Iron in PDB 8g9o: Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase

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

The structure of Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g9o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g9o:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:209.6 occ:1.00 FE1 B:SF4601 0.0 209.6 1.0 SG B:CYS373 2.3 244.9 1.0 S2 B:SF4601 2.3 209.6 1.0 S3 B:SF4601 2.3 209.6 1.0 S4 B:SF4601 2.3 209.6 1.0 HB3 B:CYS373 2.7 244.9 1.0 FE4 B:SF4601 2.7 209.6 1.0 FE3 B:SF4601 2.7 209.6 1.0 FE2 B:SF4601 2.7 209.6 1.0 CB B:CYS373 3.0 244.9 1.0 HG3 B:PRO450 3.3 261.6 1.0 HA B:CYS373 3.6 244.9 1.0 HB2 B:CYS373 3.8 244.9 1.0 S1 B:SF4601 3.9 209.6 1.0 CA B:CYS373 3.9 244.9 1.0 CG B:PRO450 4.3 261.6 1.0 HD21 B:LEU447 4.3 282.4 1.0 HD3 B:PRO450 4.3 261.6 1.0 HA B:PRO450 4.5 261.6 1.0 HB2 B:CYS390 4.6 250.9 1.0 HG B:LEU447 4.6 282.4 1.0 CD B:PRO450 4.7 261.6 1.0 HB3 B:PRO450 4.7 261.6 1.0 SG B:CYS293 4.7 301.2 1.0 HD11 B:LEU447 4.7 282.4 1.0 H B:CYS373 4.8 244.9 1.0 SG B:CYS430 4.8 277.2 1.0 N B:CYS373 4.8 244.9 1.0 SG B:CYS390 4.8 250.9 1.0 HG2 B:PRO450 4.9 261.6 1.0 N B:PRO450 4.9 261.6 1.0 HB2 B:PRO291 4.9 274.0 1.0 CB B:PRO450 4.9 261.6 1.0 HB2 B:CYS430 5.0 277.2 1.0 CA B:PRO450 5.0 261.6 1.0

Iron binding site 2 out of 4 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:209.6 occ:1.00 FE2 B:SF4601 0.0 209.6 1.0 SG B:CYS390 2.3 250.9 1.0 S3 B:SF4601 2.3 209.6 1.0 S1 B:SF4601 2.3 209.6 1.0 S4 B:SF4601 2.3 209.6 1.0 FE4 B:SF4601 2.7 209.6 1.0 FE3 B:SF4601 2.7 209.6 1.0 FE1 B:SF4601 2.7 209.6 1.0 HB2 B:CYS390 2.9 250.9 1.0 CB B:CYS390 3.1 250.9 1.0 HA B:CYS390 3.4 250.9 1.0 HD2 B:PHE392 3.4 282.2 1.0 HD2 B:PRO391 3.7 280.8 1.0 CA B:CYS390 3.8 250.9 1.0 S2 B:SF4601 3.9 209.6 1.0 HB3 B:CYS390 4.0 250.9 1.0 HD11 B:ILE377 4.1 247.3 1.0 HB3 B:CYS373 4.1 244.9 1.0 HB3 B:CYS293 4.2 301.2 1.0 CD2 B:PHE392 4.2 282.2 1.0 H B:PHE392 4.3 282.2 1.0 HB2 B:PHE392 4.3 282.2 1.0 HB2 B:CYS430 4.4 277.2 1.0 CD B:PRO391 4.4 280.8 1.0 C B:CYS390 4.5 250.9 1.0 HE2 B:PHE392 4.6 282.2 1.0 HD3 B:PRO391 4.6 280.8 1.0 N B:PRO391 4.7 280.8 1.0 SG B:CYS293 4.7 301.2 1.0 SG B:CYS430 4.8 277.2 1.0 SG B:CYS373 4.9 244.9 1.0 CE2 B:PHE392 4.9 282.2 1.0 CB B:CYS373 4.9 244.9 1.0 HG12 B:ILE377 4.9 247.3 1.0 H B:CYS293 5.0 301.2 1.0 CB B:CYS293 5.0 301.2 1.0 N B:CYS390 5.0 250.9 1.0

