Iron in PDB 2d60: Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules

The structure of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules, PDB code: 2d60 was solved by T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.364, 81.384, 53.505, 90.00, 99.34, 90.00
R / Rfree (%)	19.5 / 24

The structure of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules (pdb code 2d60). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules, PDB code: 2d60:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:13.3 occ:1.00 FE A:HEM142 0.0 13.3 1.0 NB A:HEM142 2.1 13.4 1.0 ND A:HEM142 2.1 13.2 1.0 NC A:HEM142 2.1 11.5 1.0 NA A:HEM142 2.2 13.2 1.0 NE2 A:HIS87 2.2 11.9 1.0 C4D A:HEM142 3.1 12.3 1.0 C1C A:HEM142 3.1 10.6 1.0 C4B A:HEM142 3.1 9.3 1.0 C1D A:HEM142 3.1 12.0 1.0 CE1 A:HIS87 3.1 11.7 1.0 C1A A:HEM142 3.1 12.3 1.0 C4C A:HEM142 3.1 12.7 1.0 C1B A:HEM142 3.2 11.7 1.0 O A:HOH206 3.2 48.1 1.0 C4A A:HEM142 3.2 13.7 1.0 CD2 A:HIS87 3.2 10.1 1.0 CHC A:HEM142 3.4 11.3 1.0 CHA A:HEM142 3.4 12.7 1.0 CHD A:HEM142 3.5 14.0 1.0 CHB A:HEM142 3.6 13.1 1.0 CE1 A:HIS58 4.1 14.5 1.0 ND1 A:HIS87 4.3 9.3 1.0 C3D A:HEM142 4.3 12.1 1.0 C2D A:HEM142 4.3 12.5 1.0 C3B A:HEM142 4.3 9.0 1.0 C2C A:HEM142 4.3 10.6 1.0 C3C A:HEM142 4.3 10.6 1.0 C2B A:HEM142 4.3 8.9 1.0 CG A:HIS87 4.4 13.7 1.0 NE2 A:HIS58 4.4 15.3 1.0 C2A A:HEM142 4.4 13.5 1.0 CD1 A:LEU91 4.4 16.8 1.0 C3A A:HEM142 4.4 12.8 1.0 CG2 A:VAL62 5.0 8.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:14.3 occ:1.00 FE B:HEM147 0.0 14.3 1.0 NB B:HEM147 2.1 12.5 1.0 NA B:HEM147 2.1 12.9 1.0 NC B:HEM147 2.1 12.0 1.0 ND B:HEM147 2.1 11.3 1.0 NE2 B:HIS92 2.2 9.5 1.0 C1B B:HEM147 3.0 11.0 1.0 C4A B:HEM147 3.1 13.4 1.0 C4B B:HEM147 3.1 10.3 1.0 C1C B:HEM147 3.1 11.1 1.0 C1A B:HEM147 3.1 14.5 1.0 CD2 B:HIS92 3.1 9.4 1.0 C4C B:HEM147 3.2 13.3 1.0 C4D B:HEM147 3.2 11.2 1.0 CE1 B:HIS92 3.2 14.1 1.0 C1D B:HEM147 3.2 12.8 1.0 CHB B:HEM147 3.4 12.7 1.0 CHC B:HEM147 3.5 12.3 1.0 CHA B:HEM147 3.5 11.4 1.0 CHD B:HEM147 3.5 9.2 1.0 CG2 B:VAL67 4.2 13.7 1.0 C2B B:HEM147 4.2 10.1 1.0 C3B B:HEM147 4.2 9.2 1.0 ND1 B:HIS92 4.3 9.8 1.0 CG B:HIS92 4.3 11.0 1.0 C3A B:HEM147 4.3 15.0 1.0 C2C B:HEM147 4.3 14.3 1.0 C2A B:HEM147 4.3 16.1 1.0 C3C B:HEM147 4.4 13.2 1.0 NE2 B:HIS63 4.4 19.8 1.0 C3D B:HEM147 4.4 13.1 1.0 C2D B:HEM147 4.4 12.0 1.0 CE1 B:HIS63 4.8 21.3 1.0 CD1 B:LEU96 4.9 10.