Iron in PDB 5ni1: Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate

The binding sites of Iron atom in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate (pdb code 5ni1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate, PDB code: 5ni1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:11.9 occ:1.00 FE A:HEM201 0.0 11.9 1.0 ND A:HEM201 1.9 13.7 1.0 NE2 A:HIS87 2.0 12.8 1.0 NA A:HEM201 2.0 14.0 1.0 NC A:HEM201 2.1 11.3 1.0 NB A:HEM201 2.1 11.1 1.0 CE1 A:HIS87 2.8 13.1 1.0 C1D A:HEM201 2.9 13.9 1.0 C4D A:HEM201 2.9 15.6 1.0 C4A A:HEM201 3.0 14.2 1.0 C1A A:HEM201 3.0 16.0 1.0 C1B A:HEM201 3.0 11.1 1.0 C4C A:HEM201 3.1 11.0 1.0 C4B A:HEM201 3.1 10.5 1.0 CD2 A:HIS87 3.1 13.2 1.0 C1C A:HEM201 3.1 10.5 1.0 CHD A:HEM201 3.4 12.4 1.0 CHB A:HEM201 3.4 12.4 1.0 CHA A:HEM201 3.4 15.4 1.0 CHC A:HEM201 3.5 10.4 1.0 ND1 A:HIS87 4.0 13.0 1.0 C2D A:HEM201 4.2 15.8 1.0 C3D A:HEM201 4.2 18.7 1.0 CG A:HIS87 4.2 13.5 1.0 C3A A:HEM201 4.2 16.3 1.0 C2A A:HEM201 4.2 19.2 1.0 C2B A:HEM201 4.2 10.6 1.0 C3C A:HEM201 4.3 10.3 1.0 C2C A:HEM201 4.3 10.0 1.0 C3B A:HEM201 4.3 10.6 1.0 CE1 A:HIS58 4.4 46.2 1.0 NE2 A:HIS58 4.5 48.4 1.0 CG2 A:VAL62 4.9 21.6 1.0

Iron binding site 2 out of 4 in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:28.8 occ:1.00 FE B:HEM201 0.0 28.8 1.0 ND B:HEM201 1.9 31.2 1.0 NE2 B:HIS92 2.0 30.8 1.0 NA B:HEM201 2.0 34.8 1.0 NC B:HEM201 2.1 27.6 1.0 NB B:HEM201 2.1 29.0 1.0 CE1 B:HIS92 2.9 29.6 1.0 C1D B:HEM201 2.9 30.8 1.0 C4D B:HEM201 2.9 33.6 1.0 C1A B:HEM201 3.0 37.7 1.0 C4A B:HEM201 3.0 36.0 1.0 C4C B:HEM201 3.1 27.2 1.0 C1B B:HEM201 3.1 29.9 1.0 CD2 B:HIS92 3.1 31.9 1.0 C4B B:HEM201 3.1 27.9 1.0 C1C B:HEM201 3.1 26.8 1.0 CHD B:HEM201 3.4 28.9 1.0 CHA B:HEM201 3.4 34.3 1.0 CHB B:HEM201 3.4 32.7 1.0 CHC B:HEM201 3.5 26.8 1.0 ND1 B:HIS92 4.0 29.0 1.0 CG B:HIS92 4.2 30.3 1.0 C2D B:HEM201 4.2 32.8 1.0 C3D B:HEM201 4.2 37.1 1.0 C2A B:HEM201 4.2 45.7 1.0 C3A B:HEM201 4.2 39.8 1.0 C2C B:HEM201 4.3 25.7 1.0 C3C B:HEM201 4.3 26.1 1.0 C2B B:HEM201 4.3 28.7 1.0 C3B B:HEM201 4.4 28.2 1.0 NE2 B:HIS63 4.5 60.3 1.0 CG2 B:VAL67 4.8 42.8 1.0 CE1 B:HIS63 5.0 64.8 1.0

