Iron in PDB 8vyl: The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11

The structure of The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11, PDB code: 8vyl was solved by R.Grinter, S.Binks, D.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.89 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	188.761, 74.837, 57.875, 90, 91.44, 90
R / Rfree (%)	20.8 / 26.6

The binding sites of Iron atom in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11 (pdb code 8vyl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11, PDB code: 8vyl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.7 occ:1.00 FE A:HEM201 0.0 27.7 1.0 NC A:HEM201 2.0 25.6 1.0 NB A:HEM201 2.0 29.1 1.0 NE2 A:HIS87 2.0 30.4 1.0 NA A:HEM201 2.0 28.2 1.0 ND A:HEM201 2.1 29.6 1.0 O A:HOH307 2.3 27.2 1.0 CD2 A:HIS87 3.0 23.6 1.0 CE1 A:HIS87 3.0 31.5 1.0 C1C A:HEM201 3.0 24.4 1.0 C4B A:HEM201 3.0 28.3 1.0 C1B A:HEM201 3.0 24.3 1.0 C4C A:HEM201 3.0 22.2 1.0 C4A A:HEM201 3.1 29.3 1.0 C1A A:HEM201 3.1 29.6 1.0 C4D A:HEM201 3.1 30.1 1.0 C1D A:HEM201 3.1 26.6 1.0 CHC A:HEM201 3.4 24.5 1.0 CHB A:HEM201 3.4 28.3 1.0 CHD A:HEM201 3.5 25.8 1.0 CHA A:HEM201 3.5 29.6 1.0 ND1 A:HIS87 4.1 29.6 1.0 CG A:HIS87 4.1 31.9 1.0 C2C A:HEM201 4.2 24.5 1.0 C3C A:HEM201 4.2 21.6 1.0 C2B A:HEM201 4.2 29.9 1.0 C3B A:HEM201 4.3 25.4 1.0 C3A A:HEM201 4.3 30.1 1.0 C2A A:HEM201 4.3 34.5 1.0 C3D A:HEM201 4.3 31.8 1.0 C2D A:HEM201 4.3 27.3 1.0 NE2 A:HIS58 4.3 29.4 1.0 HHC A:HEM201 4.3 29.4 1.0 HHB A:HEM201 4.4 34.0 1.0 HHA A:HEM201 4.4 35.6 1.0 HHD A:HEM201 4.4 31.0 1.0 CE1 A:HIS58 4.5 29.8 1.0 CG2 A:VAL62 4.8 25.2 1.0

Iron binding site 2 out of 4 in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:29.5 occ:1.00 FE C:HEM201 0.0 29.5 1.0 NB C:HEM201 2.0 27.4 1.0 ND C:HEM201 2.1 27.9 1.0 NE2 C:HIS87 2.1 30.0 1.0 NA C:HEM201 2.1 31.3 1.0 NC C:HEM201 2.1 28.9 1.0 O C:HOH304 2.5 31.6 1.0 CE1 C:HIS87 3.0 32.9 1.0 C4B C:HEM201 3.0 30.1 1.0 C1B C:HEM201 3.1 34.0 1.0 C1C C:HEM201 3.1 30.0 1.0 C4A C:HEM201 3.1 33.8 1.0 C1D C:HEM201 3.1 35.1 1.0 C4D C:HEM201 3.1 31.6 1.0 C4C C:HEM201 3.1 28.5 1.0 C1A C:HEM201 3.1 32.9 1.0 CD2 C:HIS87 3.1 28.9 1.0 CHC C:HEM201 3.4 31.3 1.0 CHB C:HEM201 3.4 30.8 1.0 CHD C:HEM201 3.4 29.0 1.0 CHA C:HEM201 3.4 32.3 1.0 ND1 C:HIS87 4.1 31.3 1.0 NE2 C:HIS58 4.1 31.7 1.0 CG C:HIS87 4.2 29.2 1.0 C3B C:HEM201 4.3 32.4 1.0 C2B C:HEM201 4.3 32.8 1.0 C3A C:HEM201 4.3 32.8 1.0 C2C C:HEM201 4.3 27.3 1.0 C2D C:HEM201 4.3 31.9 1.0 C2A C:HEM201 4.3 34.7 1.0 C3D C:HEM201 4.3 32.2 1.0 C3C C:HEM201 4.3 29.9 1.0 CE1 C:HIS58 4.5 32.3 1.0 CG2 C:VAL62 4.8 33.7 1.0

