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Iron in PDB 7ml4: Rna Polymerase II Initially Transcribing Complex (Itc)

Enzymatic activity of Rna Polymerase II Initially Transcribing Complex (Itc)

All present enzymatic activity of Rna Polymerase II Initially Transcribing Complex (Itc):
2.7.7.6; 3.6.4.12;

Other elements in 7ml4:

The structure of Rna Polymerase II Initially Transcribing Complex (Itc) also contains other interesting chemical elements:

Zinc (Zn) 15 atoms
Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Rna Polymerase II Initially Transcribing Complex (Itc) (pdb code 7ml4). 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 Initially Transcribing Complex (Itc), PDB code: 7ml4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7ml4

Go back to Iron Binding Sites List in 7ml4
Iron binding site 1 out of 4 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) 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
S3 0:SF4801 2.3 0.0 1.0
SG 0:CYS115 2.3 117.6 1.0
S4 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
FE4 0:SF4801 2.7 0.0 1.0
FE2 0:SF4801 2.7 0.0 1.0
CB 0:CYS115 3.6 117.6 1.0
CA 0:CYS115 3.7 117.6 1.0
SG 0:CYS133 3.9 46.6 1.0
S1 0:SF4801 3.9 0.0 1.0
N 0:LEU116 4.1 100.9 1.0
CB 0:CYS133 4.2 46.6 1.0
CB 0:CYS191 4.2 115.3 1.0
C 0:CYS115 4.5 117.6 1.0
SG 0:CYS191 4.6 115.3 1.0
N 0:HIS117 4.7 89.3 1.0
N 0:CYS115 4.9 117.6 1.0
CG1 0:VAL120 4.9 54.5 1.0
O 0:ARG111 4.9 123.3 1.0
SG 0:CYS156 4.9 90.8 1.0
O 0:LEU114 5.0 146.6 1.0

Iron binding site 2 out of 4 in 7ml4

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Iron binding site 2 out of 4 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) 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
S4 0:SF4801 2.3 0.0 1.0
S1 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
O 0:CYS156 3.1 90.8 1.0
CB 0:CYS156 3.3 90.8 1.0
CD1 0:TYR158 3.3 101.9 1.0
CB 0:HIS117 3.6 89.3 1.0
CA 0:CYS156 3.7 90.8 1.0
C 0:CYS156 3.7 90.8 1.0
S2 0:SF4801 3.9 0.0 1.0
CB 0:TYR158 4.0 101.9 1.0
SG 0:CYS156 4.0 90.8 1.0
CG 0:TYR158 4.1 101.9 1.0
N 0:HIS117 4.1 89.3 1.0
CE1 0:TYR158 4.2 101.9 1.0
CG 0:HIS117 4.4 89.3 1.0
N 0:TYR158 4.4 101.9 1.0
CD2 0:HIS117 4.4 89.3 1.0
CA 0:HIS117 4.4 89.3 1.0
SG 0:CYS115 4.7 117.6 1.0
CB 0:CYS191 4.7 115.3 1.0
CA 0:TYR158 4.7 101.9 1.0
SG 0:CYS191 4.8 115.3 1.0
N 0:HIS159 4.8 57.3 1.0
N 0:LEU116 4.9 100.9 1.0
N 0:GLU157 4.9 215.2 1.0
SD 0:MET136 4.9 134.6 1.0
SG 0:CYS133 4.9 46.6 1.0

Iron binding site 3 out of 4 in 7ml4

Go back to Iron Binding Sites List in 7ml4
Iron binding site 3 out of 4 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) 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 2.3 46.6 1.0
S4 0:SF4801 2.3 0.0 1.0
SG 0:CYS156 2.3 90.8 1.0
S1 0:SF4801 2.3 0.0 1.0
S2 0:SF4801 2.3 0.0 1.0
FE2 0:SF4801 2.7 0.0 1.0
FE1 0:SF4801 2.7 0.0 1.0
FE4 0:SF4801 2.7 0.0 1.0
CB 0:CYS156 2.9 90.8 1.0
CB 0:CYS133 3.3 46.6 1.0
S3 0:SF4801 3.9 0.0 1.0
CA 0:CYS133 4.0 46.6 1.0
CA 0:CYS156 4.0 90.8 1.0
CE2 0:PHE194 4.4 83.2 1.0
O 0:CYS133 4.5 46.6 1.0
SG 0:CYS115 4.6 117.6 1.0
C 0:CYS133 4.6 46.6 1.0
CB 0:HIS159 4.6 57.3 1.0
SD 0:MET136 4.8 134.6 1.0
OG1 0:THR137 4.9 144.2 1.0
C 0:CYS156 4.9 90.8 1.0
SG 0:CYS191 4.9 115.3 1.0
O 0:CYS156 5.0 90.8 1.0
CD2 0:PHE194 5.0 83.2 1.0
N 0:HIS159 5.0 57.3 1.0

Iron binding site 4 out of 4 in 7ml4

Go back to Iron Binding Sites List in 7ml4
Iron binding site 4 out of 4 in the Rna Polymerase II Initially Transcribing Complex (Itc)


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 Initially Transcribing Complex (Itc) 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
S2 0:SF4801 2.3 0.0 1.0
S3 0:SF4801 2.3 0.0 1.0
S1 0:SF4801 2.3 0.0 1.0
SG 0:CYS191 2.3 115.3 1.0
FE2 0:SF4801 2.7 0.0 1.0
FE1 0:SF4801 2.7 0.0 1.0
FE3 0:SF4801 2.7 0.0 1.0
CB 0:CYS191 2.9 115.3 1.0
CB 0:TYR158 3.6 101.9 1.0
N 0:HIS159 3.6 57.3 1.0
S4 0:SF4801 3.9 0.0 1.0
CD2 0:PHE194 4.0 83.2 1.0
CB 0:CYS156 4.0 90.8 1.0
C 0:TYR158 4.2 101.9 1.0
CE2 0:PHE194 4.2 83.2 1.0
CB 0:HIS159 4.3 57.3 1.0
SG 0:CYS133 4.4 46.6 1.0
CA 0:CYS191 4.4 115.3 1.0
CA 0:TYR158 4.4 101.9 1.0
SG 0:CYS156 4.4 90.8 1.0
CA 0:HIS159 4.4 57.3 1.0
CG 0:TYR158 4.6 101.9 1.0
CD1 0:TYR158 4.6 101.9 1.0
N 0:TYR158 4.8 101.9 1.0
N 0:CYS191 4.8 115.3 1.0
SG 0:CYS115 5.0 117.6 1.0
O 0:TYR158 5.0 101.9 1.0

Reference:

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
Page generated: Thu Aug 8 09:26:40 2024

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