Iron in PDB 8j5q: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Translocation State

The binding sites of Iron atom in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Translocation State (pdb code 8j5q). 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- Translocation State, PDB code: 8j5q:
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- Translocation 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- Translocation State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2001 b:84.9 occ:1.00 FE1 D:SF42001 0.0 84.9 1.0 S2 D:SF42001 2.3 84.9 1.0 S3 D:SF42001 2.3 84.9 1.0 S4 D:SF42001 2.3 84.9 1.0 SG D:CYS286 2.4 72.2 1.0 CB D:CYS286 2.6 72.2 1.0 FE4 D:SF42001 2.7 84.9 1.0 FE2 D:SF42001 2.7 84.9 1.0 FE3 D:SF42001 2.7 84.9 1.0 S1 D:SF42001 3.9 84.9 1.0 CA D:CYS286 4.1 72.2 1.0 CB D:CYS299 4.2 87.7 1.0 CG D:PRO304 4.6 75.4 1.0 N D:ALA289 4.8 66.2 1.0 C D:CYS286 4.8 72.2 1.0 SG D:CYS299 4.9 87.7 1.0 SG D:CYS292 4.9 68.7 1.0 N D:CYS286 4.9 72.2 1.0 CB D:PHE288 4.9 65.2 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Translocation 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- Translocation State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2001 b:84.9 occ:1.00 FE2 D:SF42001 0.0 84.9 1.0 S1 D:SF42001 2.3 84.9 1.0 S4 D:SF42001 2.3 84.9 1.0 S3 D:SF42001 2.3 84.9 1.0 SG D:CYS317 2.4 79.8 1.0 FE3 D:SF42001 2.7 84.9 1.0 FE1 D:SF42001 2.7 84.9 1.0 FE4 D:SF42001 2.7 84.9 1.0 CB D:CYS317 3.5 79.8 1.0 S2 D:SF42001 3.9 84.9 1.0 CA D:CYS317 4.0 79.8 1.0 N D:ILE318 4.2 81.5 1.0 SG D:CYS292 4.5 68.7 1.0 CG D:PRO249 4.6 66.5 1.0 C D:CYS317 4.6 79.8 1.0 SG D:CYS286 4.7 72.2 1.0 CD D:PRO249 4.7 66.5 1.0 N D:ARG319 4.8 83.4 1.0 CG D:ARG319 4.9 83.4 1.0 CE D:MET248 4.9 69.2 1.0 SG D:CYS299 5.0 87.7 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Translocation 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- Translocation State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2001 b:84.9 occ:1.00 FE3 D:SF42001 0.0 84.9 1.0 S4 D:SF42001 2.3 84.9 1.0 S2 D:SF42001 2.3 84.9 1.0 S1 D:SF42001 2.3 84.9 1.0 SG D:CYS292 2.3 68.7 1.0 FE2 D:SF42001 2.7 84.9 1.0 FE4 D:SF42001 2.7 84.9 1.0 FE1 D:SF42001 2.7 84.9 1.0 CB D:CYS292 3.1 68.7 1.0 S3 D:SF42001 3.9 84.9 1.0 CA D:VAL295 4.2 78.5 1.0 N D:VAL295 4.5 78.5 1.0 CB D:VAL295 4.5 78.5 1.0 CA D:CYS292 4.6 68.7 1.0 C D:LEU294 4.6 74.5 1.0 SG D:CYS286 4.6 72.2 1.0 O D:LEU294 4.7 74.5 1.0 CG2 D:VAL295 4.8 78.5 1.0 SG D:CYS299 4.9 87.7 1.0 CG D:PRO249 4.9 66.5 1.0 SG D:CYS317 4.9 79.8 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Translocation 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- Translocation State within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe2001 b:84.9 occ:1.00 FE4 D:SF42001 0.0 84.9 1.0 S2 D:SF42001 2.3 84.9 1.0 S3 D:SF42001 2.3 84.9 1.0 S1 D:SF42001 2.3 84.9 1.0 SG D:CYS299 2.4 87.7 1.0 CB D:CYS299 2.7 87.7 1.0 FE3 D:SF42001 2.7 84.9 1.0 FE1 D:SF42001 2.7 84.9 1.0 FE2 D:SF42001 2.7 84.9 1.0 S4 D:SF42001 3.9 84.9 1.0 CD D:ARG319 4.0 83.4 1.0 CA D:CYS299 4.2 87.7 1.0 CG D:ARG319 4.3 83.4 1.0 CG1 D:ILE318 4.5 81.5 1.0 SG D:CYS317 4.7 79.8 1.0 CB D:CYS286 4.7 72.2 1.0 SG D:CYS292 4.9 68.7 1.0 CD1 D:ILE318 4.9 81.5 1.0 CA D:VAL295 4.9 78.5 1.0 N D:CYS299 5.0 87.7 1.0 N D:ILE296 5.0 84.7 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