Iron in PDB 5y8a: Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)

The structure of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form), PDB code: 5y8a was solved by N.Nakamura, Y.Naoe, M.M.Rahman, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.72 / 2.00
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.088, 45.553, 113.002, 90.00, 100.35, 90.00
R / Rfree (%)	20.1 / 26

The structure of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) (pdb code 5y8a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form), PDB code: 5y8a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:37.1 occ:1.00 FE A:HEM401 0.0 37.1 1.0 NC A:HEM401 2.0 40.2 1.0 ND A:HEM401 2.0 39.4 1.0 OH A:TYR87 2.1 28.6 1.0 NB A:HEM401 2.1 41.1 1.0 NA A:HEM401 2.1 38.2 1.0 C4C A:HEM401 3.0 42.3 1.0 C1D A:HEM401 3.0 44.8 1.0 CZ A:TYR87 3.0 24.2 1.0 C1C A:HEM401 3.0 39.6 1.0 C4D A:HEM401 3.0 40.7 1.0 C1A A:HEM401 3.1 43.9 1.0 C4B A:HEM401 3.1 40.7 1.0 C1B A:HEM401 3.2 43.4 1.0 C4A A:HEM401 3.2 37.4 1.0 CHD A:HEM401 3.3 43.0 1.0 CHA A:HEM401 3.4 41.8 1.0 CHC A:HEM401 3.5 38.7 1.0 CHB A:HEM401 3.6 44.6 1.0 CE1 A:TYR87 3.6 20.3 1.0 FE A:HEM402 3.8 45.8 1.0 CE2 A:TYR87 3.9 23.7 1.0 ND A:HEM402 3.9 45.2 1.0 NA A:HEM402 4.1 41.3 1.0 C2D A:HEM401 4.2 48.2 1.0 C3C A:HEM401 4.2 43.5 1.0 C2C A:HEM401 4.2 42.5 1.0 C3D A:HEM401 4.2 49.8 1.0 NE2 A:GLN88 4.3 26.5 1.0 C3B A:HEM401 4.3 44.4 1.0 C2A A:HEM401 4.3 47.3 1.0 C2B A:HEM401 4.4 44.1 1.0 C4D A:HEM402 4.4 44.7 1.0 C3A A:HEM401 4.4 42.8 1.0 C1D A:HEM402 4.4 47.8 1.0 NC A:HEM402 4.5 47.7 1.0 NH1 A:ARG89 4.5 35.5 1.0 C1A A:HEM402 4.5 41.5 1.0 NB A:HEM402 4.6 43.4 1.0 CHA A:HEM402 4.7 40.8 1.0 CD A:ARG89 4.7 33.5 1.0 C4A A:HEM402 4.7 39.9 1.0 C4C A:HEM402 4.8 49.0 1.0 CHD A:HEM402 4.8 49.4 1.0 CD1 A:TYR87 4.8 19.3 1.0

Iron binding site 2 out of 4 in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:45.8 occ:1.00 FE A:HEM402 0.0 45.8 1.0 NB A:HEM402 1.9 43.4 1.0 NC A:HEM402 2.1 47.7 1.0 NA A:HEM402 2.1 41.3 1.0 ND A:HEM402 2.2 45.2 1.0 C1B A:HEM402 2.8 43.0 1.0 C4A A:HEM402 2.9 39.9 1.0 C4B A:HEM402 3.0 45.6 1.0 C4C A:HEM402 3.1 49.0 1.0 C1D A:HEM402 3.1 47.8 1.0 C1C A:HEM402 3.1 47.7 1.0 CHB A:HEM402 3.2 39.6 1.0 C1A A:HEM402 3.2 41.5 1.0 C4D A:HEM402 3.3 44.7 1.0 CHD A:HEM402 3.4 49.4 1.0 CHC A:HEM402 3.5 47.5 1.0 NA A:HEM401 3.6 38.2 1.0 CHA A:HEM402 3.7 40.8 1.0 FE A:HEM401 3.8 37.1 1.0 O A:HOH529 4.0 33.7 1.0 C2B A:HEM402 4.0 44.4 1.0 NB A:HEM401 4.1 41.1 1.0 ND A:HEM401 4.1 39.4 1.0 C3B A:HEM402 4.1 45.6 1.0 C4A A:HEM401 4.2 37.4 1.0 C1A A:HEM401 4.2 43.9 1.0 C3A A:HEM402 4.2 40.2 1.0 C3C A:HEM402 4.3 50.0 1.0 C2C A:HEM402 4.3 48.7 1.0 C2D A:HEM402 4.4 48.8 1.0 CD2 A:LEU190 4.4 28.1 0.5 C2A A:HEM402 4.4 42.4 1.0 C3D A:HEM402 4.5 48.0 1.0 NC A:HEM401 4.5 40.2 1.0 CHB A:HEM401 4.5 44.6 1.0 C1B A:HEM401 4.5 43.4 1.0 CHA A:HEM401 4.5 41.8 1.0 C4D A:HEM401 4.5 40.7 1.0 CD2 A:LEU190 4.5 27.6 0.6 C1D A:HEM401 4.9 44.8 1.0 C4B A:HEM401 4.9 40.7 1.0 C3A A:HEM401 5.0 42.8 1.0

