Iron in PDB 8fdl: Human Hemoglobin with Nitrosochloramphenicol

The structure of Human Hemoglobin with Nitrosochloramphenicol, PDB code: 8fdl was solved by S.M.Powell, G.B.Richter-Addo, L.M.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.41 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.551, 82.683, 62.586, 90, 100.02, 90
R / Rfree (%)	15.1 / 21

The structure of Human Hemoglobin with Nitrosochloramphenicol also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Human Hemoglobin with Nitrosochloramphenicol (pdb code 8fdl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Hemoglobin with Nitrosochloramphenicol, PDB code: 8fdl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Hemoglobin with Nitrosochloramphenicol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Hemoglobin with Nitrosochloramphenicol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:11.0 occ:1.00 FE A:HEM201 0.0 11.0 1.0 NA A:HEM201 2.1 9.5 1.0 ND A:HEM201 2.1 8.3 1.0 NC A:HEM201 2.1 9.0 1.0 NB A:HEM201 2.1 8.5 1.0 NE2 A:HIS87 2.2 8.6 1.0 CE1 A:HIS87 3.0 8.6 1.0 C1D A:HEM201 3.1 6.9 1.0 C4C A:HEM201 3.1 12.1 1.0 C1C A:HEM201 3.1 7.0 1.0 C4A A:HEM201 3.1 7.1 1.0 C4D A:HEM201 3.1 11.4 1.0 C1A A:HEM201 3.1 8.2 1.0 HE1 A:HIS87 3.1 10.3 1.0 C4B A:HEM201 3.1 7.7 1.0 C1B A:HEM201 3.1 8.6 1.0 CD2 A:HIS87 3.3 7.4 1.0 O A:HOH333 3.4 16.4 1.0 CHD A:HEM201 3.4 8.7 1.0 CHA A:HEM201 3.5 8.9 1.0 CHC A:HEM201 3.5 7.9 1.0 CHB A:HEM201 3.5 9.7 1.0 HD2 A:HIS87 3.5 8.9 1.0 HE1 A:HIS58 3.7 15.2 1.0 HD13 A:LEU91 3.9 10.5 1.0 HE2 A:HIS58 3.9 14.9 1.0 ND1 A:HIS87 4.2 7.9 1.0 HD12 A:LEU91 4.3 10.5 1.0 C2D A:HEM201 4.3 12.3 1.0 C2C A:HEM201 4.3 5.2 1.0 C3A A:HEM201 4.3 8.8 1.0 C3D A:HEM201 4.3 9.6 1.0 C3C A:HEM201 4.3 7.6 1.0 CE1 A:HIS58 4.3 12.6 1.0 CG A:HIS87 4.3 9.4 1.0 C2A A:HEM201 4.3 10.4 1.0 C3B A:HEM201 4.4 6.1 1.0 HG22 A:VAL62 4.4 10.7 1.0 C2B A:HEM201 4.4 10.0 1.0 HHA A:HEM201 4.4 10.7 1.0 HHD A:HEM201 4.4 10.4 1.0 CD1 A:LEU91 4.4 8.7 1.0 HHC A:HEM201 4.4 9.5 1.0 NE2 A:HIS58 4.5 12.4 1.0 HHB A:HEM201 4.5 11.7 1.0 HD11 A:LEU91 4.5 10.5 1.0 HG21 A:VAL93 4.8 13.1 1.0 HE2 A:PHE98 5.0 11.2 1.0 HD1 A:HIS87 5.0 9.6 1.0

