Fluorine in PDB 7nvx: Tfiih in A Post-Translocated State (with Adp-BEF3)
Enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3)
All present enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3):
3.6.4.12;
Other elements in 7nvx:
The structure of Tfiih in A Post-Translocated State (with Adp-BEF3) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Tfiih in A Post-Translocated State (with Adp-BEF3)
(pdb code 7nvx). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Tfiih in A Post-Translocated State (with Adp-BEF3), PDB code: 7nvx:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7nvx
Go back to
Fluorine Binding Sites List in 7nvx
Fluorine binding site 1 out
of 3 in the Tfiih in A Post-Translocated State (with Adp-BEF3)
![](/pictures/F/pdb/nv/7nvx-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/nv/7nvx-F-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
7:F903
b:40.3
occ:1.00
|
F1
|
7:BEF903
|
0.0
|
40.3
|
1.0
|
BE
|
7:BEF903
|
1.5
|
40.3
|
1.0
|
MG
|
7:MG902
|
2.2
|
32.4
|
1.0
|
F3
|
7:BEF903
|
2.6
|
40.3
|
1.0
|
F2
|
7:BEF903
|
2.7
|
40.3
|
1.0
|
O3B
|
7:ADP901
|
2.7
|
40.7
|
1.0
|
O2B
|
7:ADP901
|
2.9
|
40.7
|
1.0
|
PB
|
7:ADP901
|
3.3
|
40.7
|
1.0
|
OE2
|
7:GLU442
|
4.0
|
13.3
|
1.0
|
CA
|
7:SER614
|
4.0
|
27.0
|
1.0
|
CE
|
7:LYS346
|
4.0
|
28.5
|
1.0
|
NH2
|
7:ARG645
|
4.1
|
35.0
|
1.0
|
N
|
7:SER614
|
4.3
|
27.0
|
1.0
|
O1B
|
7:ADP901
|
4.4
|
40.7
|
1.0
|
OG
|
7:SER614
|
4.4
|
27.0
|
1.0
|
OD2
|
7:ASP441
|
4.5
|
18.1
|
1.0
|
OD1
|
7:ASP441
|
4.5
|
18.1
|
1.0
|
O2A
|
7:ADP901
|
4.5
|
40.7
|
1.0
|
O3A
|
7:ADP901
|
4.5
|
40.7
|
1.0
|
NZ
|
7:LYS346
|
4.7
|
28.5
|
1.0
|
CB
|
7:SER614
|
4.7
|
27.0
|
1.0
|
NH1
|
7:ARG642
|
4.9
|
28.0
|
1.0
|
CG
|
7:ASP441
|
4.9
|
18.1
|
1.0
|
CD
|
7:GLU442
|
4.9
|
13.3
|
1.0
|
C
|
7:SER614
|
5.0
|
27.0
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7nvx
Go back to
Fluorine Binding Sites List in 7nvx
Fluorine binding site 2 out
of 3 in the Tfiih in A Post-Translocated State (with Adp-BEF3)
![](/pictures/F/pdb/nv/7nvx-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/nv/7nvx-F-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
7:F903
b:40.3
occ:1.00
|
F2
|
7:BEF903
|
0.0
|
40.3
|
1.0
|
BE
|
7:BEF903
|
1.6
|
40.3
|
1.0
|
F3
|
7:BEF903
|
2.6
|
40.3
|
1.0
|
F1
|
7:BEF903
|
2.7
|
40.3
|
1.0
|
O3B
|
7:ADP901
|
2.7
|
40.7
|
1.0
|
NZ
|
7:LYS346
|
2.8
|
28.5
|