Iron binding site 3 out of 4 in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:31.9 occ:1.00 FE B:HEM401 0.0 31.9 1.0 NC B:HEM401 2.0 31.3 1.0 NB B:HEM401 2.1 32.6 1.0 OH B:TYR87 2.1 25.3 1.0 ND B:HEM401 2.1 34.5 1.0 NA B:HEM401 2.1 38.4 1.0 C4B B:HEM401 3.0 31.0 1.0 C1C B:HEM401 3.0 30.0 1.0 C4C B:HEM401 3.1 33.4 1.0 C1B B:HEM401 3.1 34.5 1.0 C1D B:HEM401 3.1 34.8 1.0 C4A B:HEM401 3.1 41.9 1.0 C4D B:HEM401 3.1 38.0 1.0 C1A B:HEM401 3.1 40.9 1.0 CZ B:TYR87 3.1 26.2 1.0 CHC B:HEM401 3.4 28.9 1.0 CHD B:HEM401 3.4 32.9 1.0 CHB B:HEM401 3.4 41.2 1.0 CHA B:HEM401 3.5 39.8 1.0 CE1 B:TYR87 3.8 24.2 1.0 ND B:HEM402 3.9 36.1 1.0 NA B:HEM402 3.9 43.9 1.0 CE2 B:TYR87 4.0 26.4 1.0 NE2 B:GLN88 4.1 17.6 1.0 FE B:HEM402 4.1 43.6 1.0 C4D B:HEM402 4.1 40.0 1.0 C1A B:HEM402 4.2 41.1 1.0 C3B B:HEM401 4.2 40.1 1.0 C2B B:HEM401 4.3 41.5 1.0 C2C B:HEM401 4.3 31.9 1.0 C3C B:HEM401 4.3 33.0 1.0 C2D B:HEM401 4.3 36.5 1.0 CHA B:HEM402 4.3 40.2 1.0 C3D B:HEM401 4.3 39.3 1.0 C3A B:HEM401 4.3 46.8 1.0 C2A B:HEM401 4.3 45.8 1.0 C1D B:HEM402 4.5 41.2 1.0 CD B:ARG89 4.5 24.8 1.0 C4A B:HEM402 4.6 46.1 1.0 NB B:HEM402 4.8 53.6 1.0 NC B:HEM402 4.8 44.8 1.0 C3D B:HEM402 4.8 43.2 1.0

Iron binding site 4 out of 4 in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:43.6 occ:1.00 FE B:HEM402 0.0 43.6 1.0 NC B:HEM402 1.9 44.8 1.0 NB B:HEM402 2.0 53.6 1.0 ND B:HEM402 2.1 36.1 1.0 NA B:HEM402 2.2 43.9 1.0 C4C B:HEM402 2.9 43.4 1.0 C1C B:HEM402 2.9 49.7 1.0 C4B B:HEM402 3.0 56.6 1.0 C1B B:HEM402 3.0 55.0 1.0 C1D B:HEM402 3.0 41.2 1.0 C4A B:HEM402 3.1 46.1 1.0 C4D B:HEM402 3.3 40.0 1.0 C1A B:HEM402 3.3 41.1 1.0 CHD B:HEM402 3.3 42.4 1.0 CHC B:HEM402 3.3 53.2 1.0 CHB B:HEM402 3.4 51.2 1.0 NA B:HEM401 3.5 38.4 1.0 CHA B:HEM402 3.7 40.2 1.0 C1A B:HEM401 3.8 40.9 1.0 C4A B:HEM401 4.0 41.9 1.0 FE B:HEM401 4.1 31.9 1.0 C3C B:HEM402 4.1 45.0 1.0 ND B:HEM401 4.1 34.5 1.0 C2C B:HEM402 4.1 48.9 1.0 CHA B:HEM401 4.1 39.8 1.0 C2B B:HEM402 4.2 60.9 1.0 C3B B:HEM402 4.2 61.8 1.0 C4D B:HEM401 4.3 38.0 1.0 C2D B:HEM402 4.3 43.8 1.0 CE1 B:HIS192 4.3 27.4 0.4 ND1 B:HIS192 4.4 29.3 0.4 CD2 B:LEU190 4.4 38.0 0.4 CD2 B:LEU190 4.4 37.6 0.6 C3A B:HEM402 4.4 45.2 1.0 C3D B:HEM402 4.4 43.2 1.0 C2A B:HEM402 4.5 43.2 1.0 CHB B:HEM401 4.5 41.2 1.0 NB B:HEM401 4.5 32.6 1.0 C2A B:HEM401 4.6 45.8 1.0 C3A B:HEM401 4.7 46.8 1.0 CD1 B:LEU190 4.7 34.9 0.4 CG B:LEU190 4.8 38.6 0.4 C1B B:HEM401 4.8 34.5 1.0 CG B:LEU190 4.9 38.5 0.6 CD1 B:LEU190 4.9 34.8 0.6

Y.Naoe, N.Nakamura, M.M.Rahman, T.Tosha, S.Nagatoishi, K.Tsumoto, Y.Shiro, H.Sugimoto. Structural Basis For Binding and Transfer of Heme in Bacterial Heme-Acquisition Systems Proteins V. 85 2217 2017.
ISSN: ESSN 1097-0134
PubMed: 28913898
DOI: 10.1002/PROT.25386