Iron in PDB 6du0: Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L Mutant

The structure of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L Mutant, PDB code: 6du0 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)	29.28 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.462, 50.830, 90.175, 90.00, 90.00, 90.00
R / Rfree (%)	27.3 / 32.4

The binding sites of Iron atom in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L Mutant (pdb code 6du0). 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 Y395L Mutant, PDB code: 6du0:
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 Y395L 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 Y395L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:36.6 occ:0.80 FE1 A:SF4602 0.0 36.6 0.8 S2 A:SF4602 2.1 38.9 1.0 S3 A:SF4602 2.1 37.2 1.0 S4 A:SF4602 2.2 36.3 1.0 SG A:CYS474 2.2 51.0 1.0 FE3 A:SF4602 2.9 39.2 0.8 FE4 A:SF4602 3.0 32.3 0.8 FE2 A:SF4602 3.0 37.4 0.8 CB A:CYS474 3.1 48.2 1.0 S1 A:SF4602 3.6 34.9 1.0 CM A:MPD603 3.7 60.1 1.0 CB A:PRO334 4.1 39.2 1.0 CE2 A:PHE436 4.3 52.3 1.0 O A:HOH710 4.4 42.3 1.0 CA A:CYS474 4.5 50.1 1.0 CD2 A:PHE436 4.6 55.0 1.0 CD2 A:TYR503 4.6 48.4 1.0 SG A:CYS417 4.6 40.6 1.0 CG A:PRO334 4.9 40.5 1.0 SG A:CYS336 4.9 46.1 1.0 CE2 A:TYR503 4.9 48.5 1.0 C2 A:MPD603 4.9 61.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L 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 Y395L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:37.4 occ:0.80 FE2 A:SF4602 0.0 37.4 0.8 S1 A:SF4602 2.0 34.9 1.0 S4 A:SF4602 2.1 36.3 1.0 S3 A:SF4602 2.2 37.2 1.0 SG A:CYS434 2.3 49.6 1.0 FE3 A:SF4602 2.9 39.2 0.8 FE1 A:SF4602 3.0 36.6 0.8 FE4 A:SF4602 3.1 32.3 0.8 CB A:CYS434 3.3 49.7 1.0 S2 A:SF4602 3.7 38.9 1.0 CD2 A:PHE436 4.0 55.0 1.0 CA A:CYS434 4.0 48.8 1.0 CE2 A:PHE436 4.6 52.3 1.0 CB A:CYS474 4.7 48.2 1.0 C A:CYS434 4.7 43.1 1.0 SG A:CYS474 4.8 51.0 1.0 CD A:PRO435 4.9 47.6 1.0 SG A:CYS336 5.0 46.1 1.0 CB A:CYS336 5.0 40.0 1.0 CG A:PHE436 5.0 53.7 1.0 CB A:TYR470 5.0 51.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L 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 Y395L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:39.2 occ:0.80 FE3 A:SF4602 0.0 39.2 0.8 S1 A:SF4602 2.1 34.9 1.0 S4 A:SF4602 2.1 36.3 1.0 S2 A:SF4602 2.2 38.9 1.0 SG A:CYS336 2.3 46.1 1.0 FE2 A:SF4602 2.9 37.4 0.8 FE1 A:SF4602 2.9 36.6 0.8 FE4 A:SF4602 3.1 32.3 0.8 CB A:CYS336 3.1 40.0 1.0 S3 A:SF4602 3.5 37.2 1.0 N A:CYS336 3.9 51.1 1.0 CA A:CYS336 4.1 43.0 1.0 CB A:PRO334 4.4 39.2 1.0 CG A:PRO334 4.4 40.5 1.0 CG A:PRO500 4.5 46.2 1.0 SG A:CYS434 4.7 49.6 1.0 CB A:PRO500 4.8 48.2 1.0 CD1 A:ILE420 4.8 50.0 1.0 N A:LEU335 4.8 42.9 1.0 SG A:CYS474 4.9 51.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y395L 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 Y395L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:32.3 occ:0.80 FE4 A:SF4602 0.0 32.3 0.8 S3 A:SF4602 2.0 37.2 1.0 S2 A:SF4602 2.1 38.9 1.0 S1 A:SF4602 2.3 34.9 1.0 SG A:CYS417 2.4 40.6 1.0 FE1 A:SF4602 3.0 36.6 0.8 CB A:CYS417 3.0 42.5 1.0 FE3 A:SF4602 3.1 39.2 0.8 FE2 A:SF4602 3.1 37.4 0.8 CA A:CYS417 3.7 49.2 1.0 S4 A:SF4602 3.9 36.3 1.0 CM A:MPD603 4.2 60.1 1.0 CG A:PRO500 4.3 46.2 1.0 CD A:PRO500 4.5 47.5 1.0 N A:CYS417 4.6 52.1 1.0 CD1 A:ILE420 4.8 50.0 1.0 N A:PRO500 4.8 45.0 1.0 C A:CYS417 4.8 48.9 1.0 O A:CYS417 4.9 52.0 1.0 SG A:CYS336 5.0 46.1 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