Iron in PDB 8d8k: Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
Other elements in 8d8k:
The structure of Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
(pdb code 8d8k). 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 2), PDB code: 8d8k:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8d8k
Go back to
Iron Binding Sites List in 8d8k
Iron binding site 1 out
of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
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 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe701
b:38.9
occ:1.00
|
FE1
|
0:SF4701
|
0.0
|
38.9
|
1.0
|
S2
|
0:SF4701
|
2.2
|
38.9
|
1.0
|
SG
|
0:CYS400
|
2.3
|
35.0
|
1.0
|
S4
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
S3
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
FE4
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE3
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE2
|
0:SF4701
|
2.8
|
38.9
|
1.0
|
CB
|
0:CYS400
|
2.9
|
35.0
|
1.0
|
S1
|
0:SF4701
|
3.9
|
38.9
|
1.0
|
CA
|
0:CYS400
|
4.4
|
35.0
|
1.0
|
SG
|
0:CYS379
|
4.7
|
38.8
|
1.0
|
SG
|
0:CYS513
|
4.7
|
31.0
|
1.0
|
CE1
|
0:PHE317
|
4.7
|
36.6
|
1.0
|
SG
|
0:CYS373
|
4.8
|
31.9
|
1.0
|
CG2
|
0:ILE498
|
4.8
|
29.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 8d8k
Go back to
Iron Binding Sites List in 8d8k
Iron binding site 2 out
of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
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 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe701
b:38.9
occ:1.00
|
FE2
|
0:SF4701
|
0.0
|
38.9
|
1.0
|
S1
|
0:SF4701
|
2.2
|
38.9
|
1.0
|
SG
|
0:CYS373
|
2.3
|
31.9
|
1.0
|
S3
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
S4
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
FE3
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE4
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE1
|
0:SF4701
|
2.8
|
38.9
|
1.0
|
CB
|
0:CYS373
|
3.1
|
31.9
|
1.0
|
CA
|
0:CYS373
|
3.6
|
31.9
|
1.0
|
S2
|
0:SF4701
|
3.9
|
38.9
|
1.0
|
N
|
0:CYS373
|
4.1
|
31.9
|
1.0
|
NE
|
0:ARG324
|
4.4
|
38.6
|
1.0
|
C
|
0:PRO372
|
4.6
|
31.1
|
1.0
|
CZ
|
0:ARG324
|
4.6
|
38.6
|
1.0
|
CD
|
0:ARG324
|
4.6
|
38.6
|
1.0
|
O
|
0:PRO372
|
4.6
|
31.1
|
1.0
|
SG
|
0:CYS400
|
4.7
|
35.0
|
1.0
|
SG
|
0:CYS513
|
4.8
|
31.0
|
1.0
|
SG
|
0:CYS379
|
4.8
|
38.8
|
1.0
|
CG
|
0:PRO372
|
4.9
|
31.1
|
1.0
|
NH2
|
0:ARG324
|
5.0
|
38.6
|
1.0
|
NH1
|
0:ARG324
|
5.0
|
38.6
|
1.0
|
C
|
0:CYS373
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 8d8k
Go back to
Iron Binding Sites List in 8d8k
Iron binding site 3 out
of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
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 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe701
b:38.9
occ:1.00
|
FE3
|
0:SF4701
|
0.0
|
38.9
|
1.0
|
S4
|
0:SF4701
|
2.2
|
38.9
|
1.0
|
SG
|
0:CYS513
|
2.3
|
31.0
|
1.0
|
S1
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
S2
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
FE2
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE4
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE1
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
CB
|
0:CYS513
|
3.4
|
31.0
|
1.0
|
S3
|
0:SF4701
|
3.9
|
38.9
|
1.0
|
CD
|
0:PRO380
|
4.0
|
36.5
|
1.0
|
CE1
|
0:HIS375
|
4.1
|
36.7
|
1.0
|
CG
|
0:PRO380
|
4.4
|
36.5
|
1.0
|
NE2
|
0:HIS375
|
4.5
|
36.7
|
1.0
|
SG
|
0:CYS379
|
4.7
|
38.8
|
1.0
|
SG
|
0:CYS400
|
4.8
|
35.0
|
1.0
|
CA
|
0:CYS513
|
4.8
|
31.0
|
1.0
|
SG
|
0:CYS373
|
4.8
|
31.9
|
1.0
|
CD
|
0:PRO374
|
4.9
|
31.8
|
1.0
|
CA
|
0:CYS373
|
4.9
|
31.9
|
1.0
|
CB
|
0:CYS373
|
5.0
|
31.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 8d8k
Go back to
Iron Binding Sites List in 8d8k
Iron binding site 4 out
of 4 in the Yeast Mitochondrial Small Subunit Assembly Intermediate (State 2)
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 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe701
b:38.9
occ:1.00
|
FE4
|
0:SF4701
|
0.0
|
38.9
|
1.0
|
SG
|
0:CYS379
|
2.3
|
38.8
|
1.0
|
S3
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
S1
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
S2
|
0:SF4701
|
2.3
|
38.9
|
1.0
|
FE1
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE2
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
FE3
|
0:SF4701
|
2.7
|
38.9
|
1.0
|
CB
|
0:CYS379
|
3.3
|
38.8
|
1.0
|
S4
|
0:SF4701
|
3.9
|
38.9
|
1.0
|
CA
|
0:CYS379
|
3.9
|
38.8
|
1.0
|
CD
|
0:PRO380
|
4.0
|
36.5
|
1.0
|
CE1
|
0:PHE317
|
4.2
|
36.6
|
1.0
|
C
|
0:CYS379
|
4.4
|
38.8
|
1.0
|
N
|
0:PRO380
|
4.5
|
36.5
|
1.0
|
CB
|
0:CYS400
|
4.6
|
35.0
|
1.0
|
SG
|
0:CYS513
|
4.7
|
31.0
|
1.0
|
SG
|
0:CYS373
|
4.7
|
31.9
|
1.0
|
SG
|
0:CYS400
|
4.8
|
35.0
|
1.0
|
CZ
|
0:PHE317
|
4.8
|
36.6
|
1.0
|
N
|
0:LEU381
|
4.8
|
37.3
|
1.0
|
CG
|
0:PRO380
|
4.8
|
36.5
|
1.0
|
CB
|
0:LEU381
|
5.0
|
37.3
|
1.0
|
NE
|
0:ARG324
|
5.0
|
38.6
|
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 23:17:18 2024
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