Iron in PDB 8g9f: Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase

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

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

Zinc

(Zn)

3 atoms

The binding sites of Iron atom in the Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g9f). 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 Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g9f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:92.1 occ:1.00 FE1 C:SF4601 0.0 92.1 1.0 SG C:CYS373 2.3 60.4 1.0 S4 C:SF4601 2.3 89.9 1.0 S3 C:SF4601 2.3 103.1 1.0 S2 C:SF4601 2.3 101.1 1.0 FE2 C:SF4601 2.7 89.2 1.0 FE4 C:SF4601 2.7 84.2 1.0 FE3 C:SF4601 2.7 99.7 1.0 HA C:CYS373 3.2 55.2 1.0 HB3 C:CYS373 3.2 55.5 1.0 CB C:CYS373 3.3 55.3 1.0 HG3 C:PRO450 3.7 58.2 1.0 CA C:CYS373 3.7 51.6 1.0 HD21 C:LEU447 3.8 57.8 1.0 S1 C:SF4601 3.9 80.2 1.0 HG2 C:GLN427 4.0 55.9 1.0 HD11 C:ILE377 4.0 52.8 1.0 HD3 C:PRO450 4.1 57.7 1.0 HB2 C:CYS373 4.1 55.9 1.0 HG C:LEU447 4.4 56.8 1.0 HD23 C:LEU447 4.4 57.5 1.0 CD2 C:LEU447 4.5 60.5 1.0 CG C:PRO450 4.6 58.4 1.0 HA C:GLN427 4.7 56.0 1.0 CD C:PRO450 4.7 60.0 1.0 N C:CYS373 4.7 54.2 1.0 SG C:CYS390 4.8 64.7 1.0 H C:CYS373 4.8 56.1 1.0 HD12 C:ILE377 4.8 53.0 1.0 C C:CYS373 4.8 52.2 1.0 SG C:CYS430 4.8 58.0 1.0 HA C:PRO450 4.8 57.5 1.0 CD1 C:ILE377 4.8 55.4 1.0 HB2 C:CYS430 4.8 57.4 1.0 SG C:CYS293 4.9 72.8 1.0 HB C:VAL376 4.9 52.5 1.0 HD11 C:LEU447 4.9 57.2 1.0 CG C:GLN427 4.9 54.2 1.0 HG3 C:GLN427 4.9 55.9 1.0 HB3 C:CYS430 4.9 56.9 1.0 O C:CYS373 4.9 60.6 1.0 N C:PRO450 4.9 50.0 1.0 CG C:LEU447 4.9 58.2 1.0

Iron binding site 2 out of 4 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:89.2 occ:1.00 FE2 C:SF4601 0.0 89.2 1.0 SG C:CYS390 2.3 64.7 1.0 S4 C:SF4601 2.3 89.9 1.0 S1 C:SF4601 2.3 80.2 1.0 S3 C:SF4601 2.3 103.1 1.0 FE1 C:SF4601 2.7 92.1 1.0 FE3 C:SF4601 2.7 99.7 1.0 FE4 C:SF4601 2.7 84.2 1.0 HB2 C:CYS390 3.4 55.1 1.0 CB C:CYS390 3.4 49.5 1.0 HD2 C:PHE392 3.4 57.9 1.0 HB3 C:CYS293 3.5 66.0 1.0 HA C:CYS390 3.6 56.0 1.0 HD11 C:ILE377 3.8 52.8 1.0 S2 C:SF4601 3.9 101.1 1.0 HD2 C:PRO391 4.0 59.7 1.0 CA C:CYS390 4.1 51.8 1.0 HB2 C:CYS430 4.2 57.4 1.0 HB3 C:CYS390 4.2 55.2 1.0 CD2 C:PHE392 4.3 55.2 1.0 HG13 C:ILE377 4.3 52.7 1.0 HB2 C:PHE392 4.4 57.6 1.0 CB C:CYS293 4.4 66.0 1.0 H C:PHE392 4.5 57.4 1.0 SG C:CYS293 4.6 72.8 1.0 HG12 C:ILE377 4.6 52.5 1.0 CD1 C:ILE377 4.7 55.4 1.0 HE2 C:PHE392 4.7 57.7 1.0 HG12 C:VAL376 4.7 53.4 1.0 H C:CYS293 4.7 65.8 1.0 CD C:PRO391 4.7 58.8 1.0 CG1 C:ILE377 4.8 54.1 1.0 SG C:CYS430 4.8 58.0 1.0 C C:CYS390 4.8 53.3 1.0 HG11 C:VAL376 4.9 53.7 1.0 HB2 C:CYS293 4.9 65.4 1.0 HA C:CYS373 4.9 55.2 1.0 HD3 C:PRO391 4.9 60.7 1.0 CE2 C:PHE392 4.9 56.2 1.0 SG C:CYS373 4.9 60.4 1.0 CB C:CYS430 4.9 53.0 1.0 HB3 C:CYS373 5.0 55.5 1.0 HB C:VAL376 5.0 52.5 1.0

