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Iron in PDB 8dy9: Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors

Enzymatic activity of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors

All present enzymatic activity of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors:
2.7.7.6;

Other elements in 8dy9:

The structure of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors (pdb code 8dy9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors, PDB code: 8dy9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8dy9

Go back to Iron Binding Sites List in 8dy9
Iron binding site 1 out of 4 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:57.7
occ:1.00
 FE1 H:SF4101 0.0 57.7 1.0
SG H:CYS25 2.3 57.0 1.0
S3 H:SF4101 2.3 57.7 1.0
S2 H:SF4101 2.3 57.7 1.0
S4 H:SF4101 2.3 57.7 1.0
FE4 H:SF4101 2.7 57.7 1.0
FE2 H:SF4101 2.7 57.7 1.0
FE3 H:SF4101 2.7 57.7 1.0
HB3 H:CYS25 2.9 57.0 1.0
H H:CYS25 3.2 57.0 1.0
CB H:CYS25 3.2 57.0 1.0
HB1 H:ALA23 3.4 61.4 1.0
HB2 F:PRO504 3.7 65.5 1.0
HB2 H:CYS25 3.9 57.0 1.0
S1 H:SF4101 3.9 57.7 1.0
N H:CYS25 3.9 57.0 1.0
HE1 F:HIS503 4.2 69.2 1.0
CA H:CYS25 4.2 57.0 1.0
HE2 H:PHE33 4.2 65.2 1.0
HG2 F:PRO504 4.2 65.5 1.0
CB H:ALA23 4.3 61.4 1.0
H H:LEU24 4.5 56.8 1.0
HD2 F:PRO504 4.5 65.5 1.0
O F:PRO504 4.6 65.5 1.0
HB2 H:ALA23 4.6 61.4 1.0
CB F:PRO504 4.6 65.5 1.0
CE2 H:PHE33 4.7 65.2 1.0
HB2 H:CYS51 4.7 65.3 1.0
SG H:CYS51 4.7 65.3 1.0
SG H:CYS48 4.7 67.3 1.0
SG H:CYS57 4.7 75.0 1.0
HA H:ALA23 4.7 61.4 1.0
HA H:CYS25 4.8 57.0 1.0
N H:LEU24 4.8 56.8 1.0
CG F:PRO504 4.8 65.5 1.0
CE1 F:HIS503 4.9 69.2 1.0
HB3 H:ALA23 4.9 61.4 1.0
CA H:ALA23 5.0 61.4 1.0

Iron binding site 2 out of 4 in 8dy9

Go back to Iron Binding Sites List in 8dy9
Iron binding site 2 out of 4 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:57.7
occ:1.00
 FE2 H:SF4101 0.0 57.7 1.0
SG H:CYS48 2.3 67.3 1.0
S4 H:SF4101 2.3 57.7 1.0
S3 H:SF4101 2.3 57.7 1.0
S1 H:SF4101 2.3 57.7 1.0
FE1 H:SF4101 2.7 57.7 1.0
FE3 H:SF4101 2.7 57.7 1.0
FE4 H:SF4101 2.7 57.7 1.0
HA H:CYS48 3.1 67.3 1.0
HB3 H:CYS48 3.2 67.3 1.0
CB H:CYS48 3.2 67.3 1.0
HE2 H:PHE33 3.5 65.2 1.0
CA H:CYS48 3.6 67.3 1.0
H H:GLY72 3.8 73.8 1.0
S2 H:SF4101 3.9 57.7 1.0
H H:GLY73 4.0 75.4 1.0
HB2 H:CYS48 4.1 67.3 1.0
HB3 H:CYS51 4.1 65.3 1.0
HB3 H:CYS25 4.1 57.0 1.0
HA2 H:GLY72 4.3 73.8 1.0
CE2 H:PHE33 4.3 65.2 1.0
N H:GLY72 4.4 73.8 1.0
HB2 H:CYS51 4.4 65.3 1.0
N H:GLY73 4.5 75.4 1.0
N H:CYS48 4.5 67.3 1.0
CB H:CYS51 4.6 65.3 1.0
HG12 H:VAL47 4.7 61.9 1.0
HD2 H:PHE33 4.7 65.2 1.0
C H:CYS48 4.7 67.3 1.0
H H:CYS48 4.7 67.3 1.0
CA H:GLY72 4.7 73.8 1.0
HA H:TRP71 4.7 76.7 1.0
O H:CYS48 4.7 67.3 1.0
SG H:CYS25 4.7 57.0 1.0
SG H:CYS57 4.8 75.0 1.0
SG H:CYS51 4.8 65.3 1.0
CB H:CYS25 4.9 57.0 1.0
H H:CYS25 4.9 57.0 1.0
CD2 H:PHE33 5.0 65.2 1.0
C H:GLY72 5.0 73.8 1.0

