Iron in PDB 7nvr: Human Mediator with Rna Polymerase II Pre-Initiation Complex
Enzymatic activity of Human Mediator with Rna Polymerase II Pre-Initiation Complex
Other elements in 7nvr:
The structure of Human Mediator with Rna Polymerase II Pre-Initiation Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Human Mediator with Rna Polymerase II Pre-Initiation Complex
(pdb code 7nvr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Human Mediator with Rna Polymerase II Pre-Initiation Complex, PDB code: 7nvr:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7nvr
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Iron Binding Sites List in 7nvr
Iron binding site 1 out
of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex
![](/pictures/FE/pdb/nv/7nvr-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/nv/7nvr-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 Human Mediator with Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe1000
b:217.9
occ:1.00
|
FE1
|
0:SF41000
|
0.0
|
217.9
|
1.0
|
SG
|
0:CYS190
|
2.2
|
146.9
|
1.0
|
S3
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S4
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S2
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
FE4
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE3
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE2
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
CB
|
0:CYS190
|
3.7
|
146.9
|
1.0
|
S1
|
0:SF41000
|
3.9
|
217.9
|
1.0
|
CE1
|
0:PHE193
|
4.0
|
145.4
|
1.0
|
CD1
|
0:PHE193
|
4.2
|
145.4
|
1.0
|
CA
|
0:CYS190
|
4.5
|
146.9
|
1.0
|
CB
|
0:PHE157
|
4.6
|
152.0
|
1.0
|
SG
|
0:CYS155
|
4.6
|
153.8
|
1.0
|
SG
|
0:CYS134
|
4.8
|
155.1
|
1.0
|
SG
|
0:CYS116
|
4.8
|
145.2
|
1.0
|
N
|
0:TYR158
|
4.8
|
149.1
|
1.0
|
CB
|
0:TYR158
|
4.9
|
149.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 7nvr
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Iron Binding Sites List in 7nvr
Iron binding site 2 out
of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex
![](/pictures/FE/pdb/nv/7nvr-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/nv/7nvr-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 Human Mediator with Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe1000
b:217.9
occ:1.00
|
FE2
|
0:SF41000
|
0.0
|
217.9
|
1.0
|
SG
|
0:CYS116
|
2.3
|
145.2
|
1.0
|
S3
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S4
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S1
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
FE3
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE4
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE1
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
CB
|
0:CYS116
|
3.8
|
145.2
|
1.0
|
S2
|
0:SF41000
|
3.9
|
217.9
|
1.0
|
CB
|
0:HIS118
|
4.1
|
153.1
|
1.0
|
N
|
0:ILE117
|
4.4
|
153.0
|
1.0
|
N
|
0:HIS118
|
4.4
|
153.1
|
1.0
|
CA
|
0:CYS116
|
4.5
|
145.2
|
1.0
|
CG2
|
0:VAL121
|
4.7
|
148.2
|
1.0
|
SG
|
0:CYS134
|
4.8
|
155.1
|
1.0
|
SG
|
0:CYS155
|
4.8
|
153.8
|
1.0
|
SG
|
0:CYS190
|
4.8
|
146.9
|
1.0
|
CA
|
0:HIS118
|
4.9
|
153.1
|
1.0
|
C
|
0:CYS116
|
5.0
|
145.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 7nvr
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Iron Binding Sites List in 7nvr
Iron binding site 3 out
of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex
![](/pictures/FE/pdb/nv/7nvr-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/nv/7nvr-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 Human Mediator with Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe1000
b:217.9
occ:1.00
|
FE3
|
0:SF41000
|
0.0
|
217.9
|
1.0
|
SG
|
0:CYS134
|
2.3
|
155.1
|
1.0
|
S2
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S4
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S1
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
FE2
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE1
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE4
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
CB
|
0:CYS134
|
3.4
|
155.1
|
1.0
|
S3
|
0:SF41000
|
3.9
|
217.9
|
1.0
|
CA
|
0:CYS134
|
4.1
|
155.1
|
1.0
|
CE1
|
0:PHE193
|
4.2
|
145.4
|
1.0
|
O
|
0:CYS134
|
4.7
|
155.1
|
1.0
|
SG
|
0:CYS116
|
4.7
|
145.2
|
1.0
|
SG
|
0:CYS190
|
4.8
|
146.9
|
1.0
|
SG
|
0:CYS155
|
4.8
|
153.8
|
1.0
|
C
|
0:CYS134
|
4.8
|
155.1
|
1.0
|
CZ
|
0:PHE193
|
4.9
|
145.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 7nvr
Go back to
Iron Binding Sites List in 7nvr
Iron binding site 4 out
of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex
![](/pictures/FE/pdb/nv/7nvr-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/nv/7nvr-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 Human Mediator with Rna Polymerase II Pre-Initiation Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe1000
b:217.9
occ:1.00
|
FE4
|
0:SF41000
|
0.0
|
217.9
|
1.0
|
SG
|
0:CYS155
|
2.2
|
153.8
|
1.0
|
S2
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S1
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
S3
|
0:SF41000
|
2.3
|
217.9
|
1.0
|
FE1
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE2
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
FE3
|
0:SF41000
|
2.7
|
217.9
|
1.0
|
CB
|
0:CYS155
|
3.7
|
153.8
|
1.0
|
S4
|
0:SF41000
|
3.9
|
217.9
|
1.0
|
CB
|
0:HIS118
|
4.3
|
153.1
|
1.0
|
CD2
|
0:PHE157
|
4.3
|
152.0
|
1.0
|
CD2
|
0:HIS118
|
4.4
|
153.1
|
1.0
|
CG
|
0:HIS118
|
4.5
|
153.1
|
1.0
|
SG
|
0:CYS190
|
4.6
|
146.9
|
1.0
|
CB
|
0:PHE157
|
4.8
|
152.0
|
1.0
|
SG
|
0:CYS116
|
4.8
|
145.2
|
1.0
|
SG
|
0:CYS134
|
4.8
|
155.1
|
1.0
|
CA
|
0:CYS155
|
5.0
|
153.8
|
1.0
|
|
Reference:
S.Rengachari,
S.Schilbach,
S.Aibara,
C.Dienemann,
P.Cramer.
Structure of Human Mediator-Rna Polymerase II Pre-Initiation Complex. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902108
DOI: 10.1038/S41586-021-03555-7
Page generated: Thu Aug 8 09:50:39 2024
|