Iron in PDB 8ebv: Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
Enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
All present enzymatic activity of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1:
3.6.4.12;
Other elements in 8ebv:
The structure of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
(pdb code 8ebv). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1, PDB code: 8ebv:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8ebv
Go back to
Iron Binding Sites List in 8ebv
Iron binding site 1 out
of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1000
b:541.8
occ:1.00
|
FE1
|
B:SF41000
|
0.0
|
541.8
|
1.0
|
SG
|
B:CYS116
|
2.3
|
528.0
|
1.0
|
S4
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S3
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S2
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
FE2
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE4
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE3
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
CB
|
B:CYS116
|
2.9
|
528.0
|
1.0
|
CA
|
B:CYS116
|
3.2
|
528.0
|
1.0
|
N
|
B:ILE117
|
3.7
|
493.5
|
1.0
|
S1
|
B:SF41000
|
3.9
|
541.8
|
1.0
|
C
|
B:CYS116
|
3.9
|
528.0
|
1.0
|
N
|
B:HIS118
|
4.0
|
494.1
|
1.0
|
CB
|
B:HIS118
|
4.1
|
494.1
|
1.0
|
N
|
B:CYS116
|
4.4
|
528.0
|
1.0
|
CG2
|
B:VAL121
|
4.7
|
548.9
|
1.0
|
CA
|
B:HIS118
|
4.7
|
494.1
|
1.0
|
CB
|
B:VAL121
|
4.8
|
548.9
|
1.0
|
O
|
B:LEU115
|
4.8
|
497.0
|
1.0
|
SG
|
B:CYS155
|
4.8
|
411.1
|
1.0
|
SG
|
B:CYS134
|
4.8
|
513.9
|
1.0
|
SG
|
B:CYS190
|
4.8
|
448.9
|
1.0
|
CA
|
B:ILE117
|
4.8
|
493.5
|
1.0
|
CB
|
B:CYS134
|
4.9
|
513.9
|
1.0
|
C
|
B:ILE117
|
4.9
|
493.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 8ebv
Go back to
Iron Binding Sites List in 8ebv
Iron binding site 2 out
of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1000
b:541.8
occ:1.00
|
FE2
|
B:SF41000
|
0.0
|
541.8
|
1.0
|
SG
|
B:CYS155
|
2.3
|
411.1
|
1.0
|
S1
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S4
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S3
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
FE1
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE3
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE4
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
CB
|
B:CYS155
|
3.6
|
411.1
|
1.0
|
CB
|
B:HIS118
|
3.8
|
494.1
|
1.0
|
S2
|
B:SF41000
|
3.9
|
541.8
|
1.0
|
CD1
|
B:PHE157
|
4.1
|
418.7
|
1.0
|
CB
|
B:PHE157
|
4.5
|
418.7
|
1.0
|
CG
|
B:HIS118
|
4.5
|
494.1
|
1.0
|
N
|
B:HIS118
|
4.5
|
494.1
|
1.0
|
SG
|
B:CYS116
|
4.6
|
528.0
|
1.0
|
CG
|
B:PHE157
|
4.6
|
418.7
|
1.0
|
CA
|
B:HIS118
|
4.7
|
494.1
|
1.0
|
SG
|
B:CYS134
|
4.7
|
513.9
|
1.0
|
SG
|
B:CYS190
|
4.8
|
448.9
|
1.0
|
CD2
|
B:HIS118
|
4.8
|
494.1
|
1.0
|
CE1
|
B:PHE157
|
4.9
|
418.7
|
1.0
|
CA
|
B:CYS155
|
4.9
|
411.1
|
1.0
|
CG2
|
B:THR138
|
5.0
|
505.0
|
1.0
|
|
Iron binding site 3 out
of 4 in 8ebv
Go back to
Iron Binding Sites List in 8ebv
Iron binding site 3 out
of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1000
b:541.8
occ:1.00
|
FE3
|
B:SF41000
|
0.0
|
541.8
|
1.0
|
SG
|
B:CYS134
|
2.3
|
513.9
|
1.0
|
S4
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S2
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S1
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
FE4
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE2
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE1
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
CB
|
B:CYS134
|
3.0
|
513.9
|
1.0
|
CA
|
B:CYS134
|
3.9
|
513.9
|
1.0
|
S3
|
B:SF41000
|
3.9
|
541.8
|
1.0
|
CE1
|
B:PHE193
|
4.3
|
470.3
|
1.0
|
SG
|
B:CYS190
|
4.6
|
448.9
|
1.0
|
CD
|
B:ARG112
|
4.6
|
525.1
|
1.0
|
SG
|
B:CYS155
|
4.6
|
411.1
|
1.0
|
C
|
B:CYS134
|
4.7
|
513.9
|
1.0
|
CG2
|
B:THR138
|
4.7
|
505.0
|
1.0
|
O
|
B:CYS134
|
4.8
|
513.9
|
1.0
|
SG
|
B:CYS116
|
4.8
|
528.0
|
1.0
|
NH1
|
B:ARG112
|
4.9
|
525.1
|
1.0
|
CZ
|
B:PHE193
|
5.0
|
470.3
|
1.0
|
N
|
B:CYS134
|
5.0
|
513.9
|
1.0
|
OG1
|
B:THR138
|
5.0
|
505.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 8ebv
Go back to
Iron Binding Sites List in 8ebv
Iron binding site 4 out
of 4 in the Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/eb/8ebv-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Initial Dna-Lesion (Ap) Binding By Xpc and Tfiih Complex 1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1000
b:541.8
occ:1.00
|
FE4
|
B:SF41000
|
0.0
|
541.8
|
1.0
|
SG
|
B:CYS190
|
2.3
|
448.9
|
1.0
|
S1
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S2
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
S3
|
B:SF41000
|
2.3
|
541.8
|
1.0
|
FE3
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE2
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
FE1
|
B:SF41000
|
2.7
|
541.8
|
1.0
|
CB
|
B:CYS190
|
3.2
|
448.9
|
1.0
|
S4
|
B:SF41000
|
3.9
|
541.8
|
1.0
|
O
|
B:LEU115
|
4.2
|
497.0
|
1.0
|
CE1
|
B:PHE193
|
4.3
|
470.3
|
1.0
|
CA
|
B:CYS116
|
4.3
|
528.0
|
1.0
|
CA
|
B:CYS190
|
4.3
|
448.9
|
1.0
|
CD1
|
B:PHE193
|
4.5
|
470.3
|
1.0
|
N
|
B:ILE117
|
4.6
|
493.5
|
1.0
|
CB
|
B:PHE157
|
4.7
|
418.7
|
1.0
|
SG
|
B:CYS134
|
4.7
|
513.9
|
1.0
|
SG
|
B:CYS155
|
4.8
|
411.1
|
1.0
|
CB
|
B:CYS116
|
4.8
|
528.0
|
1.0
|
SG
|
B:CYS116
|
4.8
|
528.0
|
1.0
|
|
Reference:
J.Kim,
C.L.Li,
X.Chen,
Y.Cui,
F.M.Golebiowski,
H.Wang,
F.Hanaoka,
K.Sugasawa,
W.Yang.
Lesion Recognition By Xpc, Tfiih and Xpa in Dna Excision Repair Nature 2023.
ISSN: ESSN 1476-4687
Page generated: Sat Aug 10 01:07:00 2024
|