Iron in PDB 5y89: Periplasmic Heme-Binding Protein Bhut in Complex with One Heme (Holo- 1)

The structure of Periplasmic Heme-Binding Protein Bhut in Complex with One Heme (Holo- 1), PDB code: 5y89 was solved by Y.Naoe, N.Nakamura, 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)	50.00 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	199.166, 199.166, 117.736, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22

The binding sites of Iron atom in the Periplasmic Heme-Binding Protein Bhut in Complex with One Heme (Holo- 1) (pdb code 5y89). 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 One Heme (Holo- 1), PDB code: 5y89:
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 One Heme (Holo- 1)


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 One Heme (Holo- 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:38.5 occ:0.50 FE A:HEM401 0.0 38.5 0.5 FE A:HEM401 0.1 47.5 0.5 ND A:HEM401 1.9 38.5 0.5 ND A:HEM401 1.9 46.7 0.5 NA A:HEM401 1.9 46.9 0.5 OH A:TYR87 2.0 39.9 1.0 NA A:HEM401 2.0 37.4 0.5 NC A:HEM401 2.1 37.2 0.5 NB A:HEM401 2.1 44.8 0.5 NB A:HEM401 2.1 36.9 0.5 NC A:HEM401 2.2 45.7 0.5 C4D A:HEM401 2.9 46.2 0.5 C1D A:HEM401 2.9 39.9 0.5 C1A A:HEM401 2.9 47.9 0.5 C4D A:HEM401 2.9 39.1 0.5 C1D A:HEM401 2.9 44.9 0.5 C4C A:HEM401 3.0 39.2 0.5 C4A A:HEM401 3.0 48.2 0.5 C1B A:HEM401 3.0 46.9 0.5 C4B A:HEM401 3.0 45.8 0.5 CZ A:TYR87 3.0 42.7 1.0 C1A A:HEM401 3.1 37.2 0.5 C4B A:HEM401 3.1 37.2 0.5 C1C A:HEM401 3.1 38.2 0.5 C4A A:HEM401 3.1 35.8 0.5 C1B A:HEM401 3.1 35.3 0.5 C4C A:HEM401 3.1 44.0 0.5 C1C A:HEM401 3.2 46.0 0.5 CHA A:HEM401 3.3 47.1 0.5 CHD A:HEM401 3.3 39.7 0.5 CHB A:HEM401 3.4 47.6 0.5 CHA A:HEM401 3.4 38.0 0.5 CHC A:HEM401 3.4 37.0 0.5 CHC A:HEM401 3.5 45.1 0.5 CHD A:HEM401 3.5 43.4 0.5 CHB A:HEM401 3.5 34.9 0.5 CE1 A:TYR87 3.6 40.8 1.0 NH1 A:ARG89 3.9 41.9 1.0 CH3 A:ACT402 4.0 46.7 1.0 CE2 A:TYR87 4.0 39.6 1.0 C2A A:HEM401 4.1 47.5 0.5 C3A A:HEM401 4.1 48.0 0.5 C3D A:HEM401 4.2 47.5 0.5 C2D A:HEM401 4.2 39.9 0.5 C2D A:HEM401 4.2 45.1 0.5 C3D A:HEM401 4.2 39.2 0.5 C3C A:HEM401 4.2 40.2 0.5 C2B A:HEM401 4.2 47.5 0.5 C3B A:HEM401 4.2 47.0 0.5 C2A A:HEM401 4.3 37.8 0.5 C2C A:HEM401 4.3 39.5 0.5 C3A A:HEM401 4.3 36.0 0.5 C2B A:HEM401 4.3 34.7 0.5 C3C A:HEM401 4.4 42.9 0.5 C3B A:HEM401 4.4 36.5 0.5 C2C A:HEM401 4.4 45.2 0.5 O A:HOH520 4.5 49.1 1.0 CZ A:ARG89 4.8 40.6 1.0 CB A:HIS192 4.8 47.1 1.0 CD1 A:TYR87 4.9 42.3 1.0

