Iron in PDB 3lgb: Crystal Structure of the Fe-S Domain of the Yeast Dna Primase

The structure of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase, PDB code: 3lgb was solved by L.Sauguet, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 1.54
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	86.570, 86.570, 141.480, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 16.4

The structure of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase (pdb code 3lgb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase, PDB code: 3lgb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe514 b:12.6 occ:1.00 FE1 A:SF4514 0.0 12.6 1.0 SG A:CYS417 2.3 14.1 1.0 S3 A:SF4514 2.3 13.3 1.0 S4 A:SF4514 2.3 13.5 1.0 S2 A:SF4514 2.4 13.6 1.0 FE3 A:SF4514 2.7 13.2 1.0 FE4 A:SF4514 2.7 12.6 1.0 FE2 A:SF4514 2.7 12.9 1.0 CB A:CYS417 3.3 11.7 1.0 S1 A:SF4514 4.0 13.7 1.0 CA A:CYS417 4.0 11.0 1.0 CD A:PRO500 4.5 12.2 1.0 CG2 A:THR471 4.6 17.2 1.0 CG A:PRO500 4.7 17.1 1.0 SG A:CYS474 4.7 15.6 1.0 N A:CYS417 4.7 11.6 1.0 SG A:CYS434 4.8 14.3 1.0 N A:PRO500 4.9 11.3 1.0 SG A:CYS336 4.9 13.1 1.0

Iron binding site 2 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe514 b:12.9 occ:1.00 FE2 A:SF4514 0.0 12.9 1.0 S4 A:SF4514 2.3 13.5 1.0 SG A:CYS434 2.3 14.3 1.0 S3 A:SF4514 2.3 13.3 1.0 S1 A:SF4514 2.4 13.7 1.0 FE3 A:SF4514 2.7 13.2 1.0 FE1 A:SF4514 2.7 12.6 1.0 FE4 A:SF4514 2.8 12.6 1.0 CB A:CYS434 3.2 12.5 1.0 CA A:CYS434 3.9 12.1 1.0 S2 A:SF4514 4.0 13.6 1.0 CD2 A:PHE436 4.0 16.2 1.0 C A:CYS434 4.6 14.4 1.0 CD A:PRO435 4.6 13.5 1.0 CE2 A:PHE436 4.7 18.2 1.0 SG A:CYS336 4.8 13.1 1.0 N A:PRO435 4.8 12.3 1.0 SG A:CYS474 4.8 15.6 1.0 CB A:CYS336 4.8 11.5 1.0 CB A:CYS474 4.9 14.0 1.0 SG A:CYS417 4.9 14.1 1.0

Iron binding site 3 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe514 b:13.2 occ:1.00 FE3 A:SF4514 0.0 13.2 1.0 SG A:CYS474 2.3 15.6 1.0 S2 A:SF4514 2.3 13.6 1.0 S4 A:SF4514 2.3 13.5 1.0 S1 A:SF4514 2.4 13.7 1.0 FE1 A:SF4514 2.7 12.6 1.0 FE2 A:SF4514 2.7 12.9 1.0 FE4 A:SF4514 2.8 12.6 1.0 CB A:CYS474 3.1 14.0 1.0 S3 A:SF4514 4.0 13.3 1.0 CE2 A:PHE436 4.1 18.2 1.0 CB A:PRO334 4.3 12.8 1.0 O A:HOH37 4.3 15.8 1.0 CD2 A:PHE436 4.3 16.2 1.0 CA A:CYS474 4.5 14.4 1.0 SG A:CYS417 4.6 14.1 1.0 SG A:CYS336 4.8 13.1 1.0 SG A:CYS434 4.8 14.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe514 b:12.6 occ:1.00 FE4 A:SF4514 0.0 12.6 1.0 SG A:CYS336 2.3 13.1 1.0 S2 A:SF4514 2.3 13.6 1.0 S1 A:SF4514 2.4 13.7 1.0 S3 A:SF4514 2.4 13.3 1.0 FE1 A:SF4514 2.7 12.6 1.0 FE2 A:SF4514 2.8 12.9 1.0 FE3 A:SF4514 2.8 13.2 1.0 CB A:CYS336 3.2 11.5 1.0 S4 A:SF4514 4.0 13.5 1.0 N A:CYS336 4.0 12.0 1.0 CA A:CYS336 4.2 10.6 1.0 CG A:PRO500 4.3 17.1 1.0 CB A:PRO334 4.4 12.8 1.0 CG A:PRO334 4.5 15.2 1.0 CB A:PRO500 4.6 13.5 1.0 SG A:CYS417 4.7 14.1 1.0 CD1 A:ILE420 4.8 12.0 1.0 SG A:CYS434 4.9 14.3 1.0 SG A:CYS474 4.9 15.6 1.0

