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

All present enzymatic activity of Human Mediator with Rna Polymerase II Pre-Initiation Complex:
2.3.1.48; 2.7.11.22; 2.7.11.23; 2.7.7.6; 3.6.4.12;

Other elements in 7nvr:

The structure of Human Mediator with Rna Polymerase II Pre-Initiation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 18 atoms

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 site 1 out of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


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 site 2 out of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


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

Go back to Iron Binding Sites List in 7nvr
Iron binding site 3 out of 4 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


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


Mono view


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: Sat Jul 10 15:34:08 2021

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