Iron in PDB 6di2: Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L Mutant

The structure of Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L Mutant, PDB code: 6di2 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)	33.62 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.950, 50.865, 89.620, 90.00, 90.00, 90.00
R / Rfree (%)	12 / 14.1

The binding sites of Iron atom in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L Mutant (pdb code 6di2). 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 Y397L Mutant, PDB code: 6di2:
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 Y397L 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 Y397L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:9.8 occ:1.00 FE1 A:SF4601 0.0 9.8 1.0 S4 A:SF4601 2.2 9.8 1.0 SG A:CYS336 2.3 10.0 1.0 S2 A:SF4601 2.3 10.3 1.0 S3 A:SF4601 2.3 10.2 1.0 FE2 A:SF4601 2.7 10.0 1.0 FE4 A:SF4601 2.7 10.2 1.0 FE3 A:SF4601 2.7 10.0 1.0 CB A:CYS336 3.2 10.2 1.0 S1 A:SF4601 3.9 10.3 1.0 N A:CYS336 4.0 9.3 1.0 CG A:PRO500 4.1 11.6 1.0 CA A:CYS336 4.2 9.3 1.0 CB A:PRO334 4.3 10.3 1.0 CG A:PRO334 4.4 11.4 1.0 CB A:PRO500 4.5 10.7 1.0 SG A:CYS417 4.7 10.6 1.0 SG A:CYS434 4.8 11.4 1.0 CD1 A:ILE420 4.9 10.6 1.0 SG A:CYS474 4.9 10.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L 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 Y397L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:10.0 occ:1.00 FE2 A:SF4601 0.0 10.0 1.0 S3 A:SF4601 2.3 10.2 1.0 SG A:CYS417 2.3 10.6 1.0 S1 A:SF4601 2.3 10.3 1.0 S4 A:SF4601 2.3 9.8 1.0 FE3 A:SF4601 2.7 10.0 1.0 FE4 A:SF4601 2.7 10.2 1.0 FE1 A:SF4601 2.7 9.8 1.0 CB A:CYS417 3.3 11.1 1.0 S2 A:SF4601 3.9 10.3 1.0 CA A:CYS417 4.0 10.4 1.0 CG A:PRO500 4.4 11.6 1.0 CM A:MPD602 4.5 16.3 1.0 CD A:PRO500 4.5 10.7 1.0 SG A:CYS474 4.7 10.7 1.0 CG2 A:THR471 4.7 13.8 1.0 N A:PRO500 4.8 10.0 1.0 SG A:CYS434 4.8 11.4 1.0 N A:CYS417 4.8 10.7 1.0 SG A:CYS336 4.8 10.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L 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 Y397L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:10.0 occ:1.00 FE3 A:SF4601 0.0 10.0 1.0 S4 A:SF4601 2.3 9.8 1.0 S2 A:SF4601 2.3 10.3 1.0 SG A:CYS474 2.3 10.7 1.0 S1 A:SF4601 2.3 10.3 1.0 FE2 A:SF4601 2.7 10.0 1.0 FE4 A:SF4601 2.7 10.2 1.0 FE1 A:SF4601 2.7 9.8 1.0 CB A:CYS474 3.2 10.7 1.0 S3 A:SF4601 3.9 10.2 1.0 CE2 A:PHE436 4.1 11.6 1.0 CB A:PRO334 4.2 10.3 1.0 CD2 A:PHE436 4.3 10.9 1.0 CM A:MPD602 4.4 16.3 1.0 O A:HOH834 4.4 11.0 1.0 CA A:CYS474 4.5 10.3 1.0 SG A:CYS417 4.6 10.6 1.0 SG A:CYS434 4.8 11.4 1.0 SG A:CYS336 4.8 10.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Eukaryotic Dna Primase Large Subunit Iron-Sulfur Cluster Domain Y397L 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 Y397L Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:10.2 occ:1.00 FE4 A:SF4601 0.0 10.2 1.0 S1 A:SF4601 2.2 10.3 1.0 SG A:CYS434 2.3 11.4 1.0 S3 A:SF4601 2.3 10.2 1.0 S2 A:SF4601 2.3 10.3 1.0 FE2 A:SF4601 2.7 10.0 1.0 FE3 A:SF4601 2.7 10.0 1.0 FE1 A:SF4601 2.7 9.8 1.0 CB A:CYS434 3.3 11.6 1.0 S4 A:SF4601 3.9 9.8 1.0 CA A:CYS434 3.9 10.7 1.0 CD2 A:PHE436 4.1 10.9 1.0 C A:CYS434 4.6 10.1 1.0 CE2 A:PHE436 4.7 11.6 1.0 SG A:CYS336 4.7 10.0 1.0 CD A:PRO435 4.8 10.5 1.0 SG A:CYS474 4.8 10.7 1.0 CB A:CYS336 4.8 10.2 1.0 CB A:CYS474 4.8 10.7 1.0 N A:PRO435 4.9 10.1 1.0 SG A:CYS417 4.9 10.6 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