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


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 One Heme (Holo- 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:47.5 occ:0.50 FE A:HEM401 0.0 47.5 0.5 FE A:HEM401 0.1 38.5 0.5 ND A:HEM401 1.9 46.7 0.5 ND A:HEM401 1.9 38.5 0.5 NA A:HEM401 2.0 46.9 0.5 OH A:TYR87 2.0 39.9 1.0 NA A:HEM401 2.0 37.4 0.5 NC A:HEM401 2.1 37.2 0.5 NB A:HEM401 2.1 44.8 0.5 NB A:HEM401 2.1 36.9 0.5 NC A:HEM401 2.1 45.7 0.5 C4D A:HEM401 2.9 46.2 0.5 C1D A:HEM401 2.9 44.9 0.5 C1D A:HEM401 2.9 39.9 0.5 C1A A:HEM401 2.9 47.9 0.5 C4D A:HEM401 3.0 39.1 0.5 C4C A:HEM401 3.0 39.2 0.5 C4B A:HEM401 3.0 45.8 0.5 C1B A:HEM401 3.0 46.9 0.5 C4B A:HEM401 3.0 37.2 0.5 C4A A:HEM401 3.0 48.2 0.5 CZ A:TYR87 3.0 42.7 1.0 C1B A:HEM401 3.1 35.3 0.5 C1A A:HEM401 3.1 37.2 0.5 C1C A:HEM401 3.1 38.2 0.5 C4A A:HEM401 3.1 35.8 0.5 C4C A:HEM401 3.1 44.0 0.5 C1C A:HEM401 3.1 46.0 0.5 CHA A:HEM401 3.3 47.1 0.5 CHD A:HEM401 3.4 39.7 0.5 CHC A:HEM401 3.4 37.0 0.5 CHD A:HEM401 3.4 43.4 0.5 CHC A:HEM401 3.4 45.1 0.5 CHB A:HEM401 3.4 47.6 0.5 CHB A:HEM401 3.5 34.9 0.5 CHA A:HEM401 3.5 38.0 0.5 CE1 A:TYR87 3.6 40.8 1.0 NH1 A:ARG89 3.9 41.9 1.0 CH3 A:ACT402 4.0 46.7 1.0 CE2 A:TYR87 4.0 39.6 1.0 C3D A:HEM401 4.1 47.5 0.5 C2A A:HEM401 4.2 47.5 0.5 C2D A:HEM401 4.2 45.1 0.5 C3A A:HEM401 4.2 48.0 0.5 C3C A:HEM401 4.2 40.2 0.5 C2D A:HEM401 4.2 39.9 0.5 C2B A:HEM401 4.2 47.5 0.5 C3D A:HEM401 4.2 39.2 0.5 C3B A:HEM401 4.2 47.0 0.5 C2A A:HEM401 4.3 37.8 0.5 C3A A:HEM401 4.3 36.0 0.5 C2C A:HEM401 4.3 39.5 0.5 C2B A:HEM401 4.3 34.7 0.5 C3C A:HEM401 4.3 42.9 0.5 C2C A:HEM401 4.3 45.2 0.5 C3B A:HEM401 4.3 36.5 0.5 O A:HOH520 4.5 49.1 1.0 CZ A:ARG89 4.8 40.6 1.0 CB A:HIS192 4.8 47.1 1.0 CD1 A:TYR87 4.9 42.3 1.0 CD A:ARG89 5.0 43.0 1.0

Iron binding site 3 out of 4 in the Periplasmic Heme-Binding Protein Bhut in Complex with One Heme (Holo- 1)


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 One Heme (Holo- 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:25.2 occ:0.50 FE B:HEM401 0.0 25.2 0.5 FE B:HEM401 0.1 30.1 0.5 OH B:TYR87 1.9 25.9 1.0 ND B:HEM401 1.9 28.3 0.5 NC B:HEM401 1.9 28.5 0.5 ND B:HEM401 2.0 24.4 0.5 NB B:HEM401 2.0 23.9 0.5 NA B:HEM401 2.0 23.8 0.5 NB B:HEM401 2.1 28.7 0.5 NA B:HEM401 2.1 28.8 0.5 NC B:HEM401 2.1 24.6 0.5 C1D B:HEM401 2.9 29.0 0.5 C4C B:HEM401 2.9 30.4 0.5 CZ B:TYR87 2.9 25.7 1.0 C1D B:HEM401 2.9 24.0 0.5 C1B B:HEM401 2.9 25.0 0.5 C4B B:HEM401 3.0 25.5 0.5 C4D B:HEM401 3.0 24.2 0.5 C4D B:HEM401 3.0 28.2 0.5 C1C B:HEM401 3.0 30.6 0.5 C4B B:HEM401 3.0 30.8 0.5 C1A B:HEM401 3.0 23.7 0.5 C4A B:HEM401 3.0 24.0 0.5 C4A B:HEM401 3.1 28.5 0.5 C1A B:HEM401 3.1 28.8 0.5 C1B B:HEM401 3.1 28.3 0.5 C1C B:HEM401 3.1 26.6 0.5 C4C B:HEM401 3.1 24.5 0.5 CHD B:HEM401 3.3 28.2 0.5 CHC B:HEM401 3.4 30.2 0.5 CHD B:HEM401 3.4 24.8 0.5 CHB B:HEM401 3.4 23.3 0.5 CHC B:HEM401 3.4 25.4 0.5 CHA B:HEM401 3.5 23.9 0.5 CHA B:HEM401 3.5 28.4 0.5 CHB B:HEM401 3.5 29.1 0.5 CE1 B:TYR87 3.6 25.4 1.0 NH1 B:ARG89 3.9 27.6 1.0 CE2 B:TYR87 3.9 25.6 1.0 CH3 B:ACT402 4.1 26.9 1.0 C3C B:HEM401 4.1 29.6 0.5 C2C B:HEM401 4.2 30.4 0.5 C2D B:HEM401 4.2 27.9 0.5 C2B B:HEM401 4.2 24.4 0.5 C3D B:HEM401 4.2 28.7 0.5 C3D B:HEM401 4.2 24.3 0.5 C2A B:HEM401 4.2 24.1 0.5 C2D B:HEM401 4.2 23.9 0.5 C3B B:HEM401 4.2 25.5 0.5 C3A B:HEM401 4.2 23.3 0.5 C2A B:HEM401 4.3 28.9 0.5 C3B B:HEM401 4.3 29.0 0.5 C3A B:HEM401 4.3 28.2 0.5 C2B B:HEM401 4.3 28.2 0.5 C2C B:HEM401 4.3 25.9 0.5 C3C B:HEM401 4.4 24.8 0.5 CZ B:ARG89 4.7 28.1 1.0 O B:HOH610 4.7 50.3 1.0 CB B:HIS192 4.8 27.0 1.0 CD1 B:TYR87 4.9 25.4 1.0 CD B:ARG89 4.9 28.3 1.0

