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Iron in PDB 8j5t: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State

Other elements in 8j5t:

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

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State (pdb code 8j5t). 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 Catalytic Intermediate State, PDB code: 8j5t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8j5t

Go back to Iron Binding Sites List in 8j5t
Iron binding site 1 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the 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 Catalytic Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe705

b:86.0
occ:1.00
FE1 D:SF4705 0.0 86.0 1.0
SG D:CYS292 2.2 73.8 1.0
S3 D:SF4705 2.3 86.0 1.0
S4 D:SF4705 2.3 86.0 1.0
S2 D:SF4705 2.3 86.0 1.0
FE3 D:SF4705 2.7 86.0 1.0
FE4 D:SF4705 2.7 86.0 1.0
FE2 D:SF4705 2.7 86.0 1.0
CB D:CYS292 3.3 73.8 1.0
S1 D:SF4705 3.9 86.0 1.0
CG D:PRO249 3.9 74.8 1.0
CB D:PRO249 4.2 74.8 1.0
CD2 D:PHE288 4.3 69.9 1.0
CA D:CYS292 4.7 73.8 1.0
N D:VAL295 4.7 78.7 1.0
CD D:PRO249 4.7 74.8 1.0
SG D:CYS317 4.7 80.2 1.0
SG D:CYS299 4.7 84.8 1.0
SG D:CYS286 4.8 77.2 1.0
CE2 D:PHE288 4.8 69.9 1.0
CA D:VAL295 4.8 78.7 1.0
C D:LEU294 4.8 77.1 1.0
CB D:LEU294 4.8 77.1 1.0

Iron binding site 2 out of 4 in 8j5t

Go back to Iron Binding Sites List in 8j5t
Iron binding site 2 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the 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 Catalytic Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe705

b:86.0
occ:1.00
FE2 D:SF4705 0.0 86.0 1.0
SG D:CYS299 2.2 84.8 1.0
S3 D:SF4705 2.3 86.0 1.0
S4 D:SF4705 2.3 86.0 1.0
S1 D:SF4705 2.3 86.0 1.0
FE4 D:SF4705 2.7 86.0 1.0
FE3 D:SF4705 2.7 86.0 1.0
FE1 D:SF4705 2.7 86.0 1.0
CB D:CYS299 3.2 84.8 1.0
S2 D:SF4705 3.9 86.0 1.0
CA D:CYS299 4.4 84.8 1.0
CG1 D:ILE318 4.6 81.1 1.0
SG D:CYS317 4.7 80.2 1.0
CB D:CYS286 4.7 77.2 1.0
SG D:CYS292 4.8 73.8 1.0
SG D:CYS286 4.8 77.2 1.0
CD D:ARG319 4.8 81.6 1.0
CA D:VAL295 4.8 78.7 1.0
N D:ILE318 5.0 81.1 1.0
CG D:ARG319 5.0 81.6 1.0

Iron binding site 3 out of 4 in 8j5t

Go back to Iron Binding Sites List in 8j5t
Iron binding site 3 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the 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 Catalytic Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe705

b:86.0
occ:1.00
FE3 D:SF4705 0.0 86.0 1.0
S4 D:SF4705 2.3 86.0 1.0
SG D:CYS286 2.3 77.2 1.0
S2 D:SF4705 2.3 86.0 1.0
S1 D:SF4705 2.3 86.0 1.0
FE1 D:SF4705 2.7 86.0 1.0
FE2 D:SF4705 2.7 86.0 1.0
FE4 D:SF4705 2.8 86.0 1.0
CB D:CYS286 3.1 77.2 1.0
S3 D:SF4705 3.9 86.0 1.0
N D:ALA289 4.5 71.8 1.0
CA D:CYS286 4.5 77.2 1.0
CB D:PHE288 4.7 69.9 1.0
SG D:CYS299 4.7 84.8 1.0
SG D:CYS292 4.7 73.8 1.0
C D:PHE288 4.8 69.9 1.0
SG D:CYS317 4.8 80.2 1.0
CD2 D:PHE288 4.8 69.9 1.0
CA D:ALA289 4.9 71.8 1.0
O D:ALA316 5.0 76.2 1.0

Iron binding site 4 out of 4 in 8j5t

Go back to Iron Binding Sites List in 8j5t
Iron binding site 4 out of 4 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the 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 Catalytic Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe705

b:86.0
occ:1.00
FE4 D:SF4705 0.0 86.0 1.0
SG D:CYS317 2.2 80.2 1.0
S3 D:SF4705 2.3 86.0 1.0
S1 D:SF4705 2.3 86.0 1.0
S2 D:SF4705 2.3 86.0 1.0
FE2 D:SF4705 2.7 86.0 1.0
FE1 D:SF4705 2.7 86.0 1.0
FE3 D:SF4705 2.8 86.0 1.0
CB D:CYS317 3.4 80.2 1.0
CA D:CYS317 3.8 80.2 1.0
S4 D:SF4705 3.9 86.0 1.0
CD D:PRO249 3.9 74.8 1.0
CG D:PRO249 4.0 74.8 1.0
N D:ILE318 4.2 81.1 1.0
C D:CYS317 4.3 80.2 1.0
O D:ARG319 4.5 81.6 1.0
SG D:CYS299 4.7 84.8 1.0
N D:ARG319 4.7 81.6 1.0
SG D:CYS292 4.7 73.8 1.0
SG D:CYS286 4.8 77.2 1.0
O D:ALA316 4.8 76.2 1.0
CB D:PRO249 4.9 74.8 1.0
CG D:ARG319 4.9 81.6 1.0

Reference:

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
Page generated: Sat Aug 10 06:32:39 2024

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