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:12.8 occ:1.00 FE C:HEM142 0.0 12.8 1.0 NC C:HEM142 2.1 11.4 1.0 NB C:HEM142 2.1 13.2 1.0 NA C:HEM142 2.1 15.6 1.0 ND C:HEM142 2.2 11.0 1.0 NE2 C:HIS87 2.2 8.3 1.0 C1C C:HEM142 3.1 10.0 1.0 C4B C:HEM142 3.1 12.5 1.0 C1A C:HEM142 3.1 15.7 1.0 C4A C:HEM142 3.1 14.6 1.0 C4D C:HEM142 3.1 12.8 1.0 CE1 C:HIS87 3.1 13.4 1.0 C1B C:HEM142 3.1 13.3 1.0 C4C C:HEM142 3.2 9.8 1.0 CD2 C:HIS87 3.2 8.1 1.0 C1D C:HEM142 3.2 11.0 1.0 CHC C:HEM142 3.4 12.8 1.0 CHA C:HEM142 3.4 12.1 1.0 CHB C:HEM142 3.5 13.7 1.0 CHD C:HEM142 3.6 11.5 1.0 ND1 C:HIS87 4.3 7.3 1.0 C2C C:HEM142 4.3 10.0 1.0 C3B C:HEM142 4.3 13.3 1.0 CG C:HIS87 4.3 9.9 1.0 C3C C:HEM142 4.3 11.3 1.0 C2A C:HEM142 4.4 15.7 1.0 C2B C:HEM142 4.4 12.8 1.0 C3A C:HEM142 4.4 14.9 1.0 C3D C:HEM142 4.4 13.5 1.0 CD1 C:LEU91 4.4 13.6 1.0 CE1 C:HIS58 4.4 17.1 1.0 C2D C:HEM142 4.5 11.7 1.0 NE2 C:HIS58 4.5 13.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Deoxy Human Hemoglobin Complexed with Two L35 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:14.1 occ:1.00 FE D:HEM147 0.0 14.1 1.0 NC D:HEM147 2.0 11.3 1.0 NB D:HEM147 2.1 14.7 1.0 ND D:HEM147 2.1 16.6 1.0 NA D:HEM147 2.1 15.9 1.0 NE2 D:HIS92 2.2 18.5 1.0 C4C D:HEM147 3.0 14.5 1.0 C4D D:HEM147 3.1 16.5 1.0 C1D D:HEM147 3.1 15.6 1.0 C1A D:HEM147 3.1 17.9 1.0 C1C D:HEM147 3.1 10.8 1.0 C4B D:HEM147 3.1 13.2 1.0 C1B D:HEM147 3.1 15.6 1.0 CD2 D:HIS92 3.1 15.1 1.0 CE1 D:HIS92 3.2 16.1 1.0 C4A D:HEM147 3.2 18.6 1.0 CHA D:HEM147 3.4 18.0 1.0 CHD D:HEM147 3.4 13.7 1.0 CHC D:HEM147 3.5 13.6 1.0 CHB D:HEM147 3.5 14.7 1.0 CG2 D:VAL67 3.9 18.3 1.0 NE2 D:HIS63 4.2 25.9 1.0 ND1 D:HIS92 4.3 14.2 1.0 C3C D:HEM147 4.3 11.0 1.0 C3D D:HEM147 4.3 15.6 1.0 C2D D:HEM147 4.3 16.3 1.0 CG D:HIS92 4.3 15.3 1.0 C2C D:HEM147 4.3 14.0 1.0 C2B D:HEM147 4.3 14.3 1.0 C3B D:HEM147 4.3 15.8 1.0 CE1 D:HIS63 4.3 24.6 1.0 C2A D:HEM147 4.4 20.7 1.0 C3A D:HEM147 4.4 19.6 1.0 CD1 D:LEU96 4.8 14.7 1.0

T.Yokoyama, S.Neya, A.Tsuneshige, T.Yonetani, S.Y.Park, J.R.Tame. R-State Haemoglobin with Low Oxygen Affinity: Crystal Structures of Deoxy Human and Carbonmonoxy Horse Haemoglobin Bound to the Effector Molecule L35 J.Mol.Biol. V. 356 790 2006.
ISSN: ISSN 0022-2836
PubMed: 16403522
DOI: 10.1016/J.JMB.2005.12.018