Iron in PDB 1hdb: Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin

The structure of Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin, PDB code: 1hdb was solved by I.Pechik, X.Ji, C.Fronticelli, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.540, 83.190, 54.020, 90.00, 99.15, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Iron atom in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin (pdb code 1hdb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin, PDB code: 1hdb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:15.4 occ:1.00 FE A:HEM142 0.0 15.4 1.0 NB A:HEM142 2.0 13.8 1.0 ND A:HEM142 2.0 14.3 1.0 NC A:HEM142 2.1 14.1 1.0 NA A:HEM142 2.1 14.9 1.0 NE2 A:HIS87 2.2 16.2 1.0 C4D A:HEM142 3.0 14.8 1.0 C4B A:HEM142 3.0 13.9 1.0 C1B A:HEM142 3.1 14.4 1.0 C1D A:HEM142 3.1 14.4 1.0 C1C A:HEM142 3.1 13.3 1.0 C1A A:HEM142 3.1 15.0 1.0 C4C A:HEM142 3.1 13.1 1.0 C4A A:HEM142 3.1 15.0 1.0 CE1 A:HIS87 3.2 16.4 1.0 CD2 A:HIS87 3.2 15.3 1.0 CHC A:HEM142 3.4 13.4 1.0 CHA A:HEM142 3.4 14.2 1.0 CHD A:HEM142 3.5 13.4 1.0 CHB A:HEM142 3.5 14.3 1.0 O A:HOH164 3.8 29.7 1.0 C3D A:HEM142 4.2 15.0 1.0 C2D A:HEM142 4.3 14.7 1.0 C2B A:HEM142 4.3 14.0 1.0 C3B A:HEM142 4.3 13.8 1.0 C2C A:HEM142 4.3 13.0 1.0 C3C A:HEM142 4.3 13.1 1.0 C2A A:HEM142 4.3 16.0 1.0 ND1 A:HIS87 4.3 15.9 1.0 C3A A:HEM142 4.4 15.7 1.0 CG A:HIS87 4.4 16.8 1.0 CD1 A:LEU91 4.6 12.0 1.0 NE2 A:HIS58 4.6 16.1 1.0 CE1 A:HIS58 4.6 16.0 1.0

Iron binding site 2 out of 4 in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe148 b:17.8 occ:1.00 FE B:HEM148 0.0 17.8 1.0 NC B:HEM148 2.0 16.7 1.0 ND B:HEM148 2.0 18.1 1.0 NA B:HEM148 2.0 18.8 1.0 NB B:HEM148 2.1 17.1 1.0 NE2 B:HIS92 2.4 16.1 1.0 C4C B:HEM148 3.1 16.1 1.0 C1D B:HEM148 3.1 17.7 1.0 C4B B:HEM148 3.1 16.9 1.0 C1C B:HEM148 3.1 16.6 1.0 C1B B:HEM148 3.1 16.8 1.0 C4A B:HEM148 3.1 18.8 1.0 C4D B:HEM148 3.1 18.5 1.0 C1A B:HEM148 3.1 20.0 1.0 CE1 B:HIS92 3.3 17.2 1.0 CHD B:HEM148 3.4 16.6 1.0 CD2 B:HIS92 3.4 16.1 1.0 CHC B:HEM148 3.5 16.1 1.0 CHB B:HEM148 3.5 17.7 1.0 CHA B:HEM148 3.5 19.2 1.0 C3C B:HEM148 4.3 15.3 1.0 NE2 B:HIS63 4.3 21.6 1.0 C3D B:HEM148 4.3 19.1 1.0 C2C B:HEM148 4.3 15.8 1.0 C2D B:HEM148 4.3 18.0 1.0 C3B B:HEM148 4.3 17.5 1.0 C2B B:HEM148 4.3 17.2 1.0 C3A B:HEM148 4.3 19.0 1.0 C2A B:HEM148 4.3 20.1 1.0 ND1 B:HIS92 4.5 16.7 1.0 CE1 B:HIS63 4.5 20.8 1.0 CG B:HIS92 4.6 17.5 1.0 OG1 B:THR67 4.7 27.1 1.0

