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Iron in PDB 8csq: Human Mitochondrial Small Subunit Assembly Intermediate (State B)

Enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State B)

All present enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State B):
2.3.1.39;

Other elements in 8csq:

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

Zinc (Zn) 1 atom
Magnesium (Mg) 27 atoms
Potassium (K) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human Mitochondrial Small Subunit Assembly Intermediate (State B) (pdb code 8csq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Human Mitochondrial Small Subunit Assembly Intermediate (State B), PDB code: 8csq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8csq

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Iron binding site 1 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Fe501

b:30.6
occ:1.00
 FE1 7:SF4501 0.0 30.6 1.0
S2 7:SF4501 2.2 30.6 1.0
SG 7:CYS404 2.3 19.7 1.0
S4 7:SF4501 2.3 30.6 1.0
S3 7:SF4501 2.3 30.6 1.0
FE3 7:SF4501 2.7 30.6 1.0
FE4 7:SF4501 2.7 30.6 1.0
FE2 7:SF4501 2.8 30.6 1.0
CB 7:CYS404 3.2 19.7 1.0
S1 7:SF4501 3.9 30.6 1.0
CD 7:PRO340 4.4 18.1 1.0
NE2 7:HIS335 4.4 13.7 1.0
SG 7:CYS333 4.6 19.2 1.0
CA 7:CYS404 4.6 19.7 1.0
CG2 7:THR389 4.6 23.9 1.0
CA 7:CYS333 4.7 19.2 1.0
SG 7:CYS339 4.8 17.5 1.0
SD 7:MET410 4.8 19.5 1.0
CG 7:PRO340 4.8 18.1 1.0
SG 7:CYS347 4.8 30.6 1.0
CB 7:CYS333 4.8 19.2 1.0
CD 7:PRO334 4.8 17.0 1.0

Iron binding site 2 out of 8 in 8csq

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Iron binding site 2 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Fe501

b:30.6
occ:1.00
 FE2 7:SF4501 0.0 30.6 1.0
S1 7:SF4501 2.2 30.6 1.0
SG 7:CYS347 2.3 30.6 1.0
S3 7:SF4501 2.3 30.6 1.0
S4 7:SF4501 2.3 30.6 1.0
FE3 7:SF4501 2.7 30.6 1.0
FE4 7:SF4501 2.7 30.6 1.0
FE1 7:SF4501 2.8 30.6 1.0
CB 7:CYS347 3.2 30.6 1.0
S2 7:SF4501 3.9 30.6 1.0
CG2 7:THR389 4.3 23.9 1.0
OE1 7:GLN341 4.5 22.4 1.0
CG 7:PRO332 4.6 22.6 1.0
CA 7:CYS347 4.6 30.6 1.0
SG 7:CYS339 4.6 17.5 1.0
NE2 7:HIS303 4.7 16.1 1.0
SG 7:CYS333 4.8 19.2 1.0
SG 7:CYS404 4.9 19.7 1.0
CZ 7:PHE349 5.0 30.6 1.0

Iron binding site 3 out of 8 in 8csq

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Iron binding site 3 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Fe501

b:30.6
occ:1.00
 FE3 7:SF4501 0.0 30.6 1.0
S4 7:SF4501 2.2 30.6 1.0
SG 7:CYS333 2.2 19.2 1.0
S1 7:SF4501 2.3 30.6 1.0
S2 7:SF4501 2.3 30.6 1.0
FE1 7:SF4501 2.7 30.6 1.0
FE4 7:SF4501 2.7 30.6 1.0
FE2 7:SF4501 2.7 30.6 1.0
CB 7:CYS333 3.3 19.2 1.0
CA 7:CYS333 3.6 19.2 1.0
S3 7:SF4501 3.8 30.6 1.0
N 7:CYS333 3.9 19.2 1.0
CG 7:PRO332 4.3 22.6 1.0
C 7:PRO332 4.6 22.6 1.0
SG 7:CYS404 4.6 19.7 1.0
CD 7:PRO332 4.7 22.6 1.0
SG 7:CYS339 4.8 17.5 1.0
SG 7:CYS347 4.9 30.6 1.0
CE 7:MET307 5.0 21.0 1.0

Iron binding site 4 out of 8 in 8csq

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Iron binding site 4 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Fe501

b:30.6
occ:1.00
 FE4 7:SF4501 0.0 30.6 1.0
SG 7:CYS339 2.3 17.5 1.0
S3 7:SF4501 2.3 30.6 1.0
S1 7:SF4501 2.3 30.6 1.0
S2 7:SF4501 2.3 30.6 1.0
FE3 7:SF4501 2.7 30.6 1.0
FE1 7:SF4501 2.7 30.6 1.0
FE2 7:SF4501 2.7 30.6 1.0
CB 7:CYS339 3.4 17.5 1.0
S4 7:SF4501 3.9 30.6 1.0
CA 7:CYS339 3.9 17.5 1.0
CD 7:PRO340 4.0 18.1 1.0
NE2 7:HIS303 4.1 16.1 1.0
SD 7:MET307 4.5 21.0 1.0
CB 7:CYS347 4.5 30.6 1.0
SG 7:CYS347 4.6 30.6 1.0
N 7:PRO340 4.6 18.1 1.0
SG 7:CYS333 4.6 19.2 1.0
C 7:CYS339 4.7 17.5 1.0
SG 7:CYS404 4.7 19.7 1.0
CE1 7:HIS303 4.7 16.1 1.0
OE1 7:GLN341 4.8 22.4 1.0
CB 7:GLN341 4.9 22.4 1.0
CG 7:PRO340 5.0 18.1 1.0

