Iron in PDB 8qj7: Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1

The structure of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 (pdb code 8qj7). 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 Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1, PDB code: 8qj7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:85.2 occ:1.00 FE1 D:SF4601 0.0 85.2 1.0 SG D:CYS367 2.3 85.8 1.0 S4 D:SF4601 2.3 108.1 1.0 S2 D:SF4601 2.3 95.6 1.0 S3 D:SF4601 2.3 93.5 1.0 HB3 D:CYS367 2.6 72.0 1.0 FE3 D:SF4601 2.7 89.9 1.0 FE4 D:SF4601 2.7 88.2 1.0 FE2 D:SF4601 2.7 84.6 1.0 CB D:CYS367 2.9 71.5 1.0 HA D:CYS367 3.2 77.4 1.0 CA D:CYS367 3.6 74.4 1.0 HG3 D:PRO444 3.7 76.9 1.0 HB2 D:CYS367 3.8 72.9 1.0 HD11 D:LEU441 3.8 82.3 1.0 S1 D:SF4601 3.9 101.8 1.0 HD12 D:LEU441 4.0 81.5 1.0 HD3 D:PRO444 4.2 77.7 1.0 HD12 D:ILE370 4.3 81.9 1.0 CD1 D:LEU441 4.4 81.4 1.0 H D:CYS367 4.5 79.4 1.0 N D:CYS367 4.5 79.1 1.0 HD11 D:ILE371 4.5 77.2 1.0 CG D:PRO444 4.6 75.8 1.0 HG D:LEU441 4.6 84.1 1.0 HB2 D:CYS384 4.7 75.1 1.0 HG2 D:GLN421 4.7 79.7 1.0 HA D:PRO444 4.7 72.2 1.0 SG D:CYS424 4.7 74.7 1.0 C D:CYS367 4.7 73.1 1.0 CD D:PRO444 4.8 75.4 1.0 SG D:CYS287 4.8 85.9 1.0 HB2 D:CYS424 4.8 81.7 1.0 SG D:CYS384 4.9 87.4 1.0 O D:CYS367 4.9 81.0 1.0 HB3 D:CYS424 4.9 81.4 1.0 N D:PRO444 4.9 70.0 1.0 HB D:ILE370 5.0 75.2 1.0 HB2 D:PRO285 5.0 73.7 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:84.6 occ:1.00 FE2 D:SF4601 0.0 84.6 1.0 SG D:CYS384 2.3 87.4 1.0 S1 D:SF4601 2.3 101.8 1.0 S3 D:SF4601 2.3 93.5 1.0 S4 D:SF4601 2.3 108.1 1.0 FE4 D:SF4601 2.7 88.2 1.0 FE3 D:SF4601 2.7 89.9 1.0 FE1 D:SF4601 2.7 85.2 1.0 HB2 D:CYS384 2.8 75.1 1.0 CB D:CYS384 3.1 75.8 1.0 HA D:CYS384 3.5 73.2 1.0 HB3 D:CYS384 3.8 76.6 1.0 HD2 D:PRO385 3.9 75.8 1.0 S2 D:SF4601 3.9 95.6 1.0 CA D:CYS384 3.9 69.8 1.0 HD11 D:ILE371 4.0 77.2 1.0 HB2 D:CYS424 4.2 81.7 1.0 HB3 D:CYS287 4.2 79.6 1.0 HB3 D:CYS367 4.2 72.0 1.0 HG13 D:ILE371 4.3 73.8 1.0 HD2 D:PHE386 4.4 82.5 1.0 HD3 D:PRO385 4.4 76.5 1.0 CD D:PRO385 4.5 74.9 1.0 HA D:CYS367 4.7 77.4 1.0 SG D:CYS287 4.7 85.9 1.0 HG12 D:ILE371 4.7 71.4 1.0 C D:CYS384 4.7 76.7 1.0 HG22 D:ILE370 4.8 77.5 1.0 SG D:CYS424 4.8 74.7 1.0 CD2 D:PHE386 4.8 80.8 1.0 H D:PHE386 4.8 76.2 1.0 CG1 D:ILE371 4.8 70.2 1.0 CD1 D:ILE371 4.8 78.0 1.0 HG21 D:ILE370 4.9 77.9 1.0 H D:CYS287 4.9 77.7 1.0 CB D:CYS424 4.9 82.1 1.0 CB D:CYS367 4.9 71.5 1.0 SG D:CYS367 4.9 85.8 1.0 HB2 D:PHE386 4.9 79.0 1.0 CB D:CYS287 5.0 77.0 1.0 N D:PRO385 5.0 72.7 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:89.9 occ:1.00 FE3 D:SF4601 0.0 89.9 1.0 SG D:CYS424 2.3 74.7 1.0 S1 D:SF4601 2.3 101.8 1.0 S2 D:SF4601 2.3 95.6 1.0 S4 D:SF4601 2.3 108.1 1.0 FE1 D:SF4601 2.7 85.2 1.0 FE4 D:SF4601 2.7 88.2 1.0 FE2 D:SF4601 2.7 84.6 1.0 HB2 D:CYS424 2.9 81.7 1.0 CB D:CYS424 3.1 82.1 1.0 HD11 D:LEU441 3.1 82.3 1.0 HD2 D:PRO286 3.2 76.9 1.0 HB3 D:CYS424 3.3 81.4 1.0 HB2 D:PRO285 3.7 73.7 1.0 S3 D:SF4601 3.9 93.5 1.0 HD12 D:LEU441 3.9 81.5 1.0 CD1 D:LEU441 3.9 81.4 1.0 HB3 D:PRO285 4.2 73.9 1.0 HE2 D:PHE386 4.2 77.8 1.0 CD D:PRO286 4.2 79.1 1.0 HD13 D:LEU441 4.2 84.6 1.0 CB D:PRO285 4.4 73.5 1.0 CA D:CYS424 4.5 85.2 1.0 HG2 D:PRO286 4.5 78.5 1.0 H D:CYS287 4.6 77.7 1.0 HD3 D:PRO286 4.6 77.6 1.0 HA D:CYS424 4.6 83.8 1.0 SG D:CYS367 4.6 85.8 1.0 SG D:CYS384 4.7 87.4 1.0 CE2 D:PHE386 4.7 76.5 1.0 SG D:CYS287 4.8 85.9 1.0 HD2 D:PHE386 4.8 82.5 1.0 HA D:GLN421 4.8 78.4 1.0 HD1 D:PHE447 4.9 80.9 1.0 CG D:PRO286 4.9 78.9 1.0 HD2 D:PRO385 5.0 75.8 1.0 HB2 D:PRO286 5.0 73.8 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


