Iron in PDB 6nbd: Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev

The binding sites of Iron atom in the Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev (pdb code 6nbd). 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 Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev, PDB code: 6nbd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:48.8 occ:1.00 FE A:HEM201 0.0 48.8 1.0 ND A:HEM201 2.0 48.8 1.0 NA A:HEM201 2.0 48.8 1.0 NC A:HEM201 2.0 48.8 1.0 NB A:HEM201 2.0 48.8 1.0 NE2 A:HIS87 2.2 47.7 1.0 C4A A:HEM201 3.0 48.8 1.0 C1B A:HEM201 3.0 48.8 1.0 C1D A:HEM201 3.0 48.8 1.0 C4D A:HEM201 3.0 48.8 1.0 C1C A:HEM201 3.0 48.8 1.0 C1A A:HEM201 3.0 48.8 1.0 C4C A:HEM201 3.1 48.8 1.0 C4B A:HEM201 3.1 48.8 1.0 CE1 A:HIS87 3.1 47.7 1.0 CD2 A:HIS87 3.2 47.7 1.0 CHB A:HEM201 3.4 48.8 1.0 CHC A:HEM201 3.4 48.8 1.0 CHA A:HEM201 3.4 48.8 1.0 CHD A:HEM201 3.4 48.8 1.0 NE2 A:HIS58 4.1 57.3 1.0 C3A A:HEM201 4.2 48.8 1.0 C2D A:HEM201 4.2 48.8 1.0 C3D A:HEM201 4.2 48.8 1.0 C2A A:HEM201 4.2 48.8 1.0 C2B A:HEM201 4.3 48.8 1.0 ND1 A:HIS87 4.3 47.7 1.0 C2C A:HEM201 4.3 48.8 1.0 C3C A:HEM201 4.3 48.8 1.0 C3B A:HEM201 4.3 48.8 1.0 CE1 A:HIS58 4.3 57.3 1.0 CG A:HIS87 4.3 47.7 1.0 CG2 A:VAL62 4.4 55.7 1.0

Iron binding site 2 out of 4 in the Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:46.0 occ:1.00 FE B:HEM201 0.0 46.0 1.0 NC B:HEM201 2.0 46.0 1.0 NA B:HEM201 2.0 46.0 1.0 ND B:HEM201 2.0 46.0 1.0 NB B:HEM201 2.0 46.0 1.0 NE2 B:HIS92 2.2 51.5 1.0 C1C B:HEM201 3.0 46.0 1.0 C4A B:HEM201 3.0 46.0 1.0 C4C B:HEM201 3.0 46.0 1.0 C1A B:HEM201 3.0 46.0 1.0 C1B B:HEM201 3.0 46.0 1.0 C1D B:HEM201 3.0 46.0 1.0 C4D B:HEM201 3.0 46.0 1.0 C4B B:HEM201 3.1 46.0 1.0 CE1 B:HIS92 3.1 51.5 1.0 CD2 B:HIS92 3.1 51.5 1.0 CHC B:HEM201 3.4 46.0 1.0 CHB B:HEM201 3.4 46.0 1.0 CHA B:HEM201 3.4 46.0 1.0 CHD B:HEM201 3.4 46.0 1.0 ND1 B:HIS92 4.2 51.5 1.0 NE2 B:HIS63 4.2 49.3 1.0 C2C B:HEM201 4.2 46.0 1.0 C3A B:HEM201 4.2 46.0 1.0 C3C B:HEM201 4.2 46.0 1.0 C2A B:HEM201 4.2 46.0 1.0 CG B:HIS92 4.2 51.5 1.0 C2B B:HEM201 4.3 46.0 1.0 C2D B:HEM201 4.3 46.0 1.0 C3D B:HEM201 4.3 46.0 1.0 C3B B:HEM201 4.3 46.0 1.0 CG2 B:VAL67 4.7 47.8 1.0 CE1 B:HIS63 4.8 49.3 1.0

