Iron in PDB 6dtv: Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant

The structure of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant, PDB code: 6dtv was solved by L.E.Salay, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.44 / 1.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.990, 50.873, 89.911, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 13.7

The binding sites of Iron atom in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant (pdb code 6dtv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant, PDB code: 6dtv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.2 occ:1.00 FE1 A:SF4601 0.0 11.2 1.0 S4 A:SF4601 2.3 11.3 1.0 SG A:CYS336 2.3 11.3 1.0 S2 A:SF4601 2.3 11.7 1.0 S3 A:SF4601 2.3 11.8 1.0 FE2 A:SF4601 2.7 11.4 1.0 FE4 A:SF4601 2.7 11.6 1.0 FE3 A:SF4601 2.7 11.3 1.0 HB3 A:CYS336 2.9 14.3 1.0 HG3 A:PRO500 3.2 15.2 1.0 CB A:CYS336 3.2 11.9 1.0 H A:CYS336 3.3 12.5 1.0 HB2 A:PRO334 3.5 13.9 1.0 S1 A:SF4601 3.9 11.8 1.0 HB2 A:CYS336 3.9 14.3 1.0 HG2 A:PRO334 4.0 15.2 1.0 N A:CYS336 4.0 10.4 1.0 HB3 A:PRO500 4.1 14.3 1.0 CG A:PRO500 4.1 12.6 1.0 HD13 A:ILE420 4.2 14.6 1.0 CA A:CYS336 4.2 11.4 1.0 HA A:CYS434 4.3 14.6 1.0 CB A:PRO334 4.3 11.6 1.0 HG3 A:PRO334 4.4 15.2 1.0 HD2 A:PRO435 4.4 14.6 1.0 CG A:PRO334 4.4 12.6 1.0 HG2 A:PRO500 4.5 15.2 1.0 CB A:PRO500 4.6 11.9 1.0 HA A:PRO500 4.6 14.0 1.0 SG A:CYS417 4.7 12.0 1.0 HB3 A:PRO334 4.7 13.9 1.0 HD12 A:ILE420 4.8 14.6 1.0 H A:ILE337 4.8 12.9 1.0 HB2 A:CYS434 4.8 15.1 1.0 HG21 A:ILE420 4.8 15.3 1.0 SG A:CYS434 4.8 12.8 1.0 HA A:CYS336 4.8 13.8 1.0 HE21 A:GLN357 4.9 14.1 1.0 CD1 A:ILE420 4.9 12.1 1.0 SG A:CYS474 4.9 12.1 1.0 H A:LEU335 4.9 14.2 0.5 HG12 A:ILE337 5.0 13.1 1.0 H A:LEU335 5.0 14.2 0.5