Iron binding site 5 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:15.8 occ:1.00 FE1 B:SF4514 0.0 15.8 1.0 SG B:CYS336 2.3 16.4 1.0 S2 B:SF4514 2.3 16.4 1.0 S3 B:SF4514 2.4 17.0 1.0 S4 B:SF4514 2.4 17.9 1.0 FE3 B:SF4514 2.7 16.1 1.0 FE4 B:SF4514 2.7 15.8 1.0 FE2 B:SF4514 2.7 16.8 1.0 CB B:CYS336 3.2 14.9 1.0 S1 B:SF4514 4.0 17.2 1.0 N B:CYS336 4.0 15.5 1.0 CA B:CYS336 4.2 14.7 1.0 CG B:PRO500 4.3 21.0 1.0 CB B:PRO334 4.3 14.5 1.0 CG B:PRO334 4.4 16.9 1.0 CB B:PRO500 4.7 15.2 1.0 SG B:CYS417 4.7 17.9 1.0 SG B:CYS434 4.8 18.7 1.0 CD1 B:ILE420 4.9 15.7 1.0 SG B:CYS474 4.9 16.5 1.0

Iron binding site 6 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:16.8 occ:1.00 FE2 B:SF4514 0.0 16.8 1.0 S1 B:SF4514 2.3 17.2 1.0 SG B:CYS434 2.3 18.7 1.0 S4 B:SF4514 2.3 17.9 1.0 S3 B:SF4514 2.4 17.0 1.0 FE3 B:SF4514 2.7 16.1 1.0 FE4 B:SF4514 2.7 15.8 1.0 FE1 B:SF4514 2.7 15.8 1.0 CB B:CYS434 3.2 16.4 1.0 CA B:CYS434 3.9 16.5 1.0 S2 B:SF4514 4.0 16.4 1.0 CD2 B:PHE436 4.1 17.1 1.0 C B:CYS434 4.6 18.3 1.0 CD B:PRO435 4.6 18.2 1.0 CE2 B:PHE436 4.7 18.5 1.0 SG B:CYS336 4.7 16.4 1.0 SG B:CYS474 4.7 16.5 1.0 CB B:CYS336 4.8 14.9 1.0 N B:PRO435 4.8 17.2 1.0 CB B:CYS474 4.8 15.0 1.0 SG B:CYS417 4.8 17.9 1.0

Iron binding site 7 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:16.1 occ:1.00 FE3 B:SF4514 0.0 16.1 1.0 SG B:CYS417 2.2 17.9 1.0 S4 B:SF4514 2.3 17.9 1.0 S1 B:SF4514 2.3 17.2 1.0 S2 B:SF4514 2.3 16.4 1.0 FE4 B:SF4514 2.7 15.8 1.0 FE2 B:SF4514 2.7 16.8 1.0 FE1 B:SF4514 2.7 15.8 1.0 CB B:CYS417 3.2 16.2 1.0 S3 B:SF4514 3.9 17.0 1.0 CA B:CYS417 4.0 16.1 1.0 CD B:PRO500 4.5 16.6 1.0 CG2 B:THR471 4.6 17.7 1.0 CG B:PRO500 4.6 21.0 1.0 SG B:CYS474 4.7 16.5 1.0 SG B:CYS434 4.8 18.7 1.0 N B:CYS417 4.8 16.8 1.0 SG B:CYS336 4.8 16.4 1.0 N B:PRO500 4.8 14.7 1.0

Iron binding site 8 out of 8 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe514 b:15.8 occ:1.00 FE4 B:SF4514 0.0 15.8 1.0 SG B:CYS474 2.3 16.5 1.0 S2 B:SF4514 2.3 16.4 1.0 S3 B:SF4514 2.3 17.0 1.0 S1 B:SF4514 2.3 17.2 1.0 FE3 B:SF4514 2.7 16.1 1.0 FE2 B:SF4514 2.7 16.8 1.0 FE1 B:SF4514 2.7 15.8 1.0 CB B:CYS474 3.1 15.0 1.0 S4 B:SF4514 3.9 17.9 1.0 CE2 B:PHE436 4.2 18.5 1.0 CB B:PRO334 4.2 14.5 1.0 O B:HOH55 4.4 16.3 1.0 CD2 B:PHE436 4.4 17.1 1.0 CA B:CYS474 4.5 14.9 1.0 SG B:CYS417 4.6 17.9 1.0 SG B:CYS434 4.8 18.7 1.0 SG B:CYS336 4.8 16.4 1.0

L.Sauguet, S.Klinge, R.L.Perera, J.D.Maman, L.Pellegrini. Shared Active Site Architecture Between the Large Subunit of Eukaryotic Primase and Dna Photolyase Plos One V. 5 10083 2010.
ISSN: ESSN 1932-6203
PubMed: 20404922
DOI: 10.1371/JOURNAL.PONE.0010083