Iron in PDB 8j5r: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State

The binding sites of Iron atom in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State (pdb code 8j5r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State, PDB code: 8j5r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:54.2 occ:1.00 FE1 D:SF4701 0.0 54.2 1.0 SG D:CYS299 2.2 45.6 1.0 S2 D:SF4701 2.2 54.2 1.0 S3 D:SF4701 2.3 54.2 1.0 S4 D:SF4701 2.3 54.2 1.0 FE2 D:SF4701 2.7 54.2 1.0 FE3 D:SF4701 2.7 54.2 1.0 FE4 D:SF4701 2.7 54.2 1.0 CB D:CYS299 3.2 45.6 1.0 S1 D:SF4701 3.9 54.2 1.0 CA D:CYS299 4.3 45.6 1.0 CD D:ARG319 4.4 46.8 1.0 CB D:CYS286 4.5 40.8 1.0 SG D:CYS317 4.5 43.6 1.0 CG1 D:ILE318 4.6 45.2 1.0 SG D:CYS286 4.7 40.8 1.0 CA D:VAL295 4.8 42.8 1.0 SG D:CYS292 4.8 41.3 1.0 CD1 D:ILE318 5.0 45.2 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:54.2 occ:1.00 FE2 D:SF4701 0.0 54.2 1.0 SG D:CYS286 2.2 40.8 1.0 S1 D:SF4701 2.3 54.2 1.0 S3 D:SF4701 2.3 54.2 1.0 S4 D:SF4701 2.3 54.2 1.0 FE1 D:SF4701 2.7 54.2 1.0 FE4 D:SF4701 2.7 54.2 1.0 FE3 D:SF4701 2.8 54.2 1.0 CB D:CYS286 2.9 40.8 1.0 S2 D:SF4701 3.8 54.2 1.0 CA D:CYS286 4.4 40.8 1.0 CB D:PHE288 4.4 38.9 1.0 SG D:CYS299 4.7 45.6 1.0 CG D:PRO304 4.7 42.1 1.0 N D:ALA289 4.8 38.9 1.0 SG D:CYS317 4.8 43.6 1.0 O D:ALA316 4.9 41.0 1.0 CB D:CYS299 4.9 45.6 1.0 CE D:MET248 5.0 41.0 1.0 N D:PHE288 5.0 38.9 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:54.2 occ:1.00 FE3 D:SF4701 0.0 54.2 1.0 S2 D:SF4701 2.2 54.2 1.0 S1 D:SF4701 2.3 54.2 1.0 S4 D:SF4701 2.3 54.2 1.0 SG D:CYS292 2.4 41.3 1.0 FE4 D:SF4701 2.6 54.2 1.0 FE1 D:SF4701 2.7 54.2 1.0 FE2 D:SF4701 2.8 54.2 1.0 CB D:CYS292 3.2 41.3 1.0 S3 D:SF4701 3.9 54.2 1.0 CD1 D:PHE288 4.5 38.9 1.0 CG D:PRO249 4.5 41.2 1.0 CA D:CYS292 4.6 41.3 1.0 CA D:VAL295 4.6 42.8 1.0 SG D:CYS317 4.7 43.6 1.0 SG D:CYS299 4.7 45.6 1.0 N D:VAL295 4.7 42.8 1.0 SG D:CYS286 4.8 40.8 1.0 CB D:VAL295 4.9 42.8 1.0 CB D:PHE288 4.9 38.9 1.0 CB D:PRO249 4.9 41.2 1.0 C D:LEU294 5.0 44.3 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Resting State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe701 b:54.2 occ:1.00 FE4 D:SF4701 0.0 54.2 1.0 S2 D:SF4701 2.2 54.2 1.0 SG D:CYS317 2.3 43.6 1.0 S3 D:SF4701 2.3 54.2 1.0 S1 D:SF4701 2.3 54.2 1.0 FE3 D:SF4701 2.6 54.2 1.0 FE2 D:SF4701 2.7 54.2 1.0 FE1 D:SF4701 2.7 54.2 1.0 CB D:CYS317 3.2 43.6 1.0 CA D:CYS317 3.8 43.6 1.0 S4 D:SF4701 3.9 54.2 1.0 N D:ILE318 4.2 45.2 1.0 CD D:PRO249 4.2 41.2 1.0 CG D:PRO249 4.3 41.2 1.0 C D:CYS317 4.5 43.6 1.0 SD D:MET248 4.7 41.0 1.0 SG D:CYS292 4.7 41.3 1.0 SG D:CYS299 4.7 45.6 1.0 SG D:CYS286 4.7 40.8 1.0 N D:ARG319 4.7 46.8 1.0 O D:ALA316 5.0 41.0 1.0

X.Yang, T.Hu, J.Liang, Z.Xiong, Z.Lin, Y.Zhao, X.Zhou, Y.Gao, S.Sun, X.Yang, L.W.Guddat, H.Yang, Z.Rao, B.Zhang. An Oligopeptide Permease, Oppabcd, Requires An Iron-Sulfur Cluster Domain For Functionality Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01256-Z