Iron binding site 2 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.4 occ:1.00 FE2 A:SF4601 0.0 11.4 1.0 S3 A:SF4601 2.3 11.8 1.0 SG A:CYS417 2.3 12.0 1.0 S1 A:SF4601 2.3 11.8 1.0 S4 A:SF4601 2.3 11.3 1.0 FE3 A:SF4601 2.7 11.3 1.0 FE4 A:SF4601 2.7 11.6 1.0 FE1 A:SF4601 2.7 11.2 1.0 HB3 A:CYS417 3.1 15.2 1.0 CB A:CYS417 3.3 12.6 1.0 HG3 A:PRO500 3.5 15.2 1.0 HM1 A:MPD602 3.6 16.6 1.0 HA A:CYS417 3.6 14.4 1.0 HG22 A:THR471 3.8 18.5 1.0 S2 A:SF4601 3.9 11.7 1.0 HD3 A:PRO500 4.0 14.2 1.0 CA A:CYS417 4.0 12.0 1.0 HB2 A:CYS417 4.0 15.2 1.0 H12 A:MPD602 4.1 20.3 1.0 CG A:PRO500 4.4 12.6 1.0 HD12 A:ILE420 4.5 14.6 1.0 CM A:MPD602 4.5 16.6 1.0 CD A:PRO500 4.6 11.9 1.0 SG A:CYS474 4.7 12.1 1.0 HM3 A:MPD602 4.7 16.6 1.0 CG2 A:THR471 4.7 15.4 1.0 HA A:PRO500 4.8 14.0 1.0 HB1 A:ALA498 4.8 20.5 1.0 HA A:THR471 4.8 16.7 1.0 N A:PRO500 4.8 11.6 1.0 HD13 A:ILE420 4.8 14.6 1.0 SG A:CYS434 4.8 12.8 1.0 HB2 A:CYS474 4.8 14.3 1.0 HG21 A:THR471 4.8 18.5 1.0 N A:CYS417 4.8 12.2 1.0 HB2 A:CYS434 4.8 15.1 1.0 SG A:CYS336 4.8 11.3 1.0 H A:CYS417 4.9 14.6 1.0 HB3 A:CYS474 5.0 14.3 1.0 HG2 A:PRO500 5.0 15.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.3 occ:1.00 FE3 A:SF4601 0.0 11.3 1.0 S4 A:SF4601 2.3 11.3 1.0 S2 A:SF4601 2.3 11.7 1.0 SG A:CYS474 2.3 12.1 1.0 S1 A:SF4601 2.3 11.8 1.0 FE2 A:SF4601 2.7 11.4 1.0 FE4 A:SF4601 2.7 11.6 1.0 FE1 A:SF4601 2.7 11.2 1.0 HB2 A:CYS474 2.9 14.3 1.0 CB A:CYS474 3.1 11.9 1.0 HB2 A:PRO334 3.4 13.9 1.0 HB3 A:CYS474 3.4 14.3 1.0 HE2 A:PHE436 3.5 15.8 1.0 HM1 A:MPD602 3.8 16.6 1.0 HD2 A:PHE436 3.9 15.5 1.0 S3 A:SF4601 3.9 11.8 1.0 HM3 A:MPD602 3.9 16.6 1.0 HB3 A:PRO334 4.1 13.9 1.0 CE2 A:PHE436 4.2 13.1 1.0 CB A:PRO334 4.2 11.6 1.0 H12 A:MPD602 4.3 20.3 1.0 CM A:MPD602 4.4 16.6 1.0 O A:HOH825 4.4 13.5 1.0 CD2 A:PHE436 4.4 12.9 1.0 H A:LEU335 4.5 14.2 0.5 H A:CYS336 4.5 12.5 1.0 CA A:CYS474 4.5 12.1 1.0 H A:LEU335 4.5 14.2 0.5 SG A:CYS417 4.6 12.0 1.0 HA A:CYS474 4.6 14.5 1.0 HD2 A:TYR503 4.6 15.0 1.0 HA A:THR471 4.7 16.7 1.0 SG A:CYS434 4.8 12.8 1.0 SG A:CYS336 4.8 11.3 1.0 HG3 A:PRO500 4.9 15.2 1.0 HG3 A:PRO334 5.0 15.2 1.0 HB2 A:LEU335 5.0 16.1 0.5

Iron binding site 4 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.6 occ:1.00 FE4 A:SF4601 0.0 11.6 1.0 S1 A:SF4601 2.3 11.8 1.0 S3 A:SF4601 2.3 11.8 1.0 SG A:CYS434 2.3 12.8 1.0 S2 A:SF4601 2.4 11.7 1.0 FE2 A:SF4601 2.7 11.4 1.0 FE3 A:SF4601 2.7 11.3 1.0 FE1 A:SF4601 2.7 11.2 1.0 HB2 A:CYS434 3.1 15.1 1.0 HD2 A:PHE436 3.2 15.5 1.0 CB A:CYS434 3.3 12.5 1.0 HA A:CYS434 3.4 14.6 1.0 CA A:CYS434 3.9 12.2 1.0 S4 A:SF4601 3.9 11.3 1.0 HB3 A:CYS336 4.0 14.3 1.0 HD2 A:PRO435 4.1 14.6 1.0 HB2 A:CYS474 4.1 14.3 1.0 HB3 A:CYS434 4.1 15.1 1.0 CD2 A:PHE436 4.2 12.9 1.0 HE2 A:PHE436 4.4 15.8 1.0 H A:PHE436 4.4 15.3 1.0 HB2 A:PHE436 4.5 16.2 1.0 HB3 A:TYR470 4.5 17.8 1.0 HB3 A:CYS417 4.7 15.2 1.0 C A:CYS434 4.7 12.5 1.0 H A:CYS336 4.7 12.5 1.0 SG A:CYS336 4.7 11.3 1.0 CE2 A:PHE436 4.7 13.1 1.0 HG22 A:THR471 4.8 18.5 1.0 SG A:CYS474 4.8 12.1 1.0 CD A:PRO435 4.8 12.2 1.0 CB A:CYS336 4.8 11.9 1.0 CB A:CYS474 4.8 11.9 1.0 HD21 A:LEU421 4.9 17.7 1.0 SG A:CYS417 4.9 12.0 1.0 N A:PRO435 4.9 12.0 1.0 HD3 A:PRO435 4.9 14.6 1.0

E.O'brien, L.E.Salay, E.A.Epum, K.L.Friedman, W.J.Chazin, J.K.Barton. Yeast Require Redox Switching in Dna Primase. Proc. Natl. Acad. Sci. V. 115 13186 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30541886
DOI: 10.1073/PNAS.1810715115