1.0 CD1 C:LEU91 4.6 17.8 1.0

Iron binding site 4 out of 4 in the 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:13.2 occ:1.00 FE D:HEM147 0.0 13.2 1.0 NB D:HEM147 2.0 14.7 1.0 NA D:HEM147 2.1 15.4 1.0 NC D:HEM147 2.1 14.2 1.0 ND D:HEM147 2.1 15.3 1.0 NE2 D:HIS92 2.2 13.9 1.0 C4A D:HEM147 3.0 16.5 1.0 C4D D:HEM147 3.0 16.0 1.0 C1D D:HEM147 3.0 15.1 1.0 CE1 D:HIS92 3.0 14.7 1.0 C4B D:HEM147 3.1 14.8 1.0 C1B D:HEM147 3.1 15.2 1.0 C1A D:HEM147 3.1 16.1 1.0 C1C D:HEM147 3.1 13.1 1.0 C4C D:HEM147 3.1 14.1 1.0 CD2 D:HIS92 3.2 13.0 1.0 CHA D:HEM147 3.4 15.5 1.0 CHC D:HEM147 3.5 14.8 1.0 CHB D:HEM147 3.5 17.3 1.0 CHD D:HEM147 3.5 14.5 1.0 ND1 D:HIS92 4.2 14.2 1.0 C3D D:HEM147 4.3 17.4 1.0 CG2 D:VAL67 4.3 20.3 1.0 NE2 D:HIS63 4.3 23.1 1.0 C2D D:HEM147 4.3 17.1 1.0 C3B D:HEM147 4.3 14.9 1.0 C2A D:HEM147 4.3 18.9 1.0 C3C D:HEM147 4.3 12.9 1.0 C2C D:HEM147 4.3 12.7 1.0 CG D:HIS92 4.3 13.8 1.0 C3A D:HEM147 4.4 17.4 1.0 C2B D:HEM147 4.4 15.6 1.0 CE1 D:HIS63 4.8 25.6 1.0 CD1 D:LEU96 4.9 17.4 1.0

S.-Y.Park, T.Yokoyama, N.Shibayama, Y.Shiro, J.R.Tame. 1.25 A Resolution Crystal Structures of Human Haemoglobin in the Oxy, Deoxy and Carbonmonoxy Forms. J.Mol.Biol. V. 360 690 2006.
ISSN: ISSN 0022-2836
PubMed: 16765986
DOI: 10.1016/J.JMB.2006.05.036