Iron binding site 3 out of 4 in 8dy9

Go back to Iron Binding Sites List in 8dy9
Iron binding site 3 out of 4 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:57.7
occ:1.00
 FE3 H:SF4101 0.0 57.7 1.0
SG H:CYS57 2.3 75.0 1.0
S1 H:SF4101 2.3 57.7 1.0
S2 H:SF4101 2.3 57.7 1.0
S4 H:SF4101 2.3 57.7 1.0
FE1 H:SF4101 2.7 57.7 1.0
FE2 H:SF4101 2.7 57.7 1.0
FE4 H:SF4101 2.7 57.7 1.0
HB2 H:CYS57 2.8 75.0 1.0
CB H:CYS57 2.9 75.0 1.0
H H:GLY72 2.9 73.8 1.0
HB3 H:CYS57 3.0 75.0 1.0
HG2 F:PRO504 3.7 65.5 1.0
N H:GLY72 3.8 73.8 1.0
HA2 H:GLY72 3.8 73.8 1.0
S3 H:SF4101 3.9 57.7 1.0
HA H:TRP71 4.1 76.7 1.0
HA H:ARG54 4.2 70.2 1.0
HZ3 H:TRP19 4.3 74.4 1.0
CA H:GLY72 4.4 73.8 1.0
CA H:CYS57 4.4 75.0 1.0
HB2 F:PRO504 4.6 65.5 1.0
HG23 H:VAL53 4.6 69.4 1.0
HB3 H:TRP71 4.6 76.7 1.0
CG F:PRO504 4.7 65.5 1.0
HA H:CYS57 4.7 75.0 1.0
SG H:CYS48 4.7 67.3 1.0
SG H:CYS51 4.8 65.3 1.0
HD2 F:PRO504 4.8 65.5 1.0
C H:TRP71 4.8 76.7 1.0
SG H:CYS25 4.8 57.0 1.0
CA H:TRP71 4.9 76.7 1.0
H H:GLY73 4.9 75.4 1.0
HB1 H:ALA23 5.0 61.4 1.0
HA3 H:GLY72 5.0 73.8 1.0

Iron binding site 4 out of 4 in 8dy9

Go back to Iron Binding Sites List in 8dy9
Iron binding site 4 out of 4 in the Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:57.7
occ:1.00
 FE4 H:SF4101 0.0 57.7 1.0
SG H:CYS51 2.3 65.3 1.0
S3 H:SF4101 2.3 57.7 1.0
S2 H:SF4101 2.3 57.7 1.0
S1 H:SF4101 2.3 57.7 1.0
FE1 H:SF4101 2.7 57.7 1.0
FE2 H:SF4101 2.7 57.7 1.0
FE3 H:SF4101 2.7 57.7 1.0
HB3 H:CYS51 2.8 65.3 1.0
CB H:CYS51 2.9 65.3 1.0
HB2 H:CYS51 2.9 65.3 1.0
HG23 H:VAL53 3.6 69.4 1.0
H H:LEU24 3.8 56.8 1.0
HA H:ARG54 3.8 70.2 1.0
S4 H:SF4101 3.9 57.7 1.0
HA H:CYS48 4.0 67.3 1.0
HA H:ALA23 4.1 61.4 1.0
HB2 H:CYS57 4.1 75.0 1.0
H H:CYS25 4.1 57.0 1.0
HB1 H:ALA23 4.2 61.4 1.0
HG22 H:VAL53 4.2 69.4 1.0
CG2 H:VAL53 4.3 69.4 1.0
CA H:CYS51 4.4 65.3 1.0
HB3 H:LEU24 4.4 56.8 1.0
HB3 H:CYS57 4.4 75.0 1.0
N H:LEU24 4.5 56.8 1.0
HB2 H:ARG54 4.5 70.2 1.0
CA H:ARG54 4.6 70.2 1.0
CB H:CYS57 4.6 75.0 1.0
H H:VAL53 4.6 69.4 1.0
N H:ARG54 4.7 70.2 1.0
HG21 H:VAL53 4.7 69.4 1.0
SG H:CYS25 4.7 57.0 1.0
HA H:CYS51 4.8 65.3 1.0
HB3 H:CYS48 4.8 67.3 1.0
O H:CYS48 4.8 67.3 1.0
SG H:CYS57 4.8 75.0 1.0
SG H:CYS48 4.8 67.3 1.0
CA H:ALA23 4.8 61.4 1.0
H H:ARG54 4.8 70.2 1.0
CB H:ALA23 4.8 61.4 1.0
CA H:CYS48 4.9 67.3 1.0
HB3 H:CYS25 4.9 57.0 1.0
H H:CYS51 4.9 65.3 1.0
C H:VAL53 4.9 69.4 1.0
C H:CYS51 4.9 65.3 1.0
HB2 H:ALA23 4.9 61.4 1.0
N H:CYS25 5.0 57.0 1.0

Reference:

M.Lilic, E.A.Campbell. Streptomyces Venezuelae Rnap Unconstrained Open Promoter Complex with Whia and Whib Transcription Factors To Be Published.
Page generated: Thu Aug 7 15:59:41 2025

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