Iron in PDB 8fod: Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II

The binding sites of Iron atom in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II (pdb code 8fod). 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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II, PDB code: 8fod:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II


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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:86.1 occ:1.00 FE1 B:SF4601 0.0 86.1 1.0 SG B:CYS336 2.3 12.5 1.0 S2 B:SF4601 2.3 86.1 1.0 S3 B:SF4601 2.3 86.1 1.0 S4 B:SF4601 2.3 86.1 1.0 FE3 B:SF4601 2.7 86.1 1.0 FE2 B:SF4601 2.7 86.1 1.0 FE4 B:SF4601 2.7 86.1 1.0 CB B:CYS336 3.0 12.5 1.0 N B:CYS336 3.6 12.5 1.0 S1 B:SF4601 3.9 86.1 1.0 CA B:CYS336 3.9 12.5 1.0 CB B:PRO334 4.1 13.1 1.0 CG B:PRO334 4.2 13.1 1.0 CG B:PRO500 4.5 3.5 1.0 N B:LEU335 4.7 12.2 1.0 SG B:CYS434 4.7 8.1 1.0 SG B:CYS417 4.7 5.0 1.0 CB B:PRO500 4.7 3.5 1.0 C B:LEU335 4.8 12.2 1.0 SG B:CYS474 4.9 3.5 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II


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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:86.1 occ:1.00 FE2 B:SF4601 0.0 86.1 1.0 SG B:CYS434 2.3 8.1 1.0 S1 B:SF4601 2.3 86.1 1.0 S4 B:SF4601 2.3 86.1 1.0 S3 B:SF4601 2.3 86.1 1.0 FE3 B:SF4601 2.7 86.1 1.0 FE4 B:SF4601 2.7 86.1 1.0 FE1 B:SF4601 2.7 86.1 1.0 CB B:CYS434 3.4 8.1 1.0 S2 B:SF4601 3.9 86.1 1.0 CA B:CYS434 4.1 8.1 1.0 CD B:PRO435 4.6 5.7 1.0 SG B:CYS474 4.6 3.5 1.0 CB B:CYS336 4.7 12.5 1.0 C B:CYS434 4.8 8.1 1.0 SG B:CYS417 4.8 5.0 1.0 CD1 B:PHE436 4.8 3.5 1.0 SG B:CYS336 4.8 12.5 1.0 CB B:CYS474 4.8 3.5 1.0 N B:PRO435 4.8 5.7 1.0 CB B:PHE436 4.9 3.5 1.0 N B:CYS336 5.0 12.5 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II


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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:86.1 occ:1.00 FE3 B:SF4601 0.0 86.1 1.0 SG B:CYS417 2.2 5.0 1.0 S1 B:SF4601 2.3 86.1 1.0 S2 B:SF4601 2.3 86.1 1.0 S4 B:SF4601 2.3 86.1 1.0 FE4 B:SF4601 2.7 86.1 1.0 FE2 B:SF4601 2.7 86.1 1.0 FE1 B:SF4601 2.7 86.1 1.0 CB B:CYS417 3.6 5.0 1.0 S3 B:SF4601 3.9 86.1 1.0 CA B:CYS417 4.5 5.0 1.0 SG B:CYS474 4.5 3.5 1.0 SG B:CYS434 4.6 8.1 1.0 SG B:CYS336 4.7 12.5 1.0 CG B:PRO500 4.8 3.5 1.0 CD B:PRO500 4.9 3.5 1.0 CB B:CYS474 4.9 3.5 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II


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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in Apo State Conformation II within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:86.1 occ:1.00 FE4 B:SF4601 0.0 86.1 1.0 SG B:CYS474 2.3 3.5 1.0 S1 B:SF4601 2.3 86.1 1.0 S3 B:SF4601 2.3 86.1 1.0 S2 B:SF4601 2.3 86.1 1.0 FE3 B:SF4601 2.7 86.1 1.0 FE2 B:SF4601 2.7 86.1 1.0 FE1 B:SF4601 2.7 86.1 1.0 CB B:CYS474 3.3 3.5 1.0 S4 B:SF4601 3.9 86.1 1.0 CB B:PRO334 3.9 13.1 1.0 CA B:CYS474 4.6 3.5 1.0 N B:LEU335 4.6 12.2 1.0 CD2 B:TYR503 4.7 10.6 1.0 SG B:CYS417 4.7 5.0 1.0 SG B:CYS336 4.8 12.5 1.0 CG B:PRO334 4.8 13.1 1.0 CE2 B:TYR503 4.9 10.6 1.0 SG B:CYS434 4.9 8.1 1.0

Z.Yuan, R.Georgescu, H.Li, M.E.O'donnell. Molecular Choreography of Primer Synthesis By the Eukaryotic Pol Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205351
DOI: 10.1101/2023.05.03.539257