Iron in PDB 8ity: Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1

Enzymatic activity of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1

All present enzymatic activity of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1:
2.7.7.6;

Other elements in 8ity:

The structure of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 also contains other interesting chemical elements:

Zinc (Zn) 7 atoms
Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 (pdb code 8ity). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1, PDB code: 8ity:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ity

Go back to Iron Binding Sites List in 8ity
Iron binding site 1 out of 4 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe401

b:278.6
occ:1.00
 FE1 P:SF4401 0.0 278.6 1.0
S4 P:SF4401 2.3 278.6 1.0
SG P:CYS290 2.3 268.2 1.0
S2 P:SF4401 2.3 278.6 1.0
S3 P:SF4401 2.3 278.6 1.0
FE3 P:SF4401 2.7 278.6 1.0
FE4 P:SF4401 2.7 278.6 1.0
FE2 P:SF4401 2.7 278.6 1.0
CB P:CYS290 2.8 268.2 1.0
S1 P:SF4401 3.9 278.6 1.0
O P:PRO286 3.9 260.8 1.0
SG P:CYS307 4.1 255.5 1.0
CA P:CYS287 4.1 262.4 1.0
CA P:CYS290 4.3 268.2 1.0
CD2 P:TYR309 4.3 260.0 1.0
C P:PRO286 4.4 260.8 1.0
CG2 P:VAL292 4.4 262.4 1.0
N P:CYS287 4.5 262.4 1.0
N P:PHE293 4.6 252.9 1.0
CA P:PHE293 4.6 252.9 1.0
CG P:TYR309 4.6 260.0 1.0
CB P:TYR309 4.7 260.0 1.0
C P:VAL292 4.8 262.4 1.0
SG P:CYS287 4.8 262.4 1.0
CE2 P:TYR309 4.9 260.0 1.0
O P:CYS287 4.9 262.4 1.0
O P:VAL292 4.9 262.4 1.0
C P:CYS287 4.9 262.4 1.0
CB P:PHE293 5.0 252.9 1.0
CB P:CYS296 5.0 255.8 1.0

Iron binding site 2 out of 4 in 8ity

Go back to Iron Binding Sites List in 8ity
Iron binding site 2 out of 4 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe401

b:278.6
occ:1.00
 FE2 P:SF4401 0.0 278.6 1.0
S3 P:SF4401 2.3 278.6 1.0
SG P:CYS287 2.3 262.4 1.0
S1 P:SF4401 2.3 278.6 1.0
S4 P:SF4401 2.3 278.6 1.0
FE3 P:SF4401 2.7 278.6 1.0
FE4 P:SF4401 2.7 278.6 1.0
FE1 P:SF4401 2.7 278.6 1.0
CB P:CYS287 3.1 262.4 1.0
CA P:CYS287 3.2 262.4 1.0
CE P:MET310 3.6 256.7 1.0
N P:CYS287 3.7 262.4 1.0
S2 P:SF4401 3.9 278.6 1.0
ND2 O:ASN445 3.9 254.1 1.0
C P:PRO286 4.4 260.8 1.0
C P:CYS287 4.4 262.4 1.0
SG P:CYS296 4.5 255.8 1.0
CG O:ASN445 4.5 254.1 1.0
O P:PRO286 4.6 260.8 1.0
O P:CYS287 4.7 262.4 1.0
CB O:ASN445 4.7 254.1 1.0
CB P:CYS290 4.7 268.2 1.0
SG P:CYS290 4.9 268.2 1.0
SG P:CYS307 5.0 255.5 1.0
SD P:MET310 5.0 256.7 1.0

Iron binding site 3 out of 4 in 8ity

Go back to Iron Binding Sites List in 8ity
Iron binding site 3 out of 4 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe401

b:278.6
occ:1.00
 FE3 P:SF4401 0.0 278.6 1.0
SG P:CYS307 2.2 255.5 1.0
S2 P:SF4401 2.3 278.6 1.0
S4 P:SF4401 2.3 278.6 1.0
S1 P:SF4401 2.3 278.6 1.0
FE4 P:SF4401 2.7 278.6 1.0
FE1 P:SF4401 2.7 278.6 1.0
FE2 P:SF4401 2.7 278.6 1.0
CB P:CYS307 3.2 255.5 1.0
CE P:MET310 3.6 256.7 1.0
S3 P:SF4401 3.9 278.6 1.0
CB P:TYR309 4.2 260.0 1.0
SG P:CYS296 4.3 255.8 1.0
SD P:MET310 4.4 256.7 1.0
CD2 P:TYR309 4.5 260.0 1.0
CG P:MET310 4.5 256.7 1.0
CA P:CYS307 4.6 255.5 1.0
SG P:CYS290 4.7 268.2 1.0
SG P:CYS287 4.7 262.4 1.0
CG P:TYR309 4.7 260.0 1.0
CA P:PRO304 4.9 242.7 1.0
N P:MET310 5.0 256.7 1.0

Iron binding site 4 out of 4 in 8ity

Go back to Iron Binding Sites List in 8ity
Iron binding site 4 out of 4 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe401

b:278.6
occ:1.00
 FE4 P:SF4401 0.0 278.6 1.0
S1 P:SF4401 2.3 278.6 1.0
SG P:CYS296 2.3 255.8 1.0
S3 P:SF4401 2.3 278.6 1.0
S2 P:SF4401 2.3 278.6 1.0
CB P:CYS296 2.6 255.8 1.0
FE3 P:SF4401 2.7 278.6 1.0
FE1 P:SF4401 2.7 278.6 1.0
FE2 P:SF4401 2.7 278.6 1.0
S4 P:SF4401 3.9 278.6 1.0
CA P:CYS296 4.0 255.8 1.0
O P:VAL292 4.3 262.4 1.0
SG P:CYS307 4.3 255.5 1.0
CA P:PHE293 4.4 252.9 1.0
SG P:CYS290 4.7 268.2 1.0
SG P:CYS287 4.8 262.4 1.0
N P:CYS296 4.8 255.8 1.0
C P:VAL292 4.8 262.4 1.0
ND2 O:ASN445 4.8 254.1 1.0
O P:PHE293 4.9 252.9 1.0
N P:PHE293 4.9 252.9 1.0
CB P:CYS290 4.9 268.2 1.0
NZ O:LYS441 5.0 244.6 1.0

Reference:

H.Hou, Q.Jin, Y.Ren, Z.Chen, Q.Wang, Y.Xu. Structure of the Snapc-Bound Rna Polymerase III Preinitiation Complex. Cell Res. 2023.
ISSN: ISSN 1001-0602
PubMed: 37165065
DOI: 10.1038/S41422-023-00819-X
Page generated: Sat Aug 10 06:15:54 2024

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