Iron in PDB 8foj: Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Post Rna Handoff State

The binding sites of Iron atom in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Post Rna Handoff State (pdb code 8foj). 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 Post Rna Handoff State, PDB code: 8foj:
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 Post Rna Handoff 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 Post Rna Handoff State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:174.9 occ:1.00 FE1 B:SF4514 0.0 174.9 1.0 S4 B:SF4514 2.3 174.9 1.0 S3 B:SF4514 2.3 174.9 1.0 SG B:CYS336 2.3 158.9 1.0 S2 B:SF4514 2.3 174.9 1.0 FE4 B:SF4514 2.7 174.9 1.0 FE2 B:SF4514 2.7 174.9 1.0 FE3 B:SF4514 2.7 174.9 1.0 CB B:CYS336 3.3 158.9 1.0 S1 B:SF4514 3.9 174.9 1.0 CG B:PRO500 3.9 152.3 1.0 N B:CYS336 4.3 158.9 1.0 CB B:PRO334 4.3 128.0 1.0 CA B:CYS336 4.4 158.9 1.0 CB B:PRO500 4.4 152.3 1.0 CG B:PRO334 4.4 128.0 1.0 SG B:CYS474 4.7 120.3 1.0 CD B:PRO500 4.7 152.3 1.0 O B:GLY433 4.9 115.2 1.0 SG B:CYS417 4.9 123.6 1.0 CD B:PRO435 4.9 142.6 1.0 SG B:CYS434 5.0 139.0 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Post Rna Handoff 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 Post Rna Handoff State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:174.9 occ:1.00 FE2 B:SF4514 0.0 174.9 1.0 SG B:CYS434 2.3 139.0 1.0 S1 B:SF4514 2.3 174.9 1.0 S4 B:SF4514 2.3 174.9 1.0 S3 B:SF4514 2.3 174.9 1.0 FE3 B:SF4514 2.7 174.9 1.0 FE1 B:SF4514 2.7 174.9 1.0 FE4 B:SF4514 2.7 174.9 1.0 CB B:CYS434 3.0 139.0 1.0 CA B:CYS434 3.3 139.0 1.0 S2 B:SF4514 3.9 174.9 1.0 CD B:PRO435 3.9 142.6 1.0 C B:CYS434 4.0 139.0 1.0 CD2 B:PHE436 4.1 128.4 1.0 SG B:CYS417 4.1 123.6 1.0 N B:PRO435 4.2 142.6 1.0 SG B:CYS336 4.5 158.9 1.0 CB B:CYS336 4.6 158.9 1.0 N B:CYS434 4.6 139.0 1.0 O B:GLY433 4.7 115.2 1.0 CE2 B:PHE436 4.7 128.4 1.0 SG B:CYS474 4.9 120.3 1.0 N B:PHE436 4.9 128.4 1.0 O B:CYS434 4.9 139.0 1.0 CB B:CYS474 4.9 120.3 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Post Rna Handoff 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 Post Rna Handoff State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:174.9 occ:1.00 FE3 B:SF4514 0.0 174.9 1.0 SG B:CYS417 2.3 123.6 1.0 S1 B:SF4514 2.3 174.9 1.0 S4 B:SF4514 2.3 174.9 1.0 S2 B:SF4514 2.3 174.9 1.0 FE2 B:SF4514 2.7 174.9 1.0 FE4 B:SF4514 2.7 174.9 1.0 FE1 B:SF4514 2.7 174.9 1.0 CB B:CYS417 2.8 123.6 1.0 CA B:CYS417 3.7 123.6 1.0 S3 B:SF4514 3.9 174.9 1.0 SG B:CYS434 4.2 139.0 1.0 CB B:CYS434 4.6 139.0 1.0 N B:CYS417 4.6 123.6 1.0 CG B:PRO500 4.7 152.3 1.0 CD B:PRO500 4.7 152.3 1.0 C B:CYS417 4.7 123.6 1.0 SG B:CYS474 4.8 120.3 1.0 SG B:CYS336 4.9 158.9 1.0 O B:CYS417 4.9 123.6 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of S. Cerevisiae Dna Polymerase Alpha-Primase Complex in the Post Rna Handoff 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 Post Rna Handoff State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:174.9 occ:1.00 FE4 B:SF4514 0.0 174.9 1.0 SG B:CYS474 2.3 120.3 1.0 S1 B:SF4514 2.3 174.9 1.0 S3 B:SF4514 2.3 174.9 1.0 S2 B:SF4514 2.3 174.9 1.0 FE1 B:SF4514 2.7 174.9 1.0 FE2 B:SF4514 2.7 174.9 1.0 FE3 B:SF4514 2.7 174.9 1.0 CB B:CYS474 2.9 120.3 1.0 S4 B:SF4514 3.9 174.9 1.0 CA B:CYS474 4.3 120.3 1.0 CE2 B:PHE436 4.3 128.4 1.0 CD2 B:PHE436 4.4 128.4 1.0 SG B:CYS434 4.5 139.0 1.0 CB B:PRO334 4.6 128.0 1.0 SG B:CYS417 4.7 123.6 1.0 SG B:CYS336 4.7 158.9 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