Iron in PDB 8fdm: Human Hemoglobin in Complex with Nitrosomethane

The structure of Human Hemoglobin in Complex with Nitrosomethane, PDB code: 8fdm 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)	46.67 / 1.91
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	53.458, 53.458, 191.375, 90, 90, 90
R / Rfree (%)	19.6 / 25.3

The binding sites of Iron atom in the Human Hemoglobin in Complex with Nitrosomethane (pdb code 8fdm). 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 in Complex with Nitrosomethane, PDB code: 8fdm:
Jump to Iron binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Hemoglobin in Complex with Nitrosomethane within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:21.1 occ:1.00 FE A:HEM201 0.0 21.1 1.0 NA A:HEM201 2.0 22.2 1.0 NE2 A:HIS87 2.0 20.9 1.0 NB A:HEM201 2.1 14.9 1.0 NC A:HEM201 2.1 21.4 1.0 ND A:HEM201 2.1 19.7 1.0 O A:HOH312 2.3 20.2 1.0 CE1 A:HIS87 3.0 18.4 1.0 C4A A:HEM201 3.0 19.7 1.0 C1B A:HEM201 3.0 20.7 1.0 C1A A:HEM201 3.1 23.7 1.0 C4C A:HEM201 3.1 18.9 1.0 C1D A:HEM201 3.1 17.3 1.0 C4B A:HEM201 3.1 17.2 1.0 C1C A:HEM201 3.1 18.5 1.0 C4D A:HEM201 3.1 20.9 1.0 CD2 A:HIS87 3.1 18.6 1.0 CHB A:HEM201 3.3 22.5 1.0 CHD A:HEM201 3.4 17.2 1.0 CHC A:HEM201 3.5 18.7 1.0 CHA A:HEM201 3.5 20.1 1.0 ND1 A:HIS87 4.1 19.2 1.0 CG A:HIS87 4.2 20.9 1.0 C3A A:HEM201 4.2 23.6 1.0 C2A A:HEM201 4.3 21.8 1.0 NE2 A:HIS58 4.3 20.4 1.0 C2B A:HEM201 4.3 17.3 1.0 C3C A:HEM201 4.3 17.6 1.0 C2C A:HEM201 4.3 16.8 1.0 C3B A:HEM201 4.3 19.0 1.0 C2D A:HEM201 4.3 23.2 1.0 C3D A:HEM201 4.3 23.3 1.0 CE1 A:HIS58 4.6 22.6 1.0 CG2 A:VAL62 5.0 19.6 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Hemoglobin in Complex with Nitrosomethane within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:31.8 occ:1.00 FE B:HEM201 0.0 31.8 1.0 N B:NSM202 2.0 34.2 1.0 ND B:HEM201 2.0 27.8 1.0 NB B:HEM201 2.0 27.2 1.0 NA B:HEM201 2.1 29.1 1.0 NC B:HEM201 2.1 32.2 1.0 NE2 B:HIS92 2.3 28.3 1.0 O1 B:NSM202 2.6 34.7 1.0 C4D B:HEM201 3.0 35.7 1.0 C4B B:HEM201 3.0 30.6 1.0 C1D B:HEM201 3.1 34.0 1.0 C1A B:HEM201 3.1 33.9 1.0 C1C B:HEM201 3.1 30.9 1.0 C1B B:HEM201 3.1 27.8 1.0 C4C B:HEM201 3.1 28.4 1.0 C4A B:HEM201 3.1 25.8 1.0 CD2 B:HIS92 3.2 32.1 1.0 C1 B:NSM202 3.2 29.8 1.0 CE1 B:HIS92 3.3 36.9 1.0 CHA B:HEM201 3.4 31.7 1.0 CHC B:HEM201 3.4 28.3 1.0 CHD B:HEM201 3.5 28.3 1.0 CHB B:HEM201 3.5 28.8 1.0 C3D B:HEM201 4.3 33.1 1.0 C2D B:HEM201 4.3 31.9 1.0 C3B B:HEM201 4.3 25.3 1.0 C2C B:HEM201 4.3 30.1 1.0 C2A B:HEM201 4.3 29.0 1.0 C2B B:HEM201 4.3 29.7 1.0 C3C B:HEM201 4.3 26.9 1.0 C3A B:HEM201 4.3 26.5 1.0 CG B:HIS92 4.3 27.2 1.0 ND1 B:HIS92 4.4 32.6 1.0 NE2 B:HIS63 4.5 37.4 1.0 CG2 B:VAL67 4.7 26.1 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Hemoglobin in Complex with Nitrosomethane within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:21.9 occ:1.00 FE C:HEM201 0.0 21.9 1.0 NA C:HEM201 2.0 21.8 1.0 O C:HOH325 2.0 20.7 1.0 NB C:HEM201 2.0 16.2 1.0 ND C:HEM201 2.1 20.5 1.0 NC C:HEM201 2.1 20.7 1.0 NE2 C:HIS87 2.3 21.6 1.0 C4A C:HEM201 3.0 19.3 1.0 C1B C:HEM201 3.0 20.9 1.0 C1A C:HEM201 3.0 22.6 1.0 C4D C:HEM201 3.1 20.7 1.0 C1D C:HEM201 3.1 19.5 1.0 C4B C:HEM201 3.1 18.4 1.0 C4C C:HEM201 3.1 19.8 1.0 C1C C:HEM201 3.1 20.9 1.0 CE1 C:HIS87 3.2 19.3 1.0 CD2 C:HIS87 3.3 18.5 1.0 CHB C:HEM201 3.4 22.0 1.0 CHA C:HEM201 3.4 19.2 1.0 CHC C:HEM201 3.5 19.3 1.0 CHD C:HEM201 3.5 18.2 1.0 NE2 C:HIS58 4.2 21.5 1.0 C3A C:HEM201 4.3 21.4 1.0 C2A C:HEM201 4.3 18.8 1.0 C2B C:HEM201 4.3 18.8 1.0 C3D C:HEM201 4.3 22.6 1.0 C2D C:HEM201 4.3 21.2 1.0 C3B C:HEM201 4.3 19.7 1.0 C3C C:HEM201 4.3 20.0 1.0 ND1 C:HIS87 4.3 18.9 1.0 C2C C:HEM201 4.3 16.3 1.0 CG C:HIS87 4.4 20.8 1.0 CE1 C:HIS58 4.6 22.9 1.0 CG2 C:VAL62 4.9 22.8 1.0

