Iron in PDB 8g99: Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase

All present enzymatic activity of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase:
2.7.7.7;

The structure of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g99). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g99:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Partial Auto-Inhibitory Complex 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 Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:68.1 occ:1.00 FE1 C:SF4601 0.0 68.1 1.0 SG C:CYS373 2.3 44.0 1.0 S3 C:SF4601 2.3 69.4 1.0 S4 C:SF4601 2.3 55.5 1.0 S2 C:SF4601 2.3 58.0 1.0 FE4 C:SF4601 2.7 73.1 1.0 FE2 C:SF4601 2.7 53.2 1.0 FE3 C:SF4601 2.7 61.1 1.0 HA C:CYS373 3.3 34.2 1.0 HB3 C:CYS373 3.3 34.9 1.0 CB C:CYS373 3.3 33.8 1.0 HG3 C:PRO450 3.6 36.0 1.0 HD21 C:LEU447 3.6 36.7 1.0 CA C:CYS373 3.8 27.5 1.0 S1 C:SF4601 3.9 49.8 1.0 HG2 C:GLN427 4.1 33.0 1.0 HD3 C:PRO450 4.1 36.1 1.0 HB2 C:CYS373 4.2 35.1 1.0 HD11 C:ILE377 4.2 32.0 1.0 HG C:LEU447 4.3 36.5 1.0 HD23 C:LEU447 4.4 36.5 1.0 CD2 C:LEU447 4.4 38.2 1.0 CG C:PRO450 4.4 34.4 1.0 HA C:PRO450 4.6 36.3 1.0 CD C:PRO450 4.6 35.9 1.0 HA C:GLN427 4.7 33.0 1.0 HD11 C:LEU447 4.7 36.5 1.0 SG C:CYS430 4.7 45.2 1.0 N C:CYS373 4.8 31.9 1.0 N C:PRO450 4.8 28.9 1.0 SG C:CYS293 4.8 42.9 1.0 HB2 C:CYS430 4.8 36.1 1.0 H C:CYS373 4.8 35.0 1.0 SG C:CYS390 4.8 32.0 1.0 CG C:LEU447 4.9 38.4 1.0 HB3 C:CYS430 4.9 36.3 1.0 C C:CYS373 4.9 25.8 1.0 HB C:VAL376 4.9 32.3 1.0 CG C:GLN427 4.9 30.7 1.0 HG3 C:GLN427 5.0 32.9 1.0

Iron binding site 2 out of 4 in the Partial Auto-Inhibitory Complex 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 Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:53.2 occ:1.00 FE2 C:SF4601 0.0 53.2 1.0 S4 C:SF4601 2.3 55.5 1.0 SG C:CYS390 2.3 32.0 1.0 S3 C:SF4601 2.3 69.4 1.0 S1 C:SF4601 2.3 49.8 1.0 FE1 C:SF4601 2.7 68.1 1.0 FE3 C:SF4601 2.7 61.1 1.0 FE4 C:SF4601 2.7 73.1 1.0 HB2 C:CYS390 3.4 33.2 1.0 CB C:CYS390 3.4 31.2 1.0 HD2 C:PHE392 3.4 35.3 1.0 HA C:CYS390 3.6 33.2 1.0 HB3 C:CYS293 3.7 39.1 1.0 HD11 C:ILE377 3.8 32.0 1.0 S2 C:SF4601 3.9 58.0 1.0 HD2 C:PRO391 4.0 35.0 1.0 CA C:CYS390 4.1 31.5 1.0 HB2 C:CYS430 4.2 36.1 1.0 HB3 C:CYS390 4.2 32.8 1.0 CD2 C:PHE392 4.3 33.6 1.0 HG13 C:ILE377 4.3 32.0 1.0 HB2 C:PHE392 4.4 34.2 1.0 H C:PHE392 4.5 34.9 1.0 CB C:CYS293 4.5 40.5 1.0 HG12 C:ILE377 4.6 31.8 1.0 CD1 C:ILE377 4.6 32.4 1.0 HE2 C:PHE392 4.7 35.5 1.0 SG C:CYS293 4.7 42.9 1.0 HG12 C:VAL376 4.7 34.1 1.0 CG1 C:ILE377 4.7 30.0 1.0 CD C:PRO391 4.7 34.1 1.0 H C:CYS293 4.8 38.5 1.0 SG C:CYS430 4.8 45.2 1.0 HA C:CYS373 4.8 34.2 1.0 SG C:CYS373 4.8 44.0 1.0 C C:CYS390 4.9 33.6 1.0 HB3 C:CYS373 4.9 34.9 1.0 CB C:CYS430 4.9 31.6 1.0 HD3 C:PRO391 4.9 35.9 1.0 CE2 C:PHE392 4.9 35.6 1.0 HG11 C:VAL376 5.0 34.0 1.0 HA C:GLN427 5.0 33.0 1.0 HB C:VAL376 5.0 32.3 1.0 HB2 C:CYS293 5.0 38.3 1.0

