Iron in PDB 9vid: Cryo-Em Structure of Alligator Haemoglobin in the R Conformation

The binding sites of Iron atom in the Cryo-Em Structure of Alligator Haemoglobin in the R Conformation (pdb code 9vid). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Cryo-Em Structure of Alligator Haemoglobin in the R Conformation, PDB code: 9vid:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Cryo-Em Structure of Alligator Haemoglobin in the R Conformation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Alligator Haemoglobin in the R Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:25.1 occ:1.00 FE A:HEM201 0.0 25.1 1.0 ND A:HEM201 2.0 27.1 1.0 NA A:HEM201 2.0 25.5 1.0 NC A:HEM201 2.1 27.3 1.0 NB A:HEM201 2.1 30.6 1.0 NE2 A:HIS87 2.2 27.0 1.0 C A:CMO202 2.7 54.9 1.0 C1D A:HEM201 3.0 26.5 1.0 C4D A:HEM201 3.0 28.0 1.0 C1A A:HEM201 3.0 26.2 1.0 CE1 A:HIS87 3.1 27.2 1.0 C4A A:HEM201 3.1 27.8 1.0 C4B A:HEM201 3.1 33.8 1.0 C1C A:HEM201 3.1 32.8 1.0 C4C A:HEM201 3.1 27.2 1.0 C1B A:HEM201 3.1 26.6 1.0 CD2 A:HIS87 3.3 31.2 1.0 CHA A:HEM201 3.4 28.5 1.0 CHD A:HEM201 3.4 26.0 1.0 CHB A:HEM201 3.4 25.6 1.0 CHC A:HEM201 3.5 31.2 1.0 O A:CMO202 3.5 77.7 1.0 C2D A:HEM201 4.2 32.1 1.0 C3D A:HEM201 4.2 33.1 1.0 ND1 A:HIS87 4.2 27.1 1.0 C2A A:HEM201 4.3 32.3 1.0 NE2 A:HIS58 4.3 33.9 1.0 C3A A:HEM201 4.3 32.3 1.0 C2C A:HEM201 4.3 34.5 1.0 C3C A:HEM201 4.3 30.6 1.0 C2B A:HEM201 4.3 31.9 1.0 C3B A:HEM201 4.4 33.5 1.0 CG A:HIS87 4.4 32.9 1.0 CE1 A:HIS58 4.4 35.9 1.0 CG2 A:VAL62 4.8 31.2 1.0

Iron binding site 2 out of 2 in the Cryo-Em Structure of Alligator Haemoglobin in the R Conformation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Alligator Haemoglobin in the R Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:28.6 occ:1.00 FE B:HEM201 0.0 28.6 1.0 ND B:HEM201 2.0 33.1 1.0 NA B:HEM201 2.0 29.0 1.0 NC B:HEM201 2.1 30.7 1.0 NB B:HEM201 2.1 31.1 1.0 NE2 B:HIS92 2.3 32.9 1.0 C1D B:HEM201 3.0 29.0 1.0 C4D B:HEM201 3.0 30.1 1.0 C1A B:HEM201 3.0 30.2 1.0 C4A B:HEM201 3.1 26.8 1.0 C4C B:HEM201 3.1 30.9 1.0 C4B B:HEM201 3.1 33.2 1.0 C1B B:HEM201 3.1 28.6 1.0 C1C B:HEM201 3.1 31.2 1.0 CE1 B:HIS92 3.2 35.6 1.0 C B:CMO202 3.4 91.5 1.0 CHA B:HEM201 3.4 30.5 1.0 CHD B:HEM201 3.4 28.6 1.0 CD2 B:HIS92 3.4 38.3 1.0 CHC B:HEM201 3.5 32.4 1.0 CHB B:HEM201 3.5 24.4 1.0 O B:CMO202 4.0 95.7 1.0 C2A B:HEM201 4.2 35.3 1.0 C3A B:HEM201 4.2 33.2 1.0 C2D B:HEM201 4.3 36.6 1.0 C3D B:HEM201 4.3 37.7 1.0 C3C B:HEM201 4.3 33.6 1.0 C2C B:HEM201 4.3 31.6 1.0 C2B B:HEM201 4.3 35.6 1.0 ND1 B:HIS92 4.3 34.0 1.0 C3B B:HEM201 4.4 35.3 1.0 NE2 B:HIS63 4.4 37.1 1.0 CG2 B:VAL67 4.4 38.8 1.0 CG B:HIS92 4.5 34.6 1.0 CE1 B:HIS63 4.9 39.4 1.0

K.Takahashi, Y.Lee, T.Nishizawa, J.R.H.Tame. Conformational Analysis of Liganded Human Hemoglobin By Cryo Electron Microscopy Biorxiv 2025.
ISSN: ISSN 2692-8205
DOI: 10.1101/2025.07.07.661630