1.0
|
CE
|
7:LYS346
|
2.8
|
28.5
|
1.0
|
CA
|
7:CYS342
|
3.5
|
24.6
|
1.0
|
PB
|
7:ADP901
|
3.6
|
40.7
|
1.0
|
SG
|
7:CYS342
|
3.6
|
24.6
|
1.0
|
CB
|
7:ALA468
|
3.7
|
15.0
|
1.0
|
O1B
|
7:ADP901
|
3.8
|
40.7
|
1.0
|
CB
|
7:CYS342
|
3.8
|
24.6
|
1.0
|
O2B
|
7:ADP901
|
4.0
|
40.7
|
1.0
|
N
|
7:GLY343
|
4.2
|
33.8
|
1.0
|
N
|
7:CYS342
|
4.3
|
24.6
|
1.0
|
CD
|
7:LYS346
|
4.3
|
28.5
|
1.0
|
NH2
|
7:ARG642
|
4.4
|
28.0
|
1.0
|
C
|
7:CYS342
|
4.4
|
24.6
|
1.0
|
MG
|
7:MG902
|
4.4
|
32.4
|
1.0
|
OE1
|
7:GLN638
|
4.5
|
19.5
|
1.0
|
NH2
|
7:ARG645
|
4.5
|
35.0
|
1.0
|
N
|
7:ALA468
|
4.7
|
15.0
|
1.0
|
O
|
7:PRO341
|
4.7
|
23.0
|
1.0
|
C
|
7:PRO341
|
4.8
|
23.0
|
1.0
|
CA
|
7:ALA468
|
4.9
|
15.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7nvx
Go back to
Fluorine Binding Sites List in 7nvx
Fluorine binding site 3 out
of 3 in the Tfiih in A Post-Translocated State (with Adp-BEF3)
![](/pictures/F/pdb/nv/7nvx-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/nv/7nvx-F-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
7:F903
b:40.3
occ:1.00
|
F3
|
7:BEF903
|
0.0
|
40.3
|
1.0
|
BE
|
7:BEF903
|
1.5
|
40.3
|
1.0
|
NH2
|
7:ARG645
|
2.5
|
35.0
|
1.0
|
O3B
|
7:ADP901
|
2.6
|
40.7
|
1.0
|
F2
|
7:BEF903
|
2.6
|
40.3
|
1.0
|
F1
|
7:BEF903
|
2.6
|
40.3
|
1.0
|
NH1
|
7:ARG642
|
2.7
|
28.0
|
1.0
|
NH2
|
7:ARG642
|
2.9
|
28.0
|
1.0
|
CZ
|
7:ARG642
|
3.2
|
28.0
|
1.0
|
CZ
|
7:ARG645
|
3.3
|
35.0
|
1.0
|
NH1
|
7:ARG645
|
3.4
|
35.0
|
1.0
|
N
|
7:SER614
|
3.8
|
27.0
|
1.0
|
PB
|
7:ADP901
|
4.0
|
40.7
|
1.0
|
CA
|
7:SER614
|
4.1
|
27.0
|
1.0
|
CB
|
7:CYS342
|
4.2
|
24.6
|
1.0
|
SG
|
7:CYS342
|
4.4
|
24.6
|
1.0
|
MG
|
7:MG902
|
4.4
|
32.4
|
1.0
|
N
|
7:GLY343
|
4.4
|
33.8
|
1.0
|
CA
|
7:CYS342
|
4.5
|
24.6
|
1.0
|
NE
|
7:ARG645
|
4.5
|
35.0
|
1.0
|
NE
|
7:ARG642
|
4.5
|
28.0
|
1.0
|
OE1
|
7:GLN638
|
4.5
|
19.5
|
1.0
|
O2B
|
7:ADP901
|
4.6
|
40.7
|
1.0
|
C
|
7:SER614
|
4.6
|
27.0
|
1.0
|
N
|
7:PHE615
|
4.8
|
27.2
|
1.0
|
O3A
|
7:ADP901
|
4.9
|
40.7
|
1.0
|
O1B
|
7:ADP901
|
4.9
|
40.7
|
1.0
|
O
|
7:PHE615
|
4.9
|
27.2
|
1.0
|
C
|
7:CYS342
|
4.9
|
24.6
|
1.0
|
C
|
7:THR613
|
5.0
|
23.7
|
1.0
|
|
Reference:
S.Aibara,
S.Schilbach,
P.Cramer.
Structures of Mammalian Rna Polymerase II Pre-Initiation Complexes. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902107
DOI: 10.1038/S41586-021-03554-8
Page generated: Fri Aug 2 10:15:43 2024
|