Iron binding site 3 out of 4 in the Partial Auto-Inhibitory Complex 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 Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:61.1 occ:1.00 FE3 C:SF4601 0.0 61.1 1.0 S1 C:SF4601 2.3 49.8 1.0 S2 C:SF4601 2.3 58.0 1.0 S4 C:SF4601 2.3 55.5 1.0 SG C:CYS430 2.3 45.2 1.0 FE4 C:SF4601 2.7 73.1 1.0 FE2 C:SF4601 2.7 53.2 1.0 FE1 C:SF4601 2.7 68.1 1.0 HB2 C:CYS430 2.8 36.1 1.0 CB C:CYS430 3.1 31.6 1.0 HD21 C:LEU447 3.1 36.7 1.0 HB3 C:CYS430 3.3 36.3 1.0 HB2 C:PRO291 3.6 39.8 1.0 HE2 C:PHE392 3.7 35.5 1.0 S3 C:SF4601 3.9 69.4 1.0 CD2 C:LEU447 3.9 38.2 1.0 HD2 C:PHE392 4.0 35.3 1.0 HD23 C:LEU447 4.0 36.5 1.0 HB3 C:PRO291 4.1 39.3 1.0 HD22 C:LEU447 4.3 36.4 1.0 CE2 C:PHE392 4.3 35.6 1.0 CB C:PRO291 4.3 39.1 1.0 CD2 C:PHE392 4.4 33.6 1.0 CA C:CYS430 4.5 28.7 1.0 HD2 C:TYR453 4.5 39.0 1.0 H C:CYS293 4.6 38.5 1.0 HA C:CYS430 4.6 36.4 1.0 SG C:CYS373 4.7 44.0 1.0 HA C:GLN427 4.7 33.0 1.0 SG C:CYS390 4.7 32.0 1.0 HB3 C:CYS293 4.8 39.1 1.0 H C:LEU292 4.8 40.0 1.0 SG C:CYS293 4.8 42.9 1.0 HE2 C:TYR453 4.9 38.6 1.0 HD11 C:LEU447 4.9 36.5 1.0

Iron binding site 4 out of 4 in the Partial Auto-Inhibitory Complex 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 Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:73.1 occ:1.00 FE4 C:SF4601 0.0 73.1 1.0 S2 C:SF4601 2.3 58.0 1.0 S1 C:SF4601 2.3 49.8 1.0 S3 C:SF4601 2.3 69.4 1.0 SG C:CYS293 2.3 42.9 1.0 HB3 C:CYS293 2.7 39.1 1.0 FE1 C:SF4601 2.7 68.1 1.0 FE3 C:SF4601 2.7 61.1 1.0 FE2 C:SF4601 2.7 53.2 1.0 CB C:CYS293 3.0 40.5 1.0 HB2 C:PRO291 3.1 39.8 1.0 HG3 C:PRO450 3.3 36.0 1.0 H C:CYS293 3.4 38.5 1.0 HB2 C:CYS293 3.7 38.3 1.0 S4 C:SF4601 3.9 55.5 1.0 HB3 C:PRO450 4.0 36.7 1.0 CB C:PRO291 4.0 39.1 1.0 HG2 C:PRO291 4.0 39.4 1.0 N C:CYS293 4.1 34.7 1.0 CA C:CYS293 4.2 36.1 1.0 CG C:PRO450 4.2 34.4 1.0 HG3 C:PRO291 4.3 39.8 1.0 HB3 C:PRO291 4.3 39.3 1.0 CG C:PRO291 4.3 40.6 1.0 HD2 C:PRO391 4.5 35.0 1.0 HA C:CYS390 4.5 33.2 1.0 HE2 C:MET294 4.6 41.0 1.0 CB C:PRO450 4.6 36.3 1.0 HA C:PRO450 4.6 36.3 1.0 H C:MET294 4.6 40.3 1.0 HG2 C:PRO450 4.6 36.1 1.0 HG11 C:VAL376 4.7 34.0 1.0 SG C:CYS390 4.8 32.0 1.0 HA C:CYS293 4.8 38.7 1.0 SG C:CYS373 4.8 44.0 1.0 SG C:CYS430 4.8 45.2 1.0 HG2 C:MET294 4.9 40.4 1.0 HA C:CYS373 4.9 34.2 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