Iron binding site 4 out of 4 in the Human Hemoglobin in Complex with Nitrosomethane


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Hemoglobin in Complex with Nitrosomethane within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:32.3 occ:1.00 FE D:HEM201 0.0 32.3 1.0 N D:NSM202 2.0 31.8 1.0 NB D:HEM201 2.0 25.3 1.0 ND D:HEM201 2.1 28.5 1.0 NA D:HEM201 2.1 32.0 1.0 NC D:HEM201 2.1 30.9 1.0 NE2 D:HIS92 2.3 27.2 1.0 O1 D:NSM202 2.7 35.9 1.0 C4B D:HEM201 3.0 28.7 1.0 C1 D:NSM202 3.1 26.9 1.0 C4D D:HEM201 3.1 35.2 1.0 C1C D:HEM201 3.1 30.1 1.0 C1A D:HEM201 3.1 34.1 1.0 C1B D:HEM201 3.1 27.3 1.0 C4A D:HEM201 3.1 24.1 1.0 C1D D:HEM201 3.1 31.7 1.0 C4C D:HEM201 3.1 25.4 1.0 CD2 D:HIS92 3.2 31.6 1.0 CE1 D:HIS92 3.3 34.3 1.0 CHC D:HEM201 3.4 29.0 1.0 CHA D:HEM201 3.4 31.9 1.0 CHB D:HEM201 3.5 26.6 1.0 CHD D:HEM201 3.5 28.0 1.0 C3B D:HEM201 4.2 25.8 1.0 C2B D:HEM201 4.3 27.2 1.0 C2C D:HEM201 4.3 29.5 1.0 C3D D:HEM201 4.3 30.1 1.0 C2A D:HEM201 4.3 29.0 1.0 C3C D:HEM201 4.3 27.8 1.0 C2D D:HEM201 4.3 30.7 1.0 C3A D:HEM201 4.3 27.4 1.0 CG D:HIS92 4.4 26.6 1.0 ND1 D:HIS92 4.4 33.1 1.0 NE2 D:HIS63 4.5 35.4 1.0 CG2 D:VAL67 4.7 30.1 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