Iron binding site 2 out of 4 in the Human Hemoglobin with Nitrosochloramphenicol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Hemoglobin with Nitrosochloramphenicol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:10.5 occ:1.00 FE B:HEM201 0.0 10.5 1.0 NC B:HEM201 2.1 8.9 1.0 NA B:HEM201 2.1 11.0 1.0 ND B:HEM201 2.1 13.0 1.0 NB B:HEM201 2.1 10.9 1.0 NE2 B:HIS92 2.2 9.0 1.0 CE1 B:HIS92 3.0 11.7 1.0 C1C B:HEM201 3.1 9.8 1.0 HE1 B:HIS92 3.1 14.0 1.0 C4A B:HEM201 3.1 7.2 1.0 C1A B:HEM201 3.1 11.9 1.0 C4D B:HEM201 3.1 10.7 1.0 C4B B:HEM201 3.1 13.0 1.0 C4C B:HEM201 3.1 7.0 1.0 C1D B:HEM201 3.1 10.3 1.0 C1B B:HEM201 3.1 8.1 1.0 HG22 B:VAL67 3.2 13.8 1.0 CD2 B:HIS92 3.3 10.2 1.0 CHC B:HEM201 3.4 9.1 1.0 CHA B:HEM201 3.4 10.8 1.0 CHB B:HEM201 3.4 10.8 1.0 CHD B:HEM201 3.5 7.1 1.0 HE2 B:HIS63 3.5 16.9 1.0 HD2 B:HIS92 3.5 12.3 1.0 HG21 B:VAL67 4.0 13.8 1.0 CG2 B:VAL67 4.0 11.4 1.0 ND1 B:HIS92 4.2 11.2 1.0 NE2 B:HIS63 4.3 14.1 1.0 C2C B:HEM201 4.3 9.3 1.0 HE1 B:PHE103 4.3 14.2 1.0 C3A B:HEM201 4.3 12.3 1.0 C2B B:HEM201 4.3 8.3 1.0 C2A B:HEM201 4.3 10.7 1.0 C3C B:HEM201 4.3 14.2 1.0 C3B B:HEM201 4.3 10.7 1.0 C3D B:HEM201 4.3 11.8 1.0 C2D B:HEM201 4.3 17.3 1.0 CG B:HIS92 4.3 9.7 1.0 HD13 B:LEU96 4.4 13.5 1.0 HHC B:HEM201 4.4 10.9 1.0 HHB B:HEM201 4.4 12.9 1.0 HHA B:HEM201 4.4 13.0 1.0 HHD B:HEM201 4.4 8.6 1.0 HG23 B:VAL67 4.5 13.8 1.0 HE1 B:HIS63 4.7 19.8 1.0 HD12 B:LEU96 4.7 13.5 1.0 HG11 B:VAL67 4.7 12.6 1.0 CE1 B:HIS63 4.8 16.5 1.0 HG13 B:VAL67 4.9 12.6 1.0 CD1 B:LEU96 4.9 11.3 1.0 HD1 B:HIS92 4.9 13.4 1.0 HD11 B:LEU96 5.0 13.5 1.0

Iron binding site 3 out of 4 in the Human Hemoglobin with Nitrosochloramphenicol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Hemoglobin with Nitrosochloramphenicol within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:13.3 occ:1.00 FE C:HEM201 0.0 13.3 1.0 ND C:HEM201 2.1 11.1 1.0 NB C:HEM201 2.1 11.2 1.0 NC C:HEM201 2.1 10.9 1.0 NA C:HEM201 2.1 10.4 1.0 NE2 C:HIS87 2.2 11.8 1.0 C4D C:HEM201 3.1 10.6 1.0 C4B C:HEM201 3.1 9.3 1.0 C1C C:HEM201 3.1 12.5 1.0 C1B C:HEM201 3.1 9.9 1.0 CE1 C:HIS87 3.1 12.6 1.0 C1D C:HEM201 3.1 9.2 1.0 C1A C:HEM201 3.1 9.5 1.0 C4C C:HEM201 3.1 8.9 1.0 C4A C:HEM201 3.1 13.7 1.0 HE1 C:HIS87 3.2 15.1 1.0 CD2 C:HIS87 3.3 10.2 1.0 CHA C:HEM201 3.4 12.1 1.0 CHC C:HEM201 3.4 10.0 1.0 CHB C:HEM201 3.5 12.2 1.0 CHD C:HEM201 3.5 11.4 1.0 HD2 C:HIS87 3.5 12.3 1.0 HE1 C:HIS58 3.5 20.9 1.0 O C:HOH360 3.6 24.5 1.0 HD13 C:LEU91 3.9 20.2 1.0 CE1 C:HIS58 4.2 17.4 1.0 ND1 C:HIS87 4.3 10.7 1.0 C3B C:HEM201 4.3 12.5 1.0 C3D C:HEM201 4.3 14.5 1.0 C2B C:HEM201 4.3 9.6 1.0 C2D C:HEM201 4.3 11.7 1.0 C2C C:HEM201 4.3 9.6 1.0 HG22 C:VAL62 4.3 13.1 1.0 C3C C:HEM201 4.3 10.4 1.0 C3A C:HEM201 4.4 13.0 1.0 C2A C:HEM201 4.4 11.6 1.0 HHA C:HEM201 4.4 14.5 1.0 HHC C:HEM201 4.4 12.1 1.0 CG C:HIS87 4.4 7.4 1.0 HHB C:HEM201 4.4 14.7 1.0 NE2 C:HIS58 4.5 13.2 1.0 HHD C:HEM201 4.5 13.7 1.0 HD12 C:LEU91 4.5 20.2 1.0 CD1 C:LEU91 4.5 16.8 1.0 HD11 C:LEU91 4.6 20.2 1.0 HG21 C:VAL93 4.9 12.1 1.0 HE2 C:PHE98 5.0 12.0 1.0

