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Iron in PDB 7nw0: Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna

Enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna

All present enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna:
2.3.1.48; 2.7.7.6; 3.6.4.12;

Other elements in 7nw0:

The structure of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 15 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna (pdb code 7nw0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna, PDB code: 7nw0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7nw0

Go back to Iron Binding Sites List in 7nw0
Iron binding site 1 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:156.0
occ:1.00
 FE1 0:SF41000 0.0 156.0 1.0
SG 0:CYS190 2.2 124.6 1.0
S4 0:SF41000 2.3 156.0 1.0
S3 0:SF41000 2.3 156.0 1.0
S2 0:SF41000 2.3 156.0 1.0
FE4 0:SF41000 2.7 156.0 1.0
FE3 0:SF41000 2.7 156.0 1.0
FE2 0:SF41000 2.7 156.0 1.0
CB 0:CYS190 3.6 124.6 1.0
S1 0:SF41000 3.9 156.0 1.0
CE2 0:PHE193 3.9 115.8 1.0
CD2 0:PHE193 4.0 115.8 1.0
CA 0:CYS190 4.3 124.6 1.0
CB 0:PHE157 4.6 116.5 1.0
SG 0:CYS155 4.6 114.1 1.0
CB 0:TYR158 4.7 118.2 1.0
SG 0:CYS134 4.8 118.3 1.0
N 0:TYR158 4.8 118.2 1.0
SG 0:CYS116 4.8 119.3 1.0

Iron binding site 2 out of 4 in 7nw0

Go back to Iron Binding Sites List in 7nw0
Iron binding site 2 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:156.0
occ:1.00
 FE2 0:SF41000 0.0 156.0 1.0
SG 0:CYS116 2.3 119.3 1.0
S3 0:SF41000 2.3 156.0 1.0
S1 0:SF41000 2.3 156.0 1.0
S4 0:SF41000 2.3 156.0 1.0
FE3 0:SF41000 2.7 156.0 1.0
FE4 0:SF41000 2.7 156.0 1.0
FE1 0:SF41000 2.7 156.0 1.0
CB 0:HIS118 3.8 104.8 1.0
CB 0:CYS116 3.9 119.3 1.0
S2 0:SF41000 3.9 156.0 1.0
N 0:HIS118 4.3 104.8 1.0
N 0:ILE117 4.5 110.8 1.0
CA 0:CYS116 4.6 119.3 1.0
CA 0:HIS118 4.7 104.8 1.0
SG 0:CYS134 4.7 118.3 1.0
CG2 0:VAL121 4.7 96.0 1.0
SG 0:CYS155 4.8 114.1 1.0
SG 0:CYS190 4.8 124.6 1.0
CG 0:HIS118 4.8 104.8 1.0

Iron binding site 3 out of 4 in 7nw0

Go back to Iron Binding Sites List in 7nw0
Iron binding site 3 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:156.0
occ:1.00
 FE3 0:SF41000 0.0 156.0 1.0
SG 0:CYS134 2.3 118.3 1.0
S2 0:SF41000 2.3 156.0 1.0
S1 0:SF41000 2.3 156.0 1.0
S4 0:SF41000 2.3 156.0 1.0
FE2 0:SF41000 2.7 156.0 1.0
FE1 0:SF41000 2.7 156.0 1.0
FE4 0:SF41000 2.7 156.0 1.0
CB 0:CYS134 3.4 118.3 1.0
S3 0:SF41000 3.9 156.0 1.0
CA 0:CYS134 4.1 118.3 1.0
CE2 0:PHE193 4.1 115.8 1.0
O 0:CYS134 4.7 118.3 1.0
SG 0:CYS116 4.7 119.3 1.0
SG 0:CYS190 4.8 124.6 1.0
C 0:CYS134 4.8 118.3 1.0
SG 0:CYS155 4.8 114.1 1.0
CZ 0:PHE193 4.8 115.8 1.0
CD2 0:PHE193 5.0 115.8 1.0

Iron binding site 4 out of 4 in 7nw0

Go back to Iron Binding Sites List in 7nw0
Iron binding site 4 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:156.0
occ:1.00
 FE4 0:SF41000 0.0 156.0 1.0
SG 0:CYS155 2.2 114.1 1.0
S2 0:SF41000 2.3 156.0 1.0
S1 0:SF41000 2.3 156.0 1.0
S3 0:SF41000 2.3 156.0 1.0
FE1 0:SF41000 2.7 156.0 1.0
FE2 0:SF41000 2.7 156.0 1.0
FE3 0:SF41000 2.7 156.0 1.0
CB 0:CYS155 3.7 114.1 1.0
S4 0:SF41000 3.9 156.0 1.0
CB 0:HIS118 3.9 104.8 1.0
ND1 0:HIS118 4.0 104.8 1.0
CG 0:HIS118 4.1 104.8 1.0
CD2 0:PHE157 4.3 116.5 1.0
SG 0:CYS190 4.6 124.6 1.0
SG 0:CYS116 4.8 119.3 1.0
CB 0:PHE157 4.8 116.5 1.0
SG 0:CYS134 4.8 118.3 1.0
CE1 0:HIS118 4.8 104.8 1.0
CD2 0:HIS118 4.9 104.8 1.0
CA 0:CYS155 4.9 114.1 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: Thu Aug 8 09:54:02 2024

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