Iron binding site 3 out of 4 in the Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:48.7 occ:1.00 FE C:HEM201 0.0 48.7 1.0 NA C:HEM201 2.0 48.7 1.0 ND C:HEM201 2.0 48.7 1.0 NC C:HEM201 2.0 48.7 1.0 NB C:HEM201 2.0 48.7 1.0 NE2 C:HIS87 2.2 47.8 1.0 C1A C:HEM201 3.0 48.7 1.0 C4B C:HEM201 3.0 48.7 1.0 C1C C:HEM201 3.0 48.7 1.0 C4D C:HEM201 3.0 48.7 1.0 C4A C:HEM201 3.0 48.7 1.0 C1D C:HEM201 3.1 48.7 1.0 C4C C:HEM201 3.1 48.7 1.0 C1B C:HEM201 3.1 48.7 1.0 CE1 C:HIS87 3.2 47.8 1.0 CD2 C:HIS87 3.2 47.8 1.0 CHA C:HEM201 3.3 48.7 1.0 CHC C:HEM201 3.4 48.7 1.0 CHD C:HEM201 3.4 48.7 1.0 CHB C:HEM201 3.4 48.7 1.0 NE2 C:HIS58 4.1 57.5 1.0 C2A C:HEM201 4.2 48.7 1.0 C3A C:HEM201 4.2 48.7 1.0 C2D C:HEM201 4.3 48.7 1.0 C3B C:HEM201 4.3 48.7 1.0 C2C C:HEM201 4.3 48.7 1.0 C3D C:HEM201 4.3 48.7 1.0 C2B C:HEM201 4.3 48.7 1.0 ND1 C:HIS87 4.3 47.8 1.0 C3C C:HEM201 4.3 48.7 1.0 CG C:HIS87 4.3 47.8 1.0 CE1 C:HIS58 4.4 57.5 1.0 CG2 C:VAL62 4.5 55.9 1.0

Iron binding site 4 out of 4 in the Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Methemoglobin State 2 Determined Using Single-Particle Cryo-Em at 200 Kev within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:46.6 occ:1.00 FE D:HEM201 0.0 46.6 1.0 NA D:HEM201 2.0 46.6 1.0 NB D:HEM201 2.0 46.6 1.0 ND D:HEM201 2.0 46.6 1.0 NC D:HEM201 2.0 46.6 1.0 NE2 D:HIS92 2.2 50.7 1.0 C1A D:HEM201 3.0 46.6 1.0 C1C D:HEM201 3.0 46.6 1.0 C4B D:HEM201 3.0 46.6 1.0 C4D D:HEM201 3.0 46.6 1.0 C4A D:HEM201 3.0 46.6 1.0 C1D D:HEM201 3.1 46.6 1.0 C4C D:HEM201 3.1 46.6 1.0 C1B D:HEM201 3.1 46.6 1.0 CD2 D:HIS92 3.1 50.7 1.0 CE1 D:HIS92 3.1 50.7 1.0 CHA D:HEM201 3.4 46.6 1.0 CHC D:HEM201 3.4 46.6 1.0 CHB D:HEM201 3.4 46.6 1.0 CHD D:HEM201 3.4 46.6 1.0 C2A D:HEM201 4.2 46.6 1.0 ND1 D:HIS92 4.2 50.7 1.0 NE2 D:HIS63 4.2 49.8 1.0 C3A D:HEM201 4.2 46.6 1.0 CG D:HIS92 4.2 50.7 1.0 C2C D:HEM201 4.2 46.6 1.0 C3B D:HEM201 4.2 46.6 1.0 C3D D:HEM201 4.2 46.6 1.0 C2D D:HEM201 4.3 46.6 1.0 C3C D:HEM201 4.3 46.6 1.0 C2B D:HEM201 4.3 46.6 1.0 CG2 D:VAL67 4.7 48.2 1.0 CE1 D:HIS63 4.8 49.8 1.0

M.A.Herzik Jr., M.Wu, G.C.Lander. High-Resolution Structure Determination of Sub-100 kDa Complexes Using Conventional Cryo-Em. Nat Commun V. 10 1032 2019.
ISSN: ESSN 2041-1723
PubMed: 30833564
DOI: 10.1038/S41467-019-08991-8