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


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 One Heme (Holo- 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:30.1 occ:0.50 FE B:HEM401 0.0 30.1 0.5 FE B:HEM401 0.1 25.2 0.5 OH B:TYR87 1.8 25.9 1.0 ND B:HEM401 1.9 28.3 0.5 ND B:HEM401 1.9 24.4 0.5 NA B:HEM401 2.0 23.8 0.5 NC B:HEM401 2.0 28.5 0.5 NB B:HEM401 2.0 23.9 0.5 NA B:HEM401 2.0 28.8 0.5 NB B:HEM401 2.1 28.7 0.5 NC B:HEM401 2.2 24.6 0.5 C1D B:HEM401 2.9 29.0 0.5 C4D B:HEM401 2.9 24.2 0.5 C4D B:HEM401 2.9 28.2 0.5 C1D B:HEM401 2.9 24.0 0.5 C4C B:HEM401 2.9 30.4 0.5 CZ B:TYR87 2.9 25.7 1.0 C1A B:HEM401 3.0 23.7 0.5 C1B B:HEM401 3.0 25.0 0.5 C4B B:HEM401 3.0 25.5 0.5 C4A B:HEM401 3.0 24.0 0.5 C1A B:HEM401 3.0 28.8 0.5 C1C B:HEM401 3.0 30.6 0.5 C4B B:HEM401 3.0 30.8 0.5 C4A B:HEM401 3.1 28.5 0.5 C1B B:HEM401 3.1 28.3 0.5 C4C B:HEM401 3.1 24.5 0.5 C1C B:HEM401 3.2 26.6 0.5 CHD B:HEM401 3.3 28.2 0.5 CHA B:HEM401 3.4 23.9 0.5 CHA B:HEM401 3.4 28.4 0.5 CHD B:HEM401 3.4 24.8 0.5 CHB B:HEM401 3.4 23.3 0.5 CHC B:HEM401 3.4 30.2 0.5 CHB B:HEM401 3.5 29.1 0.5 CHC B:HEM401 3.5 25.4 0.5 CE1 B:TYR87 3.5 25.4 1.0 NH1 B:ARG89 3.8 27.6 1.0 CE2 B:TYR87 3.9 25.6 1.0 CH3 B:ACT402 4.1 26.9 1.0 C2D B:HEM401 4.1 27.9 0.5 C3D B:HEM401 4.1 28.7 0.5 C3C B:HEM401 4.2 29.6 0.5 C3D B:HEM401 4.2 24.3 0.5 C2A B:HEM401 4.2 24.1 0.5 C2D B:HEM401 4.2 23.9 0.5 C2A B:HEM401 4.2 28.9 0.5 C3A B:HEM401 4.2 23.3 0.5 C2C B:HEM401 4.2 30.4 0.5 C2B B:HEM401 4.2 24.4 0.5 C3A B:HEM401 4.2 28.2 0.5 C3B B:HEM401 4.3 25.5 0.5 C3B B:HEM401 4.3 29.0 0.5 C2B B:HEM401 4.4 28.2 0.5 C2C B:HEM401 4.4 25.9 0.5 C3C B:HEM401 4.4 24.8 0.5 CZ B:ARG89 4.7 28.1 1.0 O B:HOH610 4.8 50.3 1.0 CD B:ARG89 4.9 28.3 1.0 CD1 B:TYR87 4.9 25.4 1.0 CB B:HIS192 4.9 27.0 1.0

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