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 Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe601 b:88.2 occ:1.00 FE4 D:SF4601 0.0 88.2 1.0 SG D:CYS287 2.3 85.9 1.0 S1 D:SF4601 2.3 101.8 1.0 S2 D:SF4601 2.3 95.6 1.0 S3 D:SF4601 2.3 93.5 1.0 FE2 D:SF4601 2.7 84.6 1.0 FE3 D:SF4601 2.7 89.9 1.0 FE1 D:SF4601 2.7 85.2 1.0 HB3 D:CYS287 3.1 79.6 1.0 HB2 D:PRO285 3.1 73.7 1.0 H D:CYS287 3.3 77.7 1.0 CB D:CYS287 3.3 77.0 1.0 HG3 D:PRO444 3.5 76.9 1.0 S4 D:SF4601 3.9 108.1 1.0 HB2 D:CYS287 4.0 76.6 1.0 CB D:PRO285 4.0 73.5 1.0 N D:CYS287 4.0 79.3 1.0 HD2 D:PRO286 4.1 76.9 1.0 HD13 D:ILE370 4.2 81.1 1.0 HA D:CYS384 4.2 73.2 1.0 HB3 D:PRO444 4.2 76.2 1.0 HG2 D:PRO285 4.3 74.0 1.0 HB3 D:PRO285 4.3 73.9 1.0 CA D:CYS287 4.3 78.4 1.0 HD12 D:ILE370 4.3 81.9 1.0 HB2 D:CYS384 4.4 75.1 1.0 CG D:PRO444 4.4 75.8 1.0 HD3 D:PRO385 4.5 76.5 1.0 HG3 D:PRO285 4.5 70.7 1.0 CG D:PRO285 4.5 72.5 1.0 HD2 D:PRO385 4.6 75.8 1.0 HG21 D:ILE370 4.6 77.9 1.0 H D:MET288 4.6 78.3 1.0 SG D:CYS367 4.6 85.8 1.0 SG D:CYS384 4.7 87.4 1.0 CD1 D:ILE370 4.7 82.0 1.0 HA D:CYS367 4.8 77.4 1.0 SG D:CYS424 4.8 74.7 1.0 CB D:PRO444 4.8 76.3 1.0 HA D:PRO444 4.8 72.2 1.0 HG2 D:PRO444 4.8 76.5 1.0 CB D:CYS384 4.9 75.8 1.0 CD D:PRO286 4.9 79.1 1.0 HA D:CYS287 4.9 78.8 1.0 N D:PRO286 4.9 72.9 1.0 HE2 D:MET288 5.0 84.7 1.0 CA D:CYS384 5.0 69.8 1.0 CD D:PRO385 5.0 74.9 1.0

Z.Yin, M.L.Kilkenny, D.S.Ker, L.Pellegrini. Cryoem Insights Into Rna Primer Synthesis By the Human Primosome. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38335062
DOI: 10.1111/FEBS.17082