Iron binding site 4 out of 4 in the Human Hemoglobin with Nitrosochloramphenicol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Hemoglobin with Nitrosochloramphenicol within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:10.9 occ:1.00 FE D:HEM201 0.0 10.9 1.0 ND D:HEM201 2.1 11.9 1.0 NA D:HEM201 2.1 8.3 1.0 NB D:HEM201 2.1 8.4 1.0 NC D:HEM201 2.1 8.9 1.0 NE2 D:HIS92 2.2 8.0 1.0 C4B D:HEM201 3.1 10.3 1.0 C1D D:HEM201 3.1 9.3 1.0 C4A D:HEM201 3.1 10.5 1.0 C1B D:HEM201 3.1 7.7 1.0 CE1 D:HIS92 3.1 9.2 1.0 C1C D:HEM201 3.1 8.8 1.0 C4C D:HEM201 3.1 10.0 1.0 C1A D:HEM201 3.1 11.3 1.0 C4D D:HEM201 3.1 10.5 1.0 HG22 D:VAL67 3.2 13.2 1.0 HE1 D:HIS92 3.2 11.1 1.0 CD2 D:HIS92 3.2 10.6 1.0 CHB D:HEM201 3.4 8.9 1.0 CHC D:HEM201 3.4 8.2 1.0 CHD D:HEM201 3.4 7.8 1.0 HD2 D:HIS92 3.4 12.7 1.0 CHA D:HEM201 3.5 7.7 1.0 HE2 D:HIS63 3.5 14.4 1.0 CG2 D:VAL67 4.0 11.0 1.0 HG21 D:VAL67 4.1 13.2 1.0 HE1 D:HIS63 4.1 17.7 1.0 NE2 D:HIS63 4.2 12.0 1.0 HE1 D:PHE103 4.2 13.7 1.0 ND1 D:HIS92 4.2 13.5 1.0 C3B D:HEM201 4.3 7.6 1.0 C2B D:HEM201 4.3 7.1 1.0 C2D D:HEM201 4.3 8.4 1.0 C3A D:HEM201 4.3 9.8 1.0 C2C D:HEM201 4.3 10.4 1.0 C3C D:HEM201 4.3 9.8 1.0 C2A D:HEM201 4.3 12.6 1.0 CG D:HIS92 4.3 14.6 1.0 C3D D:HEM201 4.4 8.6 1.0 HD13 D:LEU96 4.4 14.7 1.0 HHB D:HEM201 4.4 10.7 1.0 HHD D:HEM201 4.4 9.4 1.0 HHC D:HEM201 4.4 9.8 1.0 HG23 D:VAL67 4.4 13.2 1.0 HHA D:HEM201 4.5 9.3 1.0 CE1 D:HIS63 4.5 14.7 1.0 HD12 D:LEU96 4.8 14.7 1.0 HG21 D:VAL98 4.9 15.5 1.0 HG13 D:VAL67 4.9 12.7 1.0 HG11 D:VAL67 5.0 12.7 1.0 CD1 D:LEU96 5.0 12.2 1.0 HD11 D:LEU88 5.0 23.1 1.0

S.M.Powell, B.Wang, V.E.Herrera, K.Y.Prather, N.T.Nguyen, E.G.Abucayon, L.M.Thomas, M.K.Safo, G.B.Richter-Addo. Crystal Structural Investigations of Heme Protein Derivatives Resulting From Reactions of Aryl- and Alkylhydroxylamines with Human Hemoglobin J.Inorg.Biochem. V. 246 12304 2023.
ISSN: ISSN 0162-0134
DOI: 10.1016/J.JINORGBIO.2023.112304