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

Enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Distal Position

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

Other elements in 7nvz:

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

Iron binding site 1 out of 4 in 7nvz

Go back to Iron Binding Sites List in 7nvz
Iron binding site 1 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Distal 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 Distal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:254.7
occ:1.00
 FE1 0:SF41000 0.0 254.7 1.0
SG 0:CYS190 2.2 111.7 1.0
S3 0:SF41000 2.3 254.7 1.0
S4 0:SF41000 2.3 254.7 1.0
S2 0:SF41000 2.3 254.7 1.0
FE4 0:SF41000 2.7 254.7 1.0
FE3 0:SF41000 2.7 254.7 1.0
FE2 0:SF41000 2.7 254.7 1.0
CB 0:CYS190 3.7 111.7 1.0
S1 0:SF41000 3.9 254.7 1.0
CE1 0:PHE193 4.0 106.0 1.0
CD1 0:PHE193 4.1 106.0 1.0
CA 0:CYS190 4.5 111.7 1.0
CB 0:PHE157 4.6 106.5 1.0
SG 0:CYS155 4.6 124.6 1.0
SG 0:CYS134 4.8 125.3 1.0
N 0:TYR158 4.8 118.6 1.0
SG 0:CYS116 4.8 111.6 1.0
CB 0:TYR158 4.9 118.6 1.0

Iron binding site 2 out of 4 in 7nvz

Go back to Iron Binding Sites List in 7nvz
Iron binding site 2 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Distal 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 Distal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:254.7
occ:1.00
 FE2 0:SF41000 0.0 254.7 1.0
SG 0:CYS116 2.3 111.6 1.0
S3 0:SF41000 2.3 254.7 1.0
S4 0:SF41000 2.3 254.7 1.0
S1 0:SF41000 2.3 254.7 1.0
FE3 0:SF41000 2.7 254.7 1.0
FE4 0:SF41000 2.7 254.7 1.0
FE1 0:SF41000 2.7 254.7 1.0
CB 0:CYS116 3.8 111.6 1.0
S2 0:SF41000 3.9 254.7 1.0
CB 0:HIS118 4.1 113.6 1.0
N 0:ILE117 4.4 109.4 1.0
N 0:HIS118 4.4 113.6 1.0
CA 0:CYS116 4.5 111.6 1.0
CG2 0:VAL121 4.7 114.2 1.0
SG 0:CYS134 4.7 125.3 1.0
SG 0:CYS155 4.8 124.6 1.0
SG 0:CYS190 4.8 111.7 1.0
CA 0:HIS118 4.9 113.6 1.0
C 0:CYS116 4.9 111.6 1.0

Iron binding site 3 out of 4 in 7nvz

Go back to Iron Binding Sites List in 7nvz
Iron binding site 3 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Distal 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 Distal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:254.7
occ:1.00
 FE3 0:SF41000 0.0 254.7 1.0
SG 0:CYS134 2.3 125.3 1.0
S2 0:SF41000 2.3 254.7 1.0
S1 0:SF41000 2.3 254.7 1.0
S4 0:SF41000 2.3 254.7 1.0
FE2 0:SF41000 2.7 254.7 1.0
FE1 0:SF41000 2.7 254.7 1.0
FE4 0:SF41000 2.7 254.7 1.0
CB 0:CYS134 3.4 125.3 1.0
S3 0:SF41000 3.9 254.7 1.0
CA 0:CYS134 4.1 125.3 1.0
CE1 0:PHE193 4.2 106.0 1.0
O 0:CYS134 4.7 125.3 1.0
SG 0:CYS116 4.7 111.6 1.0
SG 0:CYS190 4.8 111.7 1.0
SG 0:CYS155 4.8 124.6 1.0
C 0:CYS134 4.8 125.3 1.0
CZ 0:PHE193 4.9 106.0 1.0

Iron binding site 4 out of 4 in 7nvz

Go back to Iron Binding Sites List in 7nvz
Iron binding site 4 out of 4 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Distal 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 Distal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Fe1000

b:254.7
occ:1.00
 FE4 0:SF41000 0.0 254.7 1.0
SG 0:CYS155 2.2 124.6 1.0
S2 0:SF41000 2.3 254.7 1.0
S1 0:SF41000 2.3 254.7 1.0
S3 0:SF41000 2.3 254.7 1.0
FE1 0:SF41000 2.7 254.7 1.0
FE2 0:SF41000 2.7 254.7 1.0
FE3 0:SF41000 2.7 254.7 1.0
CB 0:CYS155 3.7 124.6 1.0
S4 0:SF41000 3.9 254.7 1.0
CB 0:HIS118 4.2 113.6 1.0
CD2 0:PHE157 4.2 106.5 1.0
CD2 0:HIS118 4.4 113.6 1.0
CG 0:HIS118 4.4 113.6 1.0
SG 0:CYS190 4.6 111.7 1.0
SG 0:CYS116 4.7 111.6 1.0
CB 0:PHE157 4.8 106.5 1.0
SG 0:CYS134 4.8 125.3 1.0
CA 0:CYS155 4.9 124.6 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 09:53:22 2024

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