Iron in PDB 7ml1: Rna Polymerase II Pre-Initiation Complex (PIC2)

All present enzymatic activity of Rna Polymerase II Pre-Initiation Complex (PIC2):
2.7.7.6; 3.6.4.12;

The structure of Rna Polymerase II Pre-Initiation Complex (PIC2) also contains other interesting chemical elements:

Zinc	(Zn)	19 atoms
Magnesium	(Mg)	1 atom

The binding sites of Iron atom in the Rna Polymerase II Pre-Initiation Complex (PIC2) (pdb code 7ml1). 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 (PIC2), PDB code: 7ml1:
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 (PIC2)


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 (PIC2) within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe801 b:0.0 occ:1.00 FE1 0:SF4801 0.0 0.0 1.0 SG 0:CYS115 2.3 117.6 1.0 S3 0:SF4801 2.3 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 S4 0:SF4801 2.3 0.0 1.0 CB 0:CYS115 2.4 117.6 1.0 CA 0:CYS115 2.6 117.6 1.0 FE3 0:SF4801 2.7 0.0 1.0 FE4 0:SF4801 2.7 0.0 1.0 FE2 0:SF4801 2.7 0.0 1.0 C 0:CYS115 3.1 117.6 1.0 N 0:LEU116 3.3 100.9 1.0 N 0:HIS117 3.7 89.3 1.0 S1 0:SF4801 3.9 0.0 1.0 O 0:CYS115 4.0 117.6 1.0 N 0:CYS115 4.0 117.6 1.0 SG 0:CYS156 4.0 90.8 1.0 CB 0:HIS117 4.1 89.3 1.0 SG 0:CYS133 4.2 46.6 1.0 CB 0:CYS133 4.2 46.6 1.0 CB 0:CYS156 4.5 90.8 1.0 CA 0:LEU116 4.5 100.9 1.0 CA 0:HIS117 4.6 89.3 1.0 C 0:LEU116 4.6 100.9 1.0 O 0:LEU114 4.6 146.6 1.0 C 0:LEU114 4.8 146.6 1.0 CG 0:ARG111 4.9 123.3 1.0

Iron binding site 2 out of 4 in the Rna Polymerase II Pre-Initiation Complex (PIC2)


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 (PIC2) within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe801 b:0.0 occ:1.00 FE2 0:SF4801 0.0 0.0 1.0 CB 0:CYS156 1.9 90.8 1.0 SG 0:CYS156 2.3 90.8 1.0 S1 0:SF4801 2.3 0.0 1.0 S4 0:SF4801 2.3 0.0 1.0 S3 0:SF4801 2.3 0.0 1.0 FE3 0:SF4801 2.7 0.0 1.0 FE4 0:SF4801 2.7 0.0 1.0 FE1 0:SF4801 2.7 0.0 1.0 CB 0:HIS117 2.9 89.3 1.0 CA 0:CYS156 3.0 90.8 1.0 CG 0:HIS117 3.8 89.3 1.0 CD1 0:TYR158 3.8 101.9 1.0 C 0:CYS156 3.8 90.8 1.0 N 0:HIS117 3.8 89.3 1.0 S2 0:SF4801 3.9 0.0 1.0 CA 0:HIS117 3.9 89.3 1.0 O 0:CYS156 4.0 90.8 1.0 CD2 0:HIS117 4.1 89.3 1.0 SG 0:CYS115 4.1 117.6 1.0 N 0:CYS156 4.2 90.8 1.0 CB 0:TYR158 4.3 101.9 1.0 CG 0:TYR158 4.4 101.9 1.0 CE1 0:TYR158 4.6 101.9 1.0 N 0:TYR158 4.7 101.9 1.0 N 0:GLU157 4.8 215.2 1.0 SD 0:MET136 4.8 134.6 1.0 SG 0:CYS133 4.8 46.6 1.0 N 0:LEU116 4.9 100.9 1.0 CB 0:CYS133 4.9 46.6 1.0 CG2 0:VAL120 4.9 54.5 1.0 ND1 0:HIS117 4.9 89.3 1.0 C 0:LEU116 5.0 100.9 1.0

