Iron in PDB 7nvy: Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position

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

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

Zinc	(Zn)	17 atoms
Magnesium	(Mg)	1 atom

The binding sites of Iron atom in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position (pdb code 7nvy). 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 Closed Promoter Dna in Proximal Position, PDB code: 7nvy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


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 Closed Promoter Dna in Proximal Position within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe1000 b:89.3 occ:1.00 FE1 0:SF41000 0.0 89.3 1.0 SG 0:CYS190 2.2 50.2 1.0 S3 0:SF41000 2.3 89.3 1.0 S4 0:SF41000 2.3 89.3 1.0 S2 0:SF41000 2.3 89.3 1.0 FE4 0:SF41000 2.7 89.3 1.0 FE3 0:SF41000 2.7 89.3 1.0 FE2 0:SF41000 2.7 89.3 1.0 CB 0:CYS190 3.7 50.2 1.0 S1 0:SF41000 3.9 89.3 1.0 CE1 0:PHE193 4.0 54.6 1.0 CD1 0:PHE193 4.1 54.6 1.0 CA 0:CYS190 4.5 50.2 1.0 CB 0:PHE157 4.6 70.8 1.0 SG 0:CYS155 4.6 72.7 1.0 SG 0:CYS134 4.7 70.7 1.0 SG 0:CYS116 4.8 57.7 1.0 N 0:TYR158 4.8 72.0 1.0 CB 0:TYR158 4.9 72.0 1.0

Iron binding site 2 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


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 Closed Promoter Dna in Proximal Position within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe1000 b:89.3 occ:1.00 FE2 0:SF41000 0.0 89.3 1.0 SG 0:CYS116 2.3 57.7 1.0 S3 0:SF41000 2.3 89.3 1.0 S4 0:SF41000 2.3 89.3 1.0 S1 0:SF41000 2.3 89.3 1.0 FE3 0:SF41000 2.7 89.3 1.0 FE4 0:SF41000 2.7 89.3 1.0 FE1 0:SF41000 2.7 89.3 1.0 CB 0:CYS116 3.8 57.7 1.0 S2 0:SF41000 3.9 89.3 1.0 CB 0:HIS118 4.1 71.2 1.0 N 0:ILE117 4.4 59.9 1.0 N 0:HIS118 4.4 71.2 1.0 CA 0:CYS116 4.5 57.7 1.0 CG2 0:VAL121 4.7 76.7 1.0 SG 0:CYS134 4.7 70.7 1.0 SG 0:CYS155 4.8 72.7 1.0 SG 0:CYS190 4.8 50.2 1.0 CA 0:HIS118 4.9 71.2 1.0 C 0:CYS116 5.0 57.7 1.0

Iron binding site 3 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


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 Closed Promoter Dna in Proximal Position within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe1000 b:89.3 occ:1.00 FE3 0:SF41000 0.0 89.3 1.0 SG 0:CYS134 2.3 70.7 1.0 S2 0:SF41000 2.3 89.3 1.0 S1 0:SF41000 2.3 89.3 1.0 S4 0:SF41000 2.3 89.3 1.0 FE2 0:SF41000 2.7 89.3 1.0 FE1 0:SF41000 2.7 89.3 1.0 FE4 0:SF41000 2.7 89.3 1.0 CB 0:CYS134 3.4 70.7 1.0 S3 0:SF41000 3.9 89.3 1.0 CA 0:CYS134 4.1 70.7 1.0 CE1 0:PHE193 4.2 54.6 1.0 O 0:CYS134 4.7 70.7 1.0 SG 0:CYS116 4.7 57.7 1.0 SG 0:CYS190 4.8 50.2 1.0 SG 0:CYS155 4.8 72.7 1.0 C 0:CYS134 4.8 70.7 1.0 CZ 0:PHE193 4.9 54.6 1.0

Iron binding site 4 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


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 Closed Promoter Dna in Proximal Position within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe1000 b:89.3 occ:1.00 FE4 0:SF41000 0.0 89.3 1.0 SG 0:CYS155 2.2 72.7 1.0 S2 0:SF41000 2.3 89.3 1.0 S1 0:SF41000 2.3 89.3 1.0 S3 0:SF41000 2.3 89.3 1.0 FE1 0:SF41000 2.7 89.3 1.0 FE2 0:SF41000 2.7 89.3 1.0 FE3 0:SF41000 2.7 89.3 1.0 CB 0:CYS155 3.7 72.7 1.0 S4 0:SF41000 3.9 89.3 1.0 CB 0:HIS118 4.3 71.2 1.0 CD2 0:PHE157 4.3 70.8 1.0 CD2 0:HIS118 4.4 71.2 1.0 CG 0:HIS118 4.5 71.2 1.0 SG 0:CYS190 4.6 50.2 1.0 SG 0:CYS116 4.8 57.7 1.0 CB 0:PHE157 4.8 70.8 1.0 SG 0:CYS134 4.8 70.7 1.0 CA 0:CYS155 5.0 72.7 1.0

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