Iron in PDB 7d59: Cryo-Em Structure of Human Rna Polymerase III in Apo State

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III in Apo State:
2.7.7.6;

The structure of Cryo-Em Structure of Human Rna Polymerase III in Apo State also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Human Rna Polymerase III in Apo State (pdb code 7d59). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Human Rna Polymerase III in Apo State, PDB code: 7d59:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:194.3 occ:1.00 FE1 P:SF4400 0.0 194.3 1.0 S4 P:SF4400 2.3 194.3 1.0 S2 P:SF4400 2.3 194.3 1.0 S3 P:SF4400 2.3 194.3 1.0 SG P:CYS290 2.6 178.4 1.0 FE3 P:SF4400 2.6 194.3 1.0 FE4 P:SF4400 2.7 194.3 1.0 FE2 P:SF4400 2.7 194.3 1.0 CB P:CYS290 3.0 178.4 1.0 S1 P:SF4400 3.8 194.3 1.0 O P:VAL292 4.0 170.2 1.0 CA P:CYS287 4.4 183.2 1.0 CA P:CYS290 4.5 178.4 1.0 SG P:CYS296 4.5 160.8 1.0 SG P:CYS287 4.5 183.2 1.0 SG P:CYS307 4.6 175.1 1.0 O P:PRO286 4.8 184.7 1.0 O P:CYS287 4.8 183.2 1.0 CB P:CYS287 5.0 183.2 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:194.3 occ:1.00 FE2 P:SF4400 0.0 194.3 1.0 SG P:CYS296 2.1 160.8 1.0 S4 P:SF4400 2.3 194.3 1.0 S3 P:SF4400 2.3 194.3 1.0 S1 P:SF4400 2.3 194.3 1.0 FE1 P:SF4400 2.7 194.3 1.0 FE3 P:SF4400 2.8 194.3 1.0 FE4 P:SF4400 2.8 194.3 1.0 CB P:CYS296 3.3 160.8 1.0 S2 P:SF4400 4.0 194.3 1.0 C P:SER303 4.1 164.1 1.0 N P:PRO304 4.2 168.4 1.0 CD P:PRO304 4.3 168.4 1.0 ND2 O:ASN445 4.4 172.3 1.0 O P:SER303 4.4 164.1 1.0 CA P:SER303 4.5 164.1 1.0 CA P:CYS296 4.5 160.8 1.0 O P:VAL292 4.5 170.2 1.0 SG P:CYS307 4.7 175.1 1.0 SG P:CYS290 4.7 178.4 1.0 CA P:PRO304 4.8 168.4 1.0 N P:SER303 4.8 164.1 1.0 CG O:ASN445 4.9 172.3 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:194.3 occ:1.00 FE3 P:SF4400 0.0 194.3 1.0 S2 P:SF4400 2.3 194.3 1.0 S4 P:SF4400 2.3 194.3 1.0 S1 P:SF4400 2.3 194.3 1.0 SG P:CYS307 2.4 175.1 1.0 FE1 P:SF4400 2.6 194.3 1.0 FE2 P:SF4400 2.8 194.3 1.0 FE4 P:SF4400 2.8 194.3 1.0 CB P:CYS307 3.3 175.1 1.0 CG P:MET310 3.8 182.0 1.0 S3 P:SF4400 3.9 194.3 1.0 SG P:CYS290 4.6 178.4 1.0 SD P:MET310 4.6 182.0 1.0 CA P:CYS307 4.7 175.1 1.0 O P:SER303 4.7 164.1 1.0 SG P:CYS296 4.7 160.8 1.0 CA P:PRO304 4.8 168.4 1.0 CD2 P:TYR309 4.8 174.7 1.0 SG P:CYS287 4.9 183.2 1.0 CB P:MET310 5.0 182.0 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:194.3 occ:1.00 FE4 P:SF4400 0.0 194.3 1.0 S3 P:SF4400 2.3 194.3 1.0 S1 P:SF4400 2.3 194.3 1.0 S2 P:SF4400 2.3 194.3 1.0 SG P:CYS287 2.6 183.2 1.0 FE1 P:SF4400 2.7 194.3 1.0 FE3 P:SF4400 2.8 194.3 1.0 FE2 P:SF4400 2.8 194.3 1.0 ND2 O:ASN445 3.1 172.3 1.0 CG O:ASN445 3.8 172.3 1.0 CB O:ASN445 3.9 172.3 1.0 CB P:CYS287 3.9 183.2 1.0 S4 P:SF4400 3.9 194.3 1.0 SG P:CYS296 4.1 160.8 1.0 CA P:CYS287 4.2 183.2 1.0 OD1 O:ASN445 4.8 172.3 1.0 N P:CYS287 4.9 183.2 1.0

Q.Wang, S.Li, F.Wan, Y.Xu, Z.Wu, M.Cao, P.Lan, M.Lei, J.Wu. Structural Insights Into Transcriptional Regulation of Human Rna Polymerase III. Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-021-00557-X