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Iron in PDB 7zsa: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)

Enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B):
2.7.7.6; 3.6.4.12;

Other elements in 7zsa:

The structure of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) (pdb code 7zsa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B), PDB code: 7zsa:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7zsa

Go back to Iron Binding Sites List in 7zsa
Iron binding site 1 out of 4 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe801

b:51.0
occ:1.00
 FE1 0:SF4801 0.0 51.0 1.0
SG 0:CYS115 2.3 49.1 1.0
S3 0:SF4801 2.3 51.0 1.0
S2 0:SF4801 2.3 51.0 1.0
S4 0:SF4801 2.3 51.0 1.0
FE2 0:SF4801 2.7 51.0 1.0
FE4 0:SF4801 2.7 51.0 1.0
FE3 0:SF4801 2.7 51.0 1.0
CB 0:CYS115 3.3 49.1 1.0
CA 0:CYS115 3.7 49.1 1.0
S1 0:SF4801 3.9 51.0 1.0
CB 0:HIS117 4.1 50.9 1.0
N 0:LEU116 4.3 49.8 1.0
N 0:HIS117 4.4 50.9 1.0
C 0:CYS115 4.4 49.1 1.0
SG 0:CYS156 4.7 83.3 1.0
O 0:LEU114 4.8 46.2 1.0
SG 0:CYS133 4.8 57.7 1.0
N 0:CYS115 4.9 49.1 1.0
CG1 0:VAL120 4.9 49.8 1.0
CA 0:HIS117 4.9 50.9 1.0
CB 0:CYS133 4.9 57.7 1.0
SG 0:CYS191 4.9 59.9 1.0

Iron binding site 2 out of 4 in 7zsa

Go back to Iron Binding Sites List in 7zsa
Iron binding site 2 out of 4 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe801

b:51.0
occ:1.00
 FE2 0:SF4801 0.0 51.0 1.0
SG 0:CYS156 2.3 83.3 1.0
S1 0:SF4801 2.3 51.0 1.0
S3 0:SF4801 2.3 51.0 1.0
S4 0:SF4801 2.3 51.0 1.0
FE4 0:SF4801 2.7 51.0 1.0
FE1 0:SF4801 2.7 51.0 1.0
FE3 0:SF4801 2.7 51.0 1.0
CB 0:CYS156 3.2 83.3 1.0
S2 0:SF4801 3.9 51.0 1.0
CB 0:HIS117 4.4 50.9 1.0
CB 0:TYR158 4.5 68.3 1.0
SG 0:CYS191 4.6 59.9 1.0
CA 0:CYS156 4.7 83.3 1.0
CB 0:CYS191 4.7 59.9 1.0
N 0:HIS159 4.7 65.0 1.0
SG 0:CYS115 4.7 49.1 1.0
CB 0:HIS159 4.8 65.0 1.0
SG 0:CYS133 4.8 57.7 1.0
CD2 0:TYR158 4.8 68.3 1.0
CG 0:HIS117 5.0 50.9 1.0

Iron binding site 3 out of 4 in 7zsa

Go back to Iron Binding Sites List in 7zsa
Iron binding site 3 out of 4 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe801

b:51.0
occ:1.00
 FE3 0:SF4801 0.0 51.0 1.0
SG 0:CYS133 2.3 57.7 1.0
S1 0:SF4801 2.3 51.0 1.0
S2 0:SF4801 2.3 51.0 1.0
S4 0:SF4801 2.3 51.0 1.0
FE4 0:SF4801 2.7 51.0 1.0
FE1 0:SF4801 2.7 51.0 1.0
FE2 0:SF4801 2.7 51.0 1.0
CB 0:CYS133 3.0 57.7 1.0
CA 0:CYS133 3.8 57.7 1.0
S3 0:SF4801 3.9 51.0 1.0
CE2 0:PHE194 4.3 50.6 1.0
SG 0:CYS191 4.6 59.9 1.0
C 0:CYS133 4.7 57.7 1.0
O 0:CYS133 4.7 57.7 1.0
CG2 0:THR137 4.7 58.9 1.0
SG 0:CYS115 4.8 49.1 1.0
CD 0:ARG111 4.8 46.0 1.0
SG 0:CYS156 4.9 83.3 1.0
CD2 0:PHE194 4.9 50.6 1.0
N 0:CYS133 5.0 57.7 1.0
OG1 0:THR137 5.0 58.9 1.0

Iron binding site 4 out of 4 in 7zsa

Go back to Iron Binding Sites List in 7zsa
Iron binding site 4 out of 4 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with the +1 Nucleosome and Ntp (Complex B) within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe801

b:51.0
occ:1.00
 FE4 0:SF4801 0.0 51.0 1.0
SG 0:CYS191 2.3 59.9 1.0
S1 0:SF4801 2.3 51.0 1.0
S2 0:SF4801 2.3 51.0 1.0
S3 0:SF4801 2.3 51.0 1.0
FE3 0:SF4801 2.7 51.0 1.0
FE2 0:SF4801 2.7 51.0 1.0
FE1 0:SF4801 2.7 51.0 1.0
CB 0:CYS191 3.2 59.9 1.0
S4 0:SF4801 3.9 51.0 1.0
O 0:LEU114 4.2 46.2 1.0
CA 0:CYS191 4.2 59.9 1.0
CD2 0:PHE194 4.4 50.6 1.0
SG 0:CYS133 4.6 57.7 1.0
CE2 0:PHE194 4.6 50.6 1.0
SG 0:CYS156 4.7 83.3 1.0
CA 0:CYS115 4.7 49.1 1.0
SG 0:CYS115 4.8 49.1 1.0
C 0:CYS191 4.9 59.9 1.0
CB 0:TYR193 4.9 45.6 1.0

Reference:

H.Wang, S.Schilbach, M.Ninov, H.Urlaub, P.Cramer. Structures of Transcription Preinitiation Complex Engaged with the +1 Nucleosome. Nat.Struct.Mol.Biol. 2022.
ISSN: ESSN 1545-9985
PubMed: 36411341
DOI: 10.1038/S41594-022-00865-W
Page generated: Fri Aug 9 15:20:29 2024

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