Iron in PDB 7d58: Cryo-Em Structure of Human Rna Polymerase III in Elongating State

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

The structure of Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State (pdb code 7d58). 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 Elongating State, PDB code: 7d58:
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 Elongating 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 Elongating State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:135.6 occ:1.00 FE1 P:SF4400 0.0 135.6 1.0 S4 P:SF4400 2.3 135.6 1.0 S2 P:SF4400 2.3 135.6 1.0 S3 P:SF4400 2.3 135.6 1.0 SG P:CYS290 2.4 109.4 1.0 FE3 P:SF4400 2.6 135.6 1.0 FE4 P:SF4400 2.7 135.6 1.0 FE2 P:SF4400 2.7 135.6 1.0 CB P:CYS290 2.9 109.4 1.0 S1 P:SF4400 3.8 135.6 1.0 O P:VAL292 4.1 104.6 1.0 CA P:CYS290 4.4 109.4 1.0 CA P:CYS287 4.4 111.1 1.0 SG P:CYS307 4.6 114.8 1.0 SG P:CYS296 4.6 109.1 1.0 SG P:CYS287 4.8 111.1 1.0 CB P:CYS287 4.8 111.1 1.0 O P:CYS287 4.8 111.1 1.0 O P:PRO286 4.9 112.1 1.0 CB P:CYS296 4.9 109.1 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:135.6 occ:1.00 FE2 P:SF4400 0.0 135.6 1.0 S4 P:SF4400 2.3 135.6 1.0 S3 P:SF4400 2.3 135.6 1.0 S1 P:SF4400 2.3 135.6 1.0 SG P:CYS296 2.4 109.1 1.0 FE1 P:SF4400 2.7 135.6 1.0 FE3 P:SF4400 2.8 135.6 1.0 FE4 P:SF4400 2.8 135.6 1.0 CB P:CYS296 3.2 109.1 1.0 S2 P:SF4400 4.0 135.6 1.0 CA P:CYS296 4.3 109.1 1.0 C P:SER303 4.3 112.2 1.0 ND2 O:ASN445 4.4 105.6 1.0 N P:PRO304 4.4 111.7 1.0 SG P:CYS290 4.5 109.4 1.0 O P:VAL292 4.5 104.6 1.0 O P:SER303 4.5 112.2 1.0 SG P:CYS307 4.7 114.8 1.0 CD P:PRO304 4.7 111.7 1.0 CA P:SER303 4.7 112.2 1.0 CA P:PRO304 4.8 111.7 1.0 CG2 P:ILE302 4.9 111.5 1.0 N P:SER303 4.9 112.2 1.0 CB P:CYS307 5.0 114.8 1.0 CG O:ASN445 5.0 105.6 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:135.6 occ:1.00 FE3 P:SF4400 0.0 135.6 1.0 S2 P:SF4400 2.3 135.6 1.0 S4 P:SF4400 2.3 135.6 1.0 S1 P:SF4400 2.3 135.6 1.0 SG P:CYS307 2.4 114.8 1.0 FE1 P:SF4400 2.6 135.6 1.0 FE2 P:SF4400 2.8 135.6 1.0 FE4 P:SF4400 2.8 135.6 1.0 CB P:CYS307 3.3 114.8 1.0 CG P:MET310 3.7 118.5 1.0 S3 P:SF4400 3.9 135.6 1.0 SG P:CYS290 4.4 109.4 1.0 SD P:MET310 4.5 118.5 1.0 CA P:CYS307 4.7 114.8 1.0 CD2 P:TYR309 4.7 116.6 1.0 CA P:PRO304 4.7 111.7 1.0 O P:SER303 4.8 112.2 1.0 N P:MET310 4.9 118.5 1.0 CB P:MET310 4.9 118.5 1.0 SG P:CYS287 4.9 111.1 1.0 CB P:TYR309 4.9 116.6 1.0 SG P:CYS296 5.0 109.1 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range: probe atom residue distance (Å) B Occ P:Fe400 b:135.6 occ:1.00 FE4 P:SF4400 0.0 135.6 1.0 S3 P:SF4400 2.3 135.6 1.0 S1 P:SF4400 2.3 135.6 1.0 S2 P:SF4400 2.3 135.6 1.0 FE1 P:SF4400 2.7 135.6 1.0 FE3 P:SF4400 2.8 135.6 1.0 FE2 P:SF4400 2.8 135.6 1.0 SG P:CYS287 2.9 111.1 1.0 ND2 O:ASN445 3.3 105.6 1.0 CB P:CYS287 3.8 111.1 1.0 CB O:ASN445 3.9 105.6 1.0 CG O:ASN445 3.9 105.6 1.0 SG P:CYS296 3.9 109.1 1.0 S4 P:SF4400 3.9 135.6 1.0 CA P:CYS287 4.2 111.1 1.0 SD P:MET310 4.9 118.5 1.0 OD1 O:ASN445 4.9 105.6 1.0 N P:CYS287 4.9 111.1 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