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Iron in PDB 8d8l: Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)

Enzymatic activity of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)

All present enzymatic activity of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3):
3.1.2.4;

Other elements in 8d8l:

The structure of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) (pdb code 8d8l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3), PDB code: 8d8l:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8d8l

Go back to Iron Binding Sites List in 8d8l
Iron binding site 1 out of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe701

b:8.2
occ:1.00
 FE1 0:SF4701 0.0 8.2 1.0
S2 0:SF4701 2.2 8.2 1.0
SG 0:CYS400 2.3 8.2 1.0
S4 0:SF4701 2.3 8.2 1.0
S3 0:SF4701 2.3 8.2 1.0
FE3 0:SF4701 2.7 8.2 1.0
FE4 0:SF4701 2.7 8.2 1.0
FE2 0:SF4701 2.8 8.2 1.0
CB 0:CYS400 3.1 8.2 1.0
S1 0:SF4701 3.9 8.2 1.0
CA 0:CYS400 4.5 8.2 1.0
SG 0:CYS513 4.7 8.2 1.0
SG 0:CYS379 4.7 9.5 1.0
SG 0:CYS373 4.7 7.8 1.0
CG2 0:ILE498 4.9 8.6 1.0
CG 0:PRO372 4.9 7.3 1.0

Iron binding site 2 out of 4 in 8d8l

Go back to Iron Binding Sites List in 8d8l
Iron binding site 2 out of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe701

b:8.2
occ:1.00
 FE2 0:SF4701 0.0 8.2 1.0
S1 0:SF4701 2.2 8.2 1.0
SG 0:CYS373 2.3 7.8 1.0
S3 0:SF4701 2.3 8.2 1.0
S4 0:SF4701 2.3 8.2 1.0
FE3 0:SF4701 2.7 8.2 1.0
FE4 0:SF4701 2.7 8.2 1.0
FE1 0:SF4701 2.8 8.2 1.0
CB 0:CYS373 3.2 7.8 1.0
CA 0:CYS373 3.7 7.8 1.0
S2 0:SF4701 3.9 8.2 1.0
N 0:CYS373 4.2 7.8 1.0
CD 0:ARG324 4.4 11.0 1.0
NE 0:ARG324 4.5 11.0 1.0
C 0:PRO372 4.6 7.3 1.0
CZ 0:ARG324 4.7 11.0 1.0
SG 0:CYS513 4.7 8.2 1.0
CG 0:PRO372 4.7 7.3 1.0
NH1 0:ARG324 4.7 11.0 1.0
SG 0:CYS379 4.8 9.5 1.0
SG 0:CYS400 4.8 8.2 1.0
O 0:PRO372 4.8 7.3 1.0

Iron binding site 3 out of 4 in 8d8l

Go back to Iron Binding Sites List in 8d8l
Iron binding site 3 out of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe701

b:8.2
occ:1.00
 FE3 0:SF4701 0.0 8.2 1.0
SG 0:CYS513 2.2 8.2 1.0
S4 0:SF4701 2.2 8.2 1.0
S2 0:SF4701 2.3 8.2 1.0
S1 0:SF4701 2.3 8.2 1.0
FE2 0:SF4701 2.7 8.2 1.0
FE4 0:SF4701 2.7 8.2 1.0
FE1 0:SF4701 2.7 8.2 1.0
CB 0:CYS513 3.3 8.2 1.0
S3 0:SF4701 3.8 8.2 1.0
CD 0:PRO380 4.2 10.2 1.0
CE1 0:HIS375 4.4 9.2 1.0
CG 0:PRO380 4.6 10.2 1.0
CA 0:CYS513 4.7 8.2 1.0
SG 0:CYS379 4.7 9.5 1.0
SG 0:CYS373 4.7 7.8 1.0
NE2 0:HIS375 4.7 9.2 1.0
CD 0:PRO374 4.8 8.4 1.0
SG 0:CYS400 4.8 8.2 1.0
CA 0:CYS373 4.9 7.8 1.0
CB 0:CYS373 4.9 7.8 1.0

Iron binding site 4 out of 4 in 8d8l

Go back to Iron Binding Sites List in 8d8l
Iron binding site 4 out of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe701

b:8.2
occ:1.00
 FE4 0:SF4701 0.0 8.2 1.0
SG 0:CYS379 2.3 9.5 1.0
S3 0:SF4701 2.3 8.2 1.0
S1 0:SF4701 2.3 8.2 1.0
S2 0:SF4701 2.3 8.2 1.0
FE3 0:SF4701 2.7 8.2 1.0
FE2 0:SF4701 2.7 8.2 1.0
FE1 0:SF4701 2.7 8.2 1.0
CB 0:CYS379 3.3 9.5 1.0
S4 0:SF4701 3.9 8.2 1.0
CA 0:CYS379 3.9 9.5 1.0
CD 0:PRO380 4.0 10.2 1.0
CE1 0:PHE317 4.4 9.9 1.0
C 0:CYS379 4.5 9.5 1.0
N 0:PRO380 4.6 10.2 1.0
CB 0:CYS400 4.6 8.2 1.0
SG 0:CYS513 4.6 8.2 1.0
SG 0:CYS400 4.7 8.2 1.0
SG 0:CYS373 4.7 7.8 1.0
CG 0:PRO380 4.9 10.2 1.0
NE 0:ARG324 4.9 11.0 1.0
CZ 0:PHE317 4.9 9.9 1.0
N 0:LEU381 5.0 10.8 1.0

Reference:

N.J.Harper, C.Burnside, S.Klinge. Principles of Mitoribosomal Small Subunit Assembly in Eukaryotes. Nature 2022.
ISSN: ESSN 1476-4687
PubMed: 36482135
DOI: 10.1038/S41586-022-05621-0
Page generated: Thu Aug 7 15:25:41 2025

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