Iron in PDB 5gj3: Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)

The structure of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2), PDB code: 5gj3 was solved by M.M.Rahman, Y.Naoe, N.Nakamura, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.21 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.326, 86.338, 118.806, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.4

The structure of Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) (pdb code 5gj3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2), PDB code: 5gj3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


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 Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:23.2 occ:0.75 FE A:HEM401 0.0 23.2 0.8 OH A:TYR140 1.9 27.0 1.0 ND A:HEM401 1.9 23.0 0.8 NA A:HEM401 2.0 22.0 0.8 NB A:HEM401 2.1 24.3 0.8 NC A:HEM401 2.1 27.4 0.8 CZ A:TYR140 2.9 21.2 1.0 C4D A:HEM401 2.9 22.2 0.8 C1A A:HEM401 3.0 21.3 0.8 C4B A:HEM401 3.0 25.8 0.8 C1D A:HEM401 3.0 23.4 0.8 C1C A:HEM401 3.1 26.4 0.8 C4A A:HEM401 3.1 23.9 0.8 C1B A:HEM401 3.1 23.6 0.8 C4C A:HEM401 3.1 26.9 0.8 CHA A:HEM401 3.3 21.7 0.8 CHC A:HEM401 3.4 24.9 0.8 CHB A:HEM401 3.5 22.0 0.8 CHD A:HEM401 3.5 25.5 0.8 CE1 A:TYR140 3.7 20.7 1.0 CE2 A:TYR140 3.7 21.1 1.0 NB A:HEM402 3.8 24.3 0.8 C1B A:HEM402 3.8 23.3 0.8 C4B A:HEM402 3.9 23.9 0.8 C2B A:HEM402 4.1 23.7 0.8 C2A A:HEM401 4.2 22.9 0.8 C3B A:HEM402 4.2 24.3 0.8 NH1 A:ARG142 4.2 34.8 1.0 C3D A:HEM401 4.2 21.8 0.8 C3A A:HEM401 4.3 23.0 0.8 C3B A:HEM401 4.3 25.3 0.8 C2D A:HEM401 4.3 23.0 0.8 C2C A:HEM401 4.3 28.8 0.8 C2B A:HEM401 4.3 23.4 0.8 C3C A:HEM401 4.3 29.1 0.8 CHB A:HEM402 4.3 24.4 0.8 NE2 A:GLN141 4.4 24.3 1.0 FE A:HEM402 4.5 22.5 0.8 CHC A:HEM402 4.5 23.4 0.8 C4A A:HEM402 4.7 23.9 0.8 NA A:HEM402 4.8 22.8 0.8 C1C A:HEM402 4.9 25.5 0.8 NC A:HEM402 4.9 23.4 0.8 CD1 A:TYR140 4.9 18.6 1.0 CMB A:HEM402 5.0 24.4 0.8 CD2 A:TYR140 5.0 19.7 1.0

Iron binding site 2 out of 2 in the Periplasmic Heme-Binding Protein Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2)


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 Rhut From Roseiflexus Sp. Rs-1 in Two-Heme Bound Form (Holo-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:22.5 occ:0.75 FE A:HEM402 0.0 22.5 0.8 ND A:HEM402 1.9 24.3 0.8 NA A:HEM402 2.0 22.8 0.8 OH A:TYR239 2.1 32.0 1.0 NC A:HEM402 2.1 23.4 0.8 NB A:HEM402 2.1 24.3 0.8 C1D A:HEM402 2.9 22.5 0.8 C4D A:HEM402 3.0 23.1 0.8 C4A A:HEM402 3.0 23.9 0.8 C1A A:HEM402 3.1 24.7 0.8 C4C A:HEM402 3.1 25.6 0.8 C1B A:HEM402 3.1 23.3 0.8 C4B A:HEM402 3.1 23.9 0.8 CZ A:TYR239 3.1 31.9 1.0 C1C A:HEM402 3.1 25.5 0.8 CHD A:HEM402 3.4 25.6 0.8 CHB A:HEM402 3.4 24.4 0.8 CHA A:HEM402 3.5 22.5 0.8 CHC A:HEM402 3.5 23.4 0.8 CE1 A:TYR239 3.6 31.2 1.0 C4D A:HEM401 3.8 22.2 0.8 CHA A:HEM401 3.8 21.7 0.8 ND A:HEM401 4.0 23.0 0.8 C1A A:HEM401 4.1 21.3 0.8 C2D A:HEM402 4.2 24.2 0.8 C3A A:HEM402 4.2 24.9 0.8 C3D A:HEM402 4.2 23.0 0.8 CE2 A:TYR239 4.2 32.2 1.0 C2A A:HEM402 4.2 26.5 0.8 C3C A:HEM402 4.3 26.2 0.8 C2B A:HEM402 4.3 23.7 0.8 C2C A:HEM402 4.3 25.1 0.8 C3B A:HEM402 4.4 24.3 0.8 C3D A:HEM401 4.4 21.8 0.8 NA A:HEM401 4.4 22.0 0.8 FE A:HEM401 4.5 23.2 0.8 NH2 A:ARG241 4.5 37.6 1.0 C1D A:HEM401 4.5 23.4 0.8 C2D A:HEM401 4.8 23.0 0.8 CD A:ARG241 4.9 35.0 1.0 CD1 A:TYR239 5.0 30.5 1.0 C2A A:HEM401 5.0 22.9 0.8

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