Iron in PDB 8g9l: Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase

All present enzymatic activity of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase:
2.7.7.7;

The structure of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase (pdb code 8g9l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase, PDB code: 8g9l:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:96.8 occ:1.00 FE1 B:SF4601 0.0 96.8 1.0 S4 B:SF4601 2.3 111.7 1.0 S2 B:SF4601 2.3 97.5 1.0 S3 B:SF4601 2.3 95.4 1.0 SG B:CYS373 2.3 111.9 1.0 FE3 B:SF4601 2.7 99.6 1.0 FE2 B:SF4601 2.7 69.3 1.0 FE4 B:SF4601 2.7 112.1 1.0 CB B:CYS373 3.7 111.0 1.0 HG3 B:PRO450 3.8 100.4 1.0 HB3 B:CYS373 3.8 109.2 1.0 S1 B:SF4601 3.9 117.2 1.0 HA B:CYS373 3.9 109.0 1.0 CA B:CYS373 4.4 108.2 1.0 HB2 B:CYS373 4.5 109.2 1.0 HD21 B:LEU447 4.5 128.4 1.0 HB2 B:CYS390 4.5 112.5 1.0 HD3 B:PRO450 4.6 100.8 1.0 HG3 B:GLN427 4.6 115.0 1.0 HG B:LEU447 4.7 128.2 1.0 CG B:PRO450 4.7 101.4 1.0 SG B:CYS430 4.8 132.1 1.0 HB2 B:CYS430 4.8 131.3 1.0 SG B:CYS390 4.8 119.8 1.0 SG B:CYS293 4.8 97.7 1.0 HA B:PRO450 5.0 100.2 1.0

Iron binding site 2 out of 4 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:69.3 occ:1.00 FE2 B:SF4601 0.0 69.3 1.0 S3 B:SF4601 2.3 95.4 1.0 S1 B:SF4601 2.3 117.2 1.0 S4 B:SF4601 2.3 111.7 1.0 SG B:CYS390 2.3 119.8 1.0 FE4 B:SF4601 2.7 112.1 1.0 FE1 B:SF4601 2.7 96.8 1.0 FE3 B:SF4601 2.7 99.6 1.0 HB2 B:CYS390 2.9 112.5 1.0 CB B:CYS390 3.1 110.2 1.0 HA B:CYS390 3.3 113.0 1.0 HD2 B:PHE392 3.4 112.2 1.0 HD2 B:PRO391 3.7 109.7 1.0 CA B:CYS390 3.8 112.1 1.0 S2 B:SF4601 3.9 97.5 1.0 HB3 B:CYS390 3.9 113.0 1.0 HD11 B:ILE377 4.1 104.3 1.0 CD2 B:PHE392 4.3 113.2 1.0 HB2 B:PHE392 4.3 112.0 1.0 H B:PHE392 4.3 111.2 1.0 HB3 B:CYS293 4.3 95.5 1.0 HB2 B:CYS430 4.4 131.3 1.0 CD B:PRO391 4.5 110.7 1.0 C B:CYS390 4.5 108.6 1.0 N B:PRO391 4.7 104.5 1.0 HD3 B:PRO391 4.7 110.0 1.0 HE2 B:PHE392 4.7 112.3 1.0 SG B:CYS293 4.8 97.7 1.0 SG B:CYS373 4.8 111.9 1.0 SG B:CYS430 4.8 132.1 1.0 CE2 B:PHE392 4.9 112.7 1.0 N B:CYS390 5.0 118.5 1.0 H B:CYS293 5.0 94.8 1.0 HB3 B:TYR426 5.0 122.0 1.0