Iron binding site 3 out of 4 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:99.7 occ:1.00 FE3 C:SF4601 0.0 99.7 1.0 S1 C:SF4601 2.3 80.2 1.0 S2 C:SF4601 2.3 101.1 1.0 S4 C:SF4601 2.3 89.9 1.0 SG C:CYS430 2.3 58.0 1.0 FE2 C:SF4601 2.7 89.2 1.0 FE4 C:SF4601 2.7 84.2 1.0 FE1 C:SF4601 2.7 92.1 1.0 HB2 C:CYS430 2.8 57.4 1.0 HD21 C:LEU447 2.9 57.8 1.0 CB C:CYS430 3.0 53.0 1.0 HB3 C:CYS430 3.2 56.9 1.0 HB2 C:PRO291 3.7 62.6 1.0 CD2 C:LEU447 3.8 60.5 1.0 HD23 C:LEU447 3.8 57.5 1.0 HE2 C:PHE392 3.8 57.7 1.0 S3 C:SF4601 3.9 103.1 1.0 HD2 C:PHE392 4.0 57.9 1.0 HD22 C:LEU447 4.2 57.1 1.0 HB3 C:PRO291 4.2 61.9 1.0 CE2 C:PHE392 4.4 56.2 1.0 CB C:PRO291 4.4 63.6 1.0 CA C:CYS430 4.4 52.5 1.0 CD2 C:PHE392 4.5 55.2 1.0 HD2 C:TYR453 4.6 59.4 1.0 HA C:GLN427 4.6 56.0 1.0 SG C:CYS373 4.6 60.4 1.0 HA C:CYS430 4.6 56.9 1.0 H C:CYS293 4.7 65.8 1.0 SG C:CYS390 4.7 64.7 1.0 HD11 C:LEU447 4.8 57.2 1.0 HB3 C:CYS293 4.8 66.0 1.0 HG C:LEU447 4.8 56.8 1.0 SG C:CYS293 4.9 72.8 1.0 CG C:LEU447 4.9 58.2 1.0 H C:LEU292 4.9 64.6 1.0 HE2 C:TYR453 4.9 60.0 1.0

Iron binding site 4 out of 4 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe601 b:84.2 occ:1.00 FE4 C:SF4601 0.0 84.2 1.0 S1 C:SF4601 2.3 80.2 1.0 S2 C:SF4601 2.3 101.1 1.0 S3 C:SF4601 2.3 103.1 1.0 SG C:CYS293 2.3 72.8 1.0 FE3 C:SF4601 2.7 99.7 1.0 FE1 C:SF4601 2.7 92.1 1.0 FE2 C:SF4601 2.7 89.2 1.0 HB3 C:CYS293 2.8 66.0 1.0 HB2 C:PRO291 3.1 62.6 1.0 CB C:CYS293 3.2 66.0 1.0 HG3 C:PRO450 3.2 58.2 1.0 H C:CYS293 3.5 65.8 1.0 HB2 C:CYS293 3.8 65.4 1.0 S4 C:SF4601 3.9 89.9 1.0 CB C:PRO291 3.9 63.6 1.0 HG2 C:PRO291 4.0 62.1 1.0 HB3 C:PRO450 4.0 58.0 1.0 CG C:PRO450 4.1 58.4 1.0 N C:CYS293 4.2 63.5 1.0 HG3 C:PRO291 4.2 62.6 1.0 HB3 C:PRO291 4.3 61.9 1.0 CG C:PRO291 4.3 65.5 1.0 CA C:CYS293 4.3 63.8 1.0 HA C:PRO450 4.5 57.5 1.0 CB C:PRO450 4.5 55.5 1.0 HE2 C:MET294 4.5 64.6 1.0 HG2 C:PRO450 4.6 57.6 1.0 H C:MET294 4.7 64.6 1.0 SG C:CYS373 4.7 60.4 1.0 HA C:CYS390 4.7 56.0 1.0 HD2 C:PRO391 4.7 59.7 1.0 SG C:CYS430 4.7 58.0 1.0 HG11 C:VAL376 4.7 53.7 1.0 SG C:CYS390 4.8 64.7 1.0 HG2 C:MET294 4.8 64.3 1.0 HD3 C:PRO450 4.9 57.7 1.0 HA C:CYS373 4.9 55.2 1.0 HA C:CYS293 4.9 65.3 1.0 HD21 C:LEU447 4.9 57.8 1.0 CA C:PRO450 5.0 55.2 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