Iron in PDB 8fok: Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State

The binding sites of Iron atom in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State (pdb code 8fok). 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 the Dna Elongation State, PDB code: 8fok:
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 the Dna Elongation 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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:136.2 occ:1.00 FE1 B:SF4601 0.0 136.2 1.0 SG B:CYS336 2.3 50.1 1.0 S2 B:SF4601 2.3 136.2 1.0 S3 B:SF4601 2.3 136.2 1.0 S4 B:SF4601 2.3 136.2 1.0 FE4 B:SF4601 2.7 136.2 1.0 FE2 B:SF4601 2.7 136.2 1.0 FE3 B:SF4601 2.7 136.2 1.0 CB B:CYS336 3.1 50.1 1.0 S1 B:SF4601 3.9 136.2 1.0 N B:CYS336 4.0 50.1 1.0 CA B:CYS336 4.2 50.1 1.0 CB B:PRO334 4.3 48.3 1.0 CG B:PRO500 4.4 47.6 1.0 CG B:PRO334 4.6 48.3 1.0 SG B:CYS434 4.7 54.2 1.0 SG B:CYS474 4.8 62.1 1.0 SG B:CYS417 4.8 45.1 1.0 CB B:PRO500 4.8 47.6 1.0 CD1 B:ILE420 4.9 37.8 1.0 CD B:PRO435 4.9 48.8 1.0 O B:GLY433 5.0 49.6 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation 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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:136.2 occ:1.00 FE2 B:SF4601 0.0 136.2 1.0 SG B:CYS434 2.3 54.2 1.0 S4 B:SF4601 2.3 136.2 1.0 S3 B:SF4601 2.3 136.2 1.0 S1 B:SF4601 2.3 136.2 1.0 FE1 B:SF4601 2.7 136.2 1.0 FE3 B:SF4601 2.7 136.2 1.0 FE4 B:SF4601 2.7 136.2 1.0 CB B:CYS434 3.3 54.2 1.0 S2 B:SF4601 3.9 136.2 1.0 CD2 B:PHE436 3.9 51.7 1.0 CA B:CYS434 3.9 54.2 1.0 CE2 B:PHE436 4.5 51.7 1.0 CD B:PRO435 4.5 48.8 1.0 C B:CYS434 4.7 54.2 1.0 CB B:CYS474 4.7 62.1 1.0 SG B:CYS336 4.8 50.1 1.0 CB B:CYS336 4.8 50.1 1.0 SG B:CYS474 4.8 62.1 1.0 N B:PRO435 4.8 48.8 1.0 SG B:CYS417 4.8 45.1 1.0 CG B:PHE436 4.9 51.7 1.0 O B:TYR470 4.9 46.6 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation 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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:136.2 occ:1.00 FE3 B:SF4601 0.0 136.2 1.0 SG B:CYS417 2.3 45.1 1.0 S1 B:SF4601 2.3 136.2 1.0 S2 B:SF4601 2.3 136.2 1.0 S4 B:SF4601 2.3 136.2 1.0 FE4 B:SF4601 2.7 136.2 1.0 FE1 B:SF4601 2.7 136.2 1.0 FE2 B:SF4601 2.7 136.2 1.0 CB B:CYS417 3.4 45.1 1.0 S3 B:SF4601 3.9 136.2 1.0 CA B:CYS417 4.2 45.1 1.0 CG B:PRO500 4.6 47.6 1.0 CD B:PRO500 4.7 47.6 1.0 SG B:CYS474 4.7 62.1 1.0 SG B:CYS336 4.8 50.1 1.0 SG B:CYS434 4.8 54.2 1.0 CB B:CYS474 4.9 62.1 1.0 N B:CYS417 4.9 45.1 1.0 N B:PRO500 5.0 47.6 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation 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 S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Dna Elongation State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:136.2 occ:1.00 FE4 B:SF4601 0.0 136.2 1.0 SG B:CYS474 2.3 62.1 1.0 S2 B:SF4601 2.3 136.2 1.0 S1 B:SF4601 2.3 136.2 1.0 S3 B:SF4601 2.3 136.2 1.0 FE3 B:SF4601 2.7 136.2 1.0 FE1 B:SF4601 2.7 136.2 1.0 FE2 B:SF4601 2.7 136.2 1.0 CB B:CYS474 2.9 62.1 1.0 S4 B:SF4601 3.9 136.2 1.0 CE2 B:PHE436 4.0 51.7 1.0 CD2 B:PHE436 4.3 51.7 1.0 CA B:CYS474 4.3 62.1 1.0 CB B:PRO334 4.4 48.3 1.0 SG B:CYS417 4.7 45.1 1.0 SG B:CYS336 4.7 50.1 1.0 SG B:CYS434 4.8 54.2 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