Iron binding site 3 out of 4 in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:11.9 occ:1.00 FE C:HEM201 0.0 11.9 1.0 ND C:HEM201 1.9 13.7 1.0 NE2 C:HIS87 2.0 12.8 1.0 NA C:HEM201 2.0 14.0 1.0 NB C:HEM201 2.1 11.1 1.0 NC C:HEM201 2.1 11.2 1.0 CE1 C:HIS87 2.8 13.1 1.0 C1D C:HEM201 2.9 13.9 1.0 C4D C:HEM201 2.9 15.6 1.0 C4A C:HEM201 3.0 14.1 1.0 C1A C:HEM201 3.0 15.9 1.0 C1B C:HEM201 3.0 11.1 1.0 C4C C:HEM201 3.1 11.0 1.0 C4B C:HEM201 3.1 10.4 1.0 CD2 C:HIS87 3.1 13.2 1.0 C1C C:HEM201 3.1 10.5 1.0 CHD C:HEM201 3.4 12.3 1.0 CHB C:HEM201 3.4 12.4 1.0 CHA C:HEM201 3.4 15.4 1.0 CHC C:HEM201 3.5 10.3 1.0 ND1 C:HIS87 4.0 12.9 1.0 C2D C:HEM201 4.2 15.7 1.0 C3D C:HEM201 4.2 18.6 1.0 CG C:HIS87 4.2 13.5 1.0 C3A C:HEM201 4.2 16.3 1.0 C2A C:HEM201 4.2 19.2 1.0 C2B C:HEM201 4.2 10.6 1.0 C3C C:HEM201 4.3 10.2 1.0 C2C C:HEM201 4.3 9.9 1.0 C3B C:HEM201 4.3 10.6 1.0 CE1 C:HIS58 4.4 46.2 1.0 NE2 C:HIS58 4.5 48.4 1.0 CG2 C:VAL62 4.9 21.6 1.0

Iron binding site 4 out of 4 in the Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryoem Structure of Haemoglobin at 3.2 A Determined with the Volta Phase Plate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:28.8 occ:1.00 FE D:HEM201 0.0 28.8 1.0 ND D:HEM201 1.9 31.2 1.0 NE2 D:HIS92 2.0 30.9 1.0 NA D:HEM201 2.0 34.7 1.0 NC D:HEM201 2.1 27.6 1.0 NB D:HEM201 2.1 29.0 1.0 CE1 D:HIS92 2.9 29.7 1.0 C1D D:HEM201 2.9 30.8 1.0 C4D D:HEM201 2.9 33.6 1.0 C1A D:HEM201 3.0 37.6 1.0 C4A D:HEM201 3.0 35.9 1.0 C4C D:HEM201 3.1 27.2 1.0 C1B D:HEM201 3.1 29.9 1.0 CD2 D:HIS92 3.1 32.0 1.0 C4B D:HEM201 3.1 27.9 1.0 C1C D:HEM201 3.1 26.8 1.0 CHD D:HEM201 3.4 28.9 1.0 CHA D:HEM201 3.4 34.3 1.0 CHB D:HEM201 3.4 32.7 1.0 CHC D:HEM201 3.5 26.8 1.0 ND1 D:HIS92 4.0 29.1 1.0 CG D:HIS92 4.2 30.4 1.0 C2D D:HEM201 4.2 32.9 1.0 C3D D:HEM201 4.2 37.1 1.0 C2A D:HEM201 4.2 45.6 1.0 C3A D:HEM201 4.2 39.7 1.0 C2C D:HEM201 4.3 25.6 1.0 C3C D:HEM201 4.3 26.0 1.0 C2B D:HEM201 4.3 28.7 1.0 C3B D:HEM201 4.4 28.1 1.0 NE2 D:HIS63 4.5 60.1 1.0 CG2 D:VAL67 4.8 42.8 1.0 CE1 D:HIS63 5.0 64.5 1.0

R.Danev, W.Baumeister. Cryo-Em Single Particle Analysis with the Volta Phase Plate. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 26949259
DOI: 10.7554/ELIFE.13046