Iron in PDB 8j5s: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate State

The structure of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate State also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate State (pdb code 8j5s). 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 Pre- Catalytic Intermediate State, PDB code: 8j5s:
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 Pre- Catalytic Intermediate 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe705 b:38.4 occ:1.00 FE1 D:SF4705 0.0 38.4 1.0 S3 D:SF4705 2.3 38.4 1.0 S2 D:SF4705 2.3 38.4 1.0 S4 D:SF4705 2.3 38.4 1.0 SG D:CYS299 2.5 42.5 1.0 FE4 D:SF4705 2.7 38.4 1.0 FE3 D:SF4705 2.7 38.4 1.0 FE2 D:SF4705 2.7 38.4 1.0 CB D:CYS299 3.0 42.5 1.0 S1 D:SF4705 3.9 38.4 1.0 CA D:CYS299 4.1 42.5 1.0 CG1 D:ILE318 4.3 39.6 1.0 CD D:ARG319 4.5 42.6 1.0 O D:LEU294 4.6 37.9 1.0 CA D:VAL295 4.6 37.9 1.0 CG D:ARG319 4.6 42.6 1.0 CD1 D:ILE318 4.7 39.6 1.0 CB D:CYS286 4.8 34.1 1.0 SG D:CYS317 4.9 37.8 1.0 SG D:CYS286 5.0 34.1 1.0 N D:ILE296 5.0 42.1 1.0 O D:CYS299 5.0 42.5 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe705 b:38.4 occ:1.00 FE2 D:SF4705 0.0 38.4 1.0 S3 D:SF4705 2.3 38.4 1.0 S1 D:SF4705 2.3 38.4 1.0 S4 D:SF4705 2.3 38.4 1.0 SG D:CYS317 2.6 37.8 1.0 FE4 D:SF4705 2.7 38.4 1.0 FE1 D:SF4705 2.7 38.4 1.0 FE3 D:SF4705 2.7 38.4 1.0 CB D:CYS317 3.6 37.8 1.0 S2 D:SF4705 3.9 38.4 1.0 CA D:CYS317 4.0 37.8 1.0 N D:ILE318 4.3 39.6 1.0 CG D:ARG319 4.4 42.6 1.0 CD D:PRO249 4.6 33.6 1.0 CG D:PRO249 4.6 33.6 1.0 C D:CYS317 4.7 37.8 1.0 SG D:CYS292 4.8 32.4 1.0 O D:ALA316 4.8 34.7 1.0 SG D:CYS286 4.8 34.1 1.0 N D:ARG319 4.9 42.6 1.0 CG1 D:ILE318 4.9 39.6 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe705 b:38.4 occ:1.00 FE3 D:SF4705 0.0 38.4 1.0 S4 D:SF4705 2.3 38.4 1.0 S2 D:SF4705 2.3 38.4 1.0 S1 D:SF4705 2.3 38.4 1.0 SG D:CYS286 2.5 34.1 1.0 FE1 D:SF4705 2.7 38.4 1.0 FE2 D:SF4705 2.7 38.4 1.0 FE4 D:SF4705 2.7 38.4 1.0 CB D:CYS286 3.1 34.1 1.0 S3 D:SF4705 3.9 38.4 1.0 CB D:PHE288 4.4 29.5 1.0 CA D:CYS286 4.6 34.1 1.0 CB D:CYS299 4.7 42.5 1.0 N D:ALA289 4.7 30.7 1.0 C D:PHE288 4.9 29.5 1.0 CB D:CYS292 4.9 32.4 1.0 SG D:CYS292 4.9 32.4 1.0 SG D:CYS299 5.0 42.5 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe705 b:38.4 occ:1.00 FE4 D:SF4705 0.0 38.4 1.0 S3 D:SF4705 2.3 38.4 1.0 S2 D:SF4705 2.3 38.4 1.0 S1 D:SF4705 2.3 38.4 1.0 SG D:CYS292 2.5 32.4 1.0 FE2 D:SF4705 2.7 38.4 1.0 FE1 D:SF4705 2.7 38.4 1.0 FE3 D:SF4705 2.7 38.4 1.0 CB D:CYS292 3.1 32.4 1.0 S4 D:SF4705 3.9 38.4 1.0 N D:VAL295 4.5 37.9 1.0 C D:LEU294 4.5 37.9 1.0 CG D:PRO249 4.5 33.6 1.0 CA D:CYS292 4.6 32.4 1.0 CA D:VAL295 4.6 37.9 1.0 O D:LEU294 4.6 37.9 1.0 CD2 D:PHE288 4.7 29.5 1.0 SG D:CYS299 4.8 42.5 1.0 CB D:PRO249 4.9 33.6 1.0 CB D:LEU294 5.0 37.9 1.0 N D:LEU294 5.0 37.9 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