Iron binding site 3 out of 4 in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:25.1 occ:1.00 FE B:HEM201 0.0 25.1 1.0 ND B:HEM201 2.0 22.6 1.0 NC B:HEM201 2.0 21.5 1.0 NB B:HEM201 2.1 21.8 1.0 NE2 B:HIS92 2.1 30.0 1.0 NA B:HEM201 2.1 23.1 1.0 O B:HOH336 2.3 26.7 1.0 C1D B:HEM201 3.0 26.3 1.0 C4C B:HEM201 3.0 21.5 1.0 C4D B:HEM201 3.0 26.8 1.0 C1C B:HEM201 3.0 22.6 1.0 CD2 B:HIS92 3.1 25.0 1.0 CE1 B:HIS92 3.1 28.8 1.0 C4B B:HEM201 3.1 21.3 1.0 C1B B:HEM201 3.1 24.3 1.0 C1A B:HEM201 3.1 25.3 1.0 C4A B:HEM201 3.1 21.8 1.0 CHD B:HEM201 3.3 23.4 1.0 CHC B:HEM201 3.4 23.6 1.0 CHA B:HEM201 3.5 23.0 1.0 CHB B:HEM201 3.5 24.7 1.0 ND1 B:HIS92 4.2 22.9 1.0 CG B:HIS92 4.2 27.8 1.0 C2D B:HEM201 4.2 26.4 1.0 C3C B:HEM201 4.2 24.4 1.0 C3D B:HEM201 4.2 27.9 1.0 C2C B:HEM201 4.3 21.4 1.0 NE2 B:HIS63 4.3 25.7 1.0 C3B B:HEM201 4.3 22.5 1.0 C2B B:HEM201 4.3 24.2 1.0 C3A B:HEM201 4.3 28.1 1.0 C2A B:HEM201 4.3 28.6 1.0 CG2 B:VAL67 4.5 23.4 1.0 CE1 B:HIS63 4.7 28.0 1.0

Iron binding site 4 out of 4 in the The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Human Hemoglobin in Complex with Nanobody BTNBE11 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:42.8 occ:1.00 FE D:HEM201 0.0 42.8 1.0 ND D:HEM201 2.0 44.8 1.0 NC D:HEM201 2.0 39.7 1.0 NA D:HEM201 2.1 45.1 1.0 NB D:HEM201 2.1 41.4 1.0 O D:HOH324 2.1 43.9 1.0 NE2 D:HIS92 2.4 41.5 1.0 C4C D:HEM201 3.0 39.4 1.0 C1D D:HEM201 3.0 42.4 1.0 C4D D:HEM201 3.0 43.1 1.0 C1C D:HEM201 3.0 39.8 1.0 C1A D:HEM201 3.1 46.3 1.0 CD2 D:HIS92 3.1 42.4 1.0 C4A D:HEM201 3.1 48.1 1.0 C4B D:HEM201 3.1 39.3 1.0 C1B D:HEM201 3.1 46.1 1.0 CHD D:HEM201 3.4 39.4 1.0 CHA D:HEM201 3.4 44.6 1.0 CHC D:HEM201 3.4 40.4 1.0 CHB D:HEM201 3.5 48.5 1.0 CE1 D:HIS92 3.6 48.2 1.0 C3C D:HEM201 4.2 38.7 1.0 C2D D:HEM201 4.2 41.8 1.0 C3D D:HEM201 4.2 42.9 1.0 C2C D:HEM201 4.2 36.6 1.0 C2A D:HEM201 4.3 49.7 1.0 C3A D:HEM201 4.3 50.0 1.0 CG D:HIS92 4.3 44.5 1.0 C3B D:HEM201 4.4 43.5 1.0 C2B D:HEM201 4.4 47.0 1.0 CE1 D:HIS63 4.4 44.8 1.0 ND1 D:HIS92 4.5 48.0 1.0 NE2 D:HIS63 4.6 42.1 1.0 CG2 D:VAL67 4.8 52.1 1.0

D.R.Fox, I.Samuels, S.Binks, R.Grinter. The Structure of A Haemoglobin-Nanobody Complex Reveals Human Beta-Subunit-Specific Interactions. Febs Lett. 2024.
ISSN: ISSN 0014-5793
PubMed: 38880764
DOI: 10.1002/1873-3468.14958