Iron in PDB 7w7d: Heme Exporter Hrtba in Complex with Heme

The structure of Heme Exporter Hrtba in Complex with Heme, PDB code: 7w7d was solved by T.Hisano, H.Nakamura, M.M.Rahman, T.Tosha, Y.Shiro, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.29 / 3.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	82.585, 135.026, 160.969, 112.49, 100.41, 93.78
R / Rfree (%)	25.5 / 28.5

The binding sites of Iron atom in the Heme Exporter Hrtba in Complex with Heme (pdb code 7w7d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Heme Exporter Hrtba in Complex with Heme, PDB code: 7w7d:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Heme Exporter Hrtba in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heme Exporter Hrtba in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:208.4 occ:0.78 FE D:HEM401 0.0 208.4 0.8 NB D:HEM401 2.0 208.4 0.8 NC D:HEM401 2.1 208.4 0.8 ND D:HEM401 2.1 208.4 0.8 NA D:HEM401 2.1 208.4 0.8 OE2 D:GLU219 2.1 188.8 1.0 OE2 B:GLU219 2.1 163.3 1.0 C1B D:HEM401 3.1 208.4 0.8 C4B D:HEM401 3.1 208.4 0.8 C4C D:HEM401 3.1 208.4 0.8 C1C D:HEM401 3.1 208.4 0.8 C4D D:HEM401 3.1 208.4 0.8 C4A D:HEM401 3.1 208.4 0.8 C1D D:HEM401 3.1 208.4 0.8 C1A D:HEM401 3.1 208.4 0.8 CD B:GLU219 3.3 163.0 1.0 CD D:GLU219 3.4 192.1 1.0 CHB D:HEM401 3.4 268.4 0.8 CHC D:HEM401 3.4 268.4 0.8 CHA D:HEM401 3.4 268.4 0.8 CHD D:HEM401 3.4 268.4 0.8 CG B:GLU219 4.0 160.3 1.0 OE1 D:GLU219 4.2 195.1 1.0 CG D:GLU219 4.3 190.7 1.0 OE1 B:GLU219 4.3 164.4 1.0 C3B D:HEM401 4.3 208.4 0.8 C2B D:HEM401 4.3 208.4 0.8 C3C D:HEM401 4.3 208.4 0.8 C2C D:HEM401 4.3 208.4 0.8 C3A D:HEM401 4.3 208.4 0.8 C3D D:HEM401 4.3 208.4 0.8 C2D D:HEM401 4.3 208.4 0.8 C2A D:HEM401 4.3 208.4 0.8 HHB D:HEM401 4.4 268.4 0.8 HHC D:HEM401 4.4 268.4 0.8 HHA D:HEM401 4.4 268.4 0.8 HHD D:HEM401 4.4 268.4 0.8 CB B:GLU219 4.7 159.4 1.0 CD1 D:LEU39 4.8 254.6 1.0 CD1 B:LEU39 5.0 166.7 1.0

Iron binding site 2 out of 2 in the Heme Exporter Hrtba in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heme Exporter Hrtba in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:288.4 occ:0.81 FE F:HEM401 0.0 288.4 0.8 ND F:HEM401 2.0 208.4 0.8 NA F:HEM401 2.0 208.4 0.8 NB F:HEM401 2.0 208.4 0.8 NC F:HEM401 2.1 208.4 0.8 OE2 F:GLU219 2.1 202.3 1.0 OE2 H:GLU219 2.1 196.8 1.0 C4B F:HEM401 3.1 238.4 0.8 C4D F:HEM401 3.1 238.4 0.8 C1B F:HEM401 3.1 238.4 0.8 C4A F:HEM401 3.1 238.4 0.8 C1A F:HEM401 3.1 238.4 0.8 C1D F:HEM401 3.1 238.4 0.8 C1C F:HEM401 3.1 238.4 0.8 C4C F:HEM401 3.1 238.4 0.8 CD F:GLU219 3.2 198.4 1.0 CD H:GLU219 3.3 198.3 1.0 CHA F:HEM401 3.4 288.4 0.8 CHC F:HEM401 3.4 288.4 0.8 CHB F:HEM401 3.4 288.4 0.8 CHD F:HEM401 3.5 288.4 0.8 CG F:GLU219 3.7 196.6 1.0 CG H:GLU219 4.2 198.3 1.0 OE1 H:GLU219 4.2 199.6 1.0 C3B F:HEM401 4.3 238.4 0.8 C2B F:HEM401 4.3 238.4 0.8 C3D F:HEM401 4.3 238.4 0.8 C3A F:HEM401 4.3 238.4 0.8 OE1 F:GLU219 4.3 195.2 1.0 C2A F:HEM401 4.3 238.4 0.8 C2D F:HEM401 4.3 238.4 0.8 C2C F:HEM401 4.3 238.4 0.8 C3C F:HEM401 4.3 238.4 0.8 HHA F:HEM401 4.4 288.4 0.8 HHC F:HEM401 4.4 288.4 0.8 HHB F:HEM401 4.4 288.4 0.8 HHD F:HEM401 4.4 288.4 0.8 CB F:GLU219 4.5 194.2 1.0 CE1 H:HIS163 4.9 207.4 1.0 CD1 H:LEU39 4.9 253.3 1.0

H.Nakamura, T.Hisano, M.M.Rahman, T.Tosha, M.Shirouzu, Y.Shiro. Structural Basis For Heme Detoxification By An Atp-Binding Cassette-Type Efflux Pump in Gram-Positive Pathogenic Bacteria. Proc.Natl.Acad.Sci.Usa V. 119 85119 2022.
ISSN: ESSN 1091-6490
PubMed: 35767641
DOI: 10.1073/PNAS.2123385119