Iron binding site 3 out of 4 in the Rna Polymerase II Pre-Initiation Complex (PIC2)


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 (PIC2) within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe801 b:0.0 occ:1.00 FE3 0:SF4801 0.0 0.0 1.0 SG 0:CYS133 2.2 46.6 1.0 S4 0:SF4801 2.3 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 S1 0:SF4801 2.3 0.0 1.0 SG 0:CYS156 2.3 90.8 1.0 FE4 0:SF4801 2.7 0.0 1.0 FE1 0:SF4801 2.7 0.0 1.0 FE2 0:SF4801 2.7 0.0 1.0 CB 0:CYS133 3.0 46.6 1.0 CB 0:CYS156 3.3 90.8 1.0 CE2 0:PHE194 3.3 83.2 1.0 OG1 0:THR137 3.4 144.2 1.0 S3 0:SF4801 3.9 0.0 1.0 CA 0:CYS133 4.0 46.6 1.0 CD2 0:PHE194 4.1 83.2 1.0 CZ 0:PHE194 4.3 83.2 1.0 O 0:CYS133 4.4 46.6 1.0 SG 0:CYS115 4.4 117.6 1.0 NE 0:ARG111 4.4 123.3 1.0 C 0:CYS133 4.5 46.6 1.0 CG2 0:THR137 4.5 144.2 1.0 CB 0:THR137 4.6 144.2 1.0 CB 0:CYS115 4.6 117.6 1.0 CA 0:CYS156 4.7 90.8 1.0 CD2 0:TYR193 5.0 84.4 1.0

Iron binding site 4 out of 4 in the Rna Polymerase II Pre-Initiation Complex (PIC2)


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 (PIC2) within 5.0Å range: probe atom residue distance (Å) B Occ 0:Fe801 b:0.0 occ:1.00 FE4 0:SF4801 0.0 0.0 1.0 S3 0:SF4801 2.3 0.0 1.0 S1 0:SF4801 2.3 0.0 1.0 S2 0:SF4801 2.3 0.0 1.0 FE3 0:SF4801 2.7 0.0 1.0 FE2 0:SF4801 2.7 0.0 1.0 FE1 0:SF4801 2.7 0.0 1.0 CB 0:CYS191 2.9 115.3 1.0 CB 0:TYR158 3.4 101.9 1.0 CB 0:CYS156 3.6 90.8 1.0 CD2 0:PHE194 3.8 83.2 1.0 S4 0:SF4801 3.9 0.0 1.0 N 0:HIS159 3.9 57.3 1.0 SG 0:CYS191 3.9 115.3 1.0 CE2 0:PHE194 4.0 83.2 1.0 SG 0:CYS156 4.0 90.8 1.0 CA 0:CYS191 4.0 115.3 1.0 CG 0:TYR158 4.2 101.9 1.0 C 0:TYR158 4.3 101.9 1.0 CA 0:TYR158 4.3 101.9 1.0 N 0:LEU116 4.4 100.9 1.0 CD1 0:TYR158 4.5 101.9 1.0 CA 0:CYS115 4.5 117.6 1.0 CB 0:HIS159 4.6 57.3 1.0 CA 0:HIS159 4.7 57.3 1.0 N 0:TYR158 4.7 101.9 1.0 SG 0:CYS133 4.7 46.6 1.0 N 0:CYS191 4.9 115.3 1.0 CB 0:CYS115 4.9 117.6 1.0 C 0:CYS115 4.9 117.6 1.0 N 0:HIS117 4.9 89.3 1.0 SG 0:CYS115 5.0 117.6 1.0

C.Yang, R.Fujiwara, H.J.Kim, P.Basnet, Y.Zhu, J.J.Gorbea Colon, S.Steimle, B.A.Garcia, C.D.Kaplan, K.Murakami. Structural Visualization of De Novo Transcription Initiation By Saccharomyces Cerevisiae Rna Polymerase II. Mol.Cell V. 82 660 2022.
ISSN: ISSN 1097-2765
PubMed: 35051353
DOI: 10.1016/J.MOLCEL.2021.12.020