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:
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
|