Iron binding site 3 out of 4 in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:14.6 occ:1.00 FE C:HEM142 0.0 14.6 1.0 NB C:HEM142 2.0 12.7 1.0 ND C:HEM142 2.0 13.4 1.0 NC C:HEM142 2.0 12.9 1.0 NA C:HEM142 2.0 14.5 1.0 NE2 C:HIS87 2.4 16.5 1.0 C4C C:HEM142 3.0 13.2 1.0 C1B C:HEM142 3.0 12.9 1.0 C1C C:HEM142 3.1 13.2 1.0 C1D C:HEM142 3.1 13.8 1.0 C4B C:HEM142 3.1 12.6 1.0 C1A C:HEM142 3.1 14.5 1.0 C4A C:HEM142 3.1 14.8 1.0 C4D C:HEM142 3.1 13.8 1.0 CD2 C:HIS87 3.2 16.3 1.0 CE1 C:HIS87 3.4 17.8 1.0 CHD C:HEM142 3.4 13.7 1.0 CHA C:HEM142 3.4 13.9 1.0 CHC C:HEM142 3.5 12.8 1.0 CHB C:HEM142 3.5 13.8 1.0 O C:HOH150 3.6 22.1 1.0 C2B C:HEM142 4.3 12.5 1.0 C2A C:HEM142 4.3 15.9 1.0 C2D C:HEM142 4.3 13.7 1.0 C3D C:HEM142 4.3 13.9 1.0 C2C C:HEM142 4.3 13.5 1.0 C3B C:HEM142 4.3 12.2 1.0 C3C C:HEM142 4.3 13.3 1.0 C3A C:HEM142 4.3 15.1 1.0 CG C:HIS87 4.4 17.3 1.0 CE1 C:HIS58 4.4 18.6 1.0 ND1 C:HIS87 4.4 17.2 1.0 NE2 C:HIS58 4.5 18.7 1.0 CD1 C:LEU91 4.5 17.7 1.0

Iron binding site 4 out of 4 in the Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Analysis of the Crystal Structure, Molecular Modeling and Infrared Spectroscopy of the Distal Beta-Heme Pocket VALINE67(E11)-Threonine Mutation of Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe148 b:19.8 occ:1.00 FE D:HEM148 0.0 19.8 1.0 ND D:HEM148 2.0 19.8 1.0 NA D:HEM148 2.0 20.1 1.0 NC D:HEM148 2.0 19.3 1.0 NB D:HEM148 2.0 19.8 1.0 NE2 D:HIS92 2.2 16.2 1.0 C4C D:HEM148 3.0 19.5 1.0 C1D D:HEM148 3.0 20.4 1.0 C4A D:HEM148 3.0 20.5 1.0 C4D D:HEM148 3.0 20.4 1.0 C1B D:HEM148 3.1 19.6 1.0 C1A D:HEM148 3.1 20.7 1.0 C1C D:HEM148 3.1 19.1 1.0 C4B D:HEM148 3.1 20.0 1.0 CD2 D:HIS92 3.2 16.7 1.0 CE1 D:HIS92 3.2 16.9 1.0 CHD D:HEM148 3.4 19.9 1.0 CHB D:HEM148 3.4 19.7 1.0 CHA D:HEM148 3.4 20.3 1.0 CHC D:HEM148 3.5 19.3 1.0 C3D D:HEM148 4.3 21.7 1.0 C3C D:HEM148 4.3 19.2 1.0 C2D D:HEM148 4.3 21.0 1.0 C3A D:HEM148 4.3 20.7 1.0 C2B D:HEM148 4.3 19.9 1.0 C2A D:HEM148 4.3 21.3 1.0 C2C D:HEM148 4.3 19.0 1.0 C3B D:HEM148 4.3 19.7 1.0 NE2 D:HIS63 4.3 12.5 1.0 CG D:HIS92 4.3 17.9 1.0 ND1 D:HIS92 4.4 17.6 1.0 CE1 D:HIS63 4.8 14.2 1.0 OG1 D:THR67 4.8 25.0 1.0

I.Pechik, X.Ji, K.Fidelis, M.Karavitis, J.Moult, W.S.Brinigar, C.Fronticelli, G.L.Gilliland. Crystallographic, Molecular Modeling, and Biophysical Characterization of the Valine Beta 67 (E11)-->Threonine Variant of Hemoglobin. Biochemistry V. 35 1935 1996.
ISSN: ISSN 0006-2960
PubMed: 8639677
DOI: 10.1021/BI9519967