Iron binding site 5 out of 8 in 8csq

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Iron binding site 5 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe201

b:73.6
occ:1.00
 FE1 P:FES201 0.0 73.6 1.0
S1 P:FES201 2.2 73.6 1.0
S2 P:FES201 2.2 73.6 1.0
SG P:CYS100 2.3 47.1 1.0
FE2 P:FES201 2.7 73.6 1.0
CB P:CYS100 2.8 47.1 1.0
SG P:CYS65 3.4 49.2 1.0
CG P:LYS103 3.8 41.7 1.0
CB P:CYS68 4.0 47.5 1.0
SG E:CYS105 4.1 59.4 1.0
CA P:CYS100 4.2 47.1 1.0
SG P:CYS68 4.4 47.5 1.0
N P:CYS100 4.4 47.1 1.0
CB P:CYS65 4.5 49.2 1.0
CB E:CYS105 4.8 59.4 1.0
CD P:LYS103 4.8 41.7 1.0
CB P:LYS103 4.8 41.7 1.0
NZ P:LYS64 4.9 57.6 1.0
CA P:CYS68 4.9 47.5 1.0
N P:CYS65 4.9 49.2 1.0

Iron binding site 6 out of 8 in 8csq

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Iron binding site 6 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe201

b:73.6
occ:1.00
 FE2 P:FES201 0.0 73.6 1.0
S2 P:FES201 2.2 73.6 1.0
S1 P:FES201 2.2 73.6 1.0
SG E:CYS105 2.3 59.4 1.0
SG P:CYS68 2.3 47.5 1.0
CB E:CYS105 2.4 59.4 1.0
FE1 P:FES201 2.7 73.6 1.0
NZ P:LYS64 2.9 57.6 1.0
CB P:CYS68 3.1 47.5 1.0
CA E:CYS105 3.8 59.4 1.0
CE P:LYS64 3.8 57.6 1.0
C E:CYS105 4.1 59.4 1.0
CA P:CYS68 4.3 47.5 1.0
N E:CYS105 4.4 59.4 1.0
O E:CYS105 4.5 59.4 1.0
N E:GLU106 4.5 61.6 1.0
SG P:CYS100 4.7 47.1 1.0
CD P:LYS64 4.9 57.6 1.0

Iron binding site 7 out of 8 in 8csq

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Iron binding site 7 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Fe201

b:51.3
occ:1.00
 FE1 T:FES201 0.0 51.3 1.0
S2 T:FES201 2.2 51.3 1.0
S1 T:FES201 2.2 51.3 1.0
SG T:CYS149 2.3 31.2 1.0
SG M:CYS26 2.3 28.1 1.0
FE2 T:FES201 2.7 51.3 1.0
CB T:CYS149 3.5 31.2 1.0
SG T:CYS141 3.6 26.9 1.0
CB M:CYS26 4.0 28.1 1.0
CA T:CYS149 4.1 31.2 1.0
N M:CYS26 4.7 28.1 1.0
C M:GLY25 4.8 24.2 1.0
CD T:PRO150 4.9 28.8 1.0
SG T:CYS139 4.9 27.8 1.0
N T:CYS149 4.9 31.2 1.0
CA M:CYS26 4.9 28.1 1.0
CB T:CYS141 5.0 26.9 1.0

Iron binding site 8 out of 8 in 8csq

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Iron binding site 8 out of 8 in the Human Mitochondrial Small Subunit Assembly Intermediate (State B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Human Mitochondrial Small Subunit Assembly Intermediate (State B) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Fe201

b:51.3
occ:1.00
 FE2 T:FES201 0.0 51.3 1.0
S2 T:FES201 2.2 51.3 1.0
S1 T:FES201 2.2 51.3 1.0
SG T:CYS141 2.3 26.9 1.0
SG T:CYS139 2.3 27.8 1.0
CB T:CYS139 2.6 27.8 1.0
FE1 T:FES201 2.7 51.3 1.0
CB T:CYS141 3.6 26.9 1.0
SG T:CYS149 3.9 31.2 1.0
CA T:CYS139 4.1 27.8 1.0
CA M:GLY25 4.2 24.2 1.0
SG M:CYS26 4.3 28.1 1.0
N T:CYS141 4.4 26.9 1.0
CA T:CYS141 4.6 26.9 1.0
C T:CYS139 4.7 27.8 1.0
C M:GLY25 4.8 24.2 1.0
N T:ILE140 4.9 24.2 1.0
N T:CYS139 5.0 27.8 1.0
N M:GLY25 5.0 24.2 1.0
CD M:ARG29 5.0 24.2 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: Fri Aug 9 23:01:41 2024

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