Iron binding site 3 out of 4 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:209.6 occ:1.00 FE3 B:SF4601 0.0 209.6 1.0 S2 B:SF4601 2.3 209.6 1.0 S1 B:SF4601 2.3 209.6 1.0 S4 B:SF4601 2.3 209.6 1.0 SG B:CYS430 2.3 277.2 1.0 FE4 B:SF4601 2.7 209.6 1.0 FE1 B:SF4601 2.7 209.6 1.0 FE2 B:SF4601 2.7 209.6 1.0 HB2 B:CYS430 3.1 277.2 1.0 CB B:CYS430 3.2 277.2 1.0 HE2 B:PHE392 3.5 282.2 1.0 HD21 B:LEU447 3.5 282.4 1.0 HB3 B:CYS430 3.6 277.2 1.0 HB2 B:PRO291 3.7 274.0 1.0 HD2 B:PHE392 3.8 282.2 1.0 S3 B:SF4601 3.9 209.6 1.0 HB3 B:PRO291 4.1 274.0 1.0 HD2 B:TYR453 4.2 271.9 1.0 CE2 B:PHE392 4.2 282.2 1.0 CD2 B:PHE392 4.4 282.2 1.0 CB B:PRO291 4.4 274.0 1.0 CD2 B:LEU447 4.4 282.4 1.0 HD23 B:LEU447 4.5 282.4 1.0 H B:LEU292 4.6 290.1 1.0 CA B:CYS430 4.6 277.2 1.0 HE2 B:TYR453 4.6 271.9 1.0 HA B:CYS430 4.6 277.2 1.0 H B:CYS293 4.7 301.2 1.0 SG B:CYS373 4.7 244.9 1.0 SG B:CYS390 4.7 250.9 1.0 SG B:CYS293 4.8 301.2 1.0 CD2 B:TYR453 4.8 271.9 1.0 HD2 B:PRO391 4.9 280.8 1.0 HD22 B:LEU447 5.0 282.4 1.0

Iron binding site 4 out of 4 in the Complete Dna Elongation 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 Complete Dna Elongation Subcomplex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:209.6 occ:1.00 FE4 B:SF4601 0.0 209.6 1.0 SG B:CYS293 2.3 301.2 1.0 S2 B:SF4601 2.3 209.6 1.0 S1 B:SF4601 2.3 209.6 1.0 S3 B:SF4601 2.3 209.6 1.0 FE1 B:SF4601 2.7 209.6 1.0 FE2 B:SF4601 2.7 209.6 1.0 FE3 B:SF4601 2.7 209.6 1.0 HB3 B:CYS293 3.0 301.2 1.0 HB2 B:PRO291 3.1 274.0 1.0 H B:CYS293 3.2 301.2 1.0 CB B:CYS293 3.2 301.2 1.0 HG3 B:PRO450 3.8 261.6 1.0 S4 B:SF4601 3.9 209.6 1.0 HD2 B:PRO391 3.9 280.8 1.0 HB2 B:CYS293 3.9 301.2 1.0 CB B:PRO291 3.9 274.0 1.0 N B:CYS293 4.0 301.2 1.0 HA B:CYS390 4.1 250.9 1.0 HG2 B:PRO291 4.1 274.0 1.0 HB3 B:PRO291 4.2 274.0 1.0 HB3 B:PRO450 4.2 261.6 1.0 CA B:CYS293 4.2 301.2 1.0 CG B:PRO291 4.4 274.0 1.0 HD3 B:PRO391 4.5 280.8 1.0 HG3 B:PRO291 4.5 274.0 1.0 HE2 B:MET294 4.5 297.1 1.0 HB2 B:CYS390 4.6 250.9 1.0 H B:MET294 4.6 297.1 1.0 CD B:PRO391 4.6 280.8 1.0 CG B:PRO450 4.7 261.6 1.0 H B:LEU292 4.7 290.1 1.0 SG B:CYS373 4.7 244.9 1.0 SG B:CYS390 4.7 250.9 1.0 HA B:CYS293 4.8 301.2 1.0 SG B:CYS430 4.8 277.2 1.0 N B:LEU292 4.8 290.1 1.0 CB B:PRO450 4.9 261.6 1.0 CA B:CYS390 4.9 250.9 1.0 C B:PRO291 4.9 274.0 1.0 CB B:CYS390 5.0 250.9 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