Iron binding site 3 out of 4 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:99.6 occ:1.00 FE3 B:SF4601 0.0 99.6 1.0 S2 B:SF4601 2.3 97.5 1.0 S4 B:SF4601 2.3 111.7 1.0 S1 B:SF4601 2.3 117.2 1.0 SG B:CYS430 2.3 132.1 1.0 FE1 B:SF4601 2.7 96.8 1.0 FE4 B:SF4601 2.7 112.1 1.0 FE2 B:SF4601 2.7 69.3 1.0 HB2 B:CYS430 2.9 131.3 1.0 CB B:CYS430 3.1 133.1 1.0 HB3 B:CYS430 3.5 131.7 1.0 HD21 B:LEU447 3.6 128.4 1.0 HE2 B:PHE392 3.6 112.3 1.0 HB2 B:PRO291 3.8 91.4 1.0 HD2 B:PHE392 3.8 112.2 1.0 S3 B:SF4601 3.9 95.4 1.0 HB3 B:PRO291 4.1 91.0 1.0 HD2 B:TYR453 4.3 115.5 1.0 CE2 B:PHE392 4.3 112.7 1.0 CD2 B:PHE392 4.4 113.2 1.0 CB B:PRO291 4.4 89.8 1.0 CD2 B:LEU447 4.5 128.5 1.0 H B:LEU292 4.5 97.2 1.0 HD23 B:LEU447 4.5 128.2 1.0 CA B:CYS430 4.5 135.9 1.0 HA B:CYS430 4.6 132.0 1.0 HE2 B:TYR453 4.7 114.9 1.0 H B:CYS293 4.7 94.8 1.0 SG B:CYS373 4.8 111.9 1.0 SG B:CYS390 4.8 119.8 1.0 SG B:CYS293 4.8 97.7 1.0 CD2 B:TYR453 4.9 115.2 1.0 HG B:LEU447 5.0 128.2 1.0

Iron binding site 4 out of 4 in the Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dna Initiation Subcomplex of Xenopus Laevis Dna Polymerase Alpha- Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:112.1 occ:1.00 FE4 B:SF4601 0.0 112.1 1.0 S3 B:SF4601 2.3 95.4 1.0 S2 B:SF4601 2.3 97.5 1.0 S1 B:SF4601 2.3 117.2 1.0 SG B:CYS293 2.3 97.7 1.0 FE2 B:SF4601 2.7 69.3 1.0 FE3 B:SF4601 2.7 99.6 1.0 FE1 B:SF4601 2.7 96.8 1.0 HB3 B:CYS293 3.1 95.5 1.0 HB2 B:PRO291 3.1 91.4 1.0 H B:CYS293 3.3 94.8 1.0 CB B:CYS293 3.3 92.8 1.0 S4 B:SF4601 3.9 111.7 1.0 HG3 B:PRO450 3.9 100.4 1.0 HB2 B:CYS293 4.0 94.3 1.0 CB B:PRO291 4.0 89.8 1.0 N B:CYS293 4.1 91.2 1.0 HA B:CYS390 4.1 113.0 1.0 HD2 B:PRO391 4.1 109.7 1.0 HB3 B:PRO291 4.3 91.0 1.0 HG2 B:PRO291 4.3 92.1 1.0 CA B:CYS293 4.3 91.9 1.0 HB3 B:PRO450 4.5 99.9 1.0 HB2 B:CYS390 4.5 112.5 1.0 CG B:PRO291 4.6 93.9 1.0 HG3 B:PRO291 4.6 91.4 1.0 HE2 B:MET294 4.6 92.7 1.0 HD3 B:PRO391 4.6 110.0 1.0 H B:LEU292 4.7 97.2 1.0 SG B:CYS390 4.8 119.8 1.0 SG B:CYS430 4.8 132.1 1.0 CG B:PRO450 4.8 101.4 1.0 CD B:PRO391 4.8 110.7 1.0 SG B:CYS373 4.8 111.9 1.0 H B:MET294 4.8 92.1 1.0 HG11 B:VAL376 4.8 99.7 1.0 N B:LEU292 4.9 83.0 1.0 HA B:CYS293 4.9 95.0 1.0 CA B:CYS390 4.9 112.1 1.0 CB B:CYS390 4.9 110.2 1.0

E.A.Mullins, L.E.Salay, C.L.Durie, J.E.Jackman, M.D.Ohi, W.J.Chazin, B.F.Eichman. A Mechanistic Model of Primer Synthesis From Catalytic Structures of Dna Polymerase Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993335
DOI: 10.1101/2023.03.16.533013