Iron in PDB 3l9q: Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain

The structure of Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain, PDB code: 3l9q was solved by S.Vaithiyalingam, B.F.Eichman, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.441, 53.050, 88.844, 90.00, 115.09, 90.00
R / Rfree (%)	13 / 16.9

The binding sites of Iron atom in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain (pdb code 3l9q). 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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain, PDB code: 3l9q:
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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:22.0 occ:1.00 FE1 A:SF4500 0.0 22.0 1.0 S3 A:SF4500 2.3 21.4 1.0 S2 A:SF4500 2.3 21.2 1.0 S4 A:SF4500 2.3 21.4 1.0 SG A:CYS424 2.3 22.0 1.0 FE4 A:SF4500 2.7 20.7 1.0 FE2 A:SF4500 2.7 21.7 1.0 FE3 A:SF4500 2.7 20.7 1.0 CB A:CYS424 3.1 20.9 1.0 S1 A:SF4500 3.9 21.0 1.0 CD2 A:LEU441 3.9 23.7 1.0 CB A:PRO285 4.2 18.1 1.0 CE2 A:PHE386 4.3 24.8 1.0 CD A:PRO286 4.4 17.4 1.0 CD2 A:PHE386 4.4 24.4 1.0 CA A:CYS424 4.6 21.9 1.0 SG A:CYS367 4.7 22.7 1.0 SG A:CYS287 4.7 19.3 1.0 SG A:CYS384 4.8 21.7 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:21.7 occ:1.00 FE2 A:SF4500 0.0 21.7 1.0 S4 A:SF4500 2.3 21.4 1.0 S1 A:SF4500 2.3 21.0 1.0 S3 A:SF4500 2.3 21.4 1.0 SG A:CYS384 2.3 21.7 1.0 FE4 A:SF4500 2.7 20.7 1.0 FE1 A:SF4500 2.7 22.0 1.0 FE3 A:SF4500 2.7 20.7 1.0 CB A:CYS384 3.3 21.1 1.0 S2 A:SF4500 3.9 21.2 1.0 CA A:CYS384 4.1 19.6 1.0 CD2 A:PHE386 4.2 24.4 1.0 CD1 A:ILE371 4.6 24.2 1.0 CB A:CYS287 4.6 19.0 1.0 CD A:PRO385 4.7 22.4 1.0 SG A:CYS287 4.7 19.3 1.0 CG1 A:ILE371 4.7 22.8 1.0 CE2 A:PHE386 4.8 24.8 1.0 C A:CYS384 4.8 20.4 1.0 SG A:CYS424 4.8 22.0 1.0 CB A:CYS424 4.9 20.9 1.0 SG A:CYS367 5.0 22.7 1.0 N A:PRO385 5.0 20.6 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:20.7 occ:1.00 FE3 A:SF4500 0.0 20.7 1.0 S1 A:SF4500 2.3 21.0 1.0 S2 A:SF4500 2.3 21.2 1.0 S4 A:SF4500 2.3 21.4 1.0 SG A:CYS367 2.3 22.7 1.0 FE4 A:SF4500 2.7 20.7 1.0 FE1 A:SF4500 2.7 22.0 1.0 FE2 A:SF4500 2.7 21.7 1.0 CB A:CYS367 3.2 21.6 1.0 CA A:CYS367 3.8 21.3 1.0 S3 A:SF4500 3.9 21.4 1.0 CD2 A:LEU441 4.3 23.7 1.0 CG A:PRO444 4.5 15.4 1.0 CD A:PRO444 4.6 15.3 1.0 CG A:GLN421 4.6 25.8 1.0 N A:CYS367 4.8 19.5 1.0 SG A:CYS424 4.8 22.0 1.0 CG A:LEU441 4.8 22.1 1.0 N A:PRO444 4.8 16.4 1.0 SG A:CYS287 4.9 19.3 1.0 SG A:CYS384 4.9 21.7 1.0 CD1 A:ILE371 4.9 24.2 1.0 C A:CYS367 4.9 22.3 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:20.7 occ:1.00 FE4 A:SF4500 0.0 20.7 1.0 S2 A:SF4500 2.3 21.2 1.0 SG A:CYS287 2.3 19.3 1.0 S3 A:SF4500 2.3 21.4 1.0 S1 A:SF4500 2.3 21.0 1.0 FE2 A:SF4500 2.7 21.7 1.0 FE1 A:SF4500 2.7 22.0 1.0 FE3 A:SF4500 2.7 20.7 1.0 CB A:CYS287 3.2 19.0 1.0 S4 A:SF4500 3.9 21.4 1.0 CB A:PRO285 4.1 18.1 1.0 N A:CYS287 4.1 17.2 1.0 CG A:PRO444 4.1 15.4 1.0 CA A:CYS287 4.3 19.0 1.0 CG A:PRO285 4.4 17.3 1.0 CB A:PRO444 4.7 14.9 1.0 SG A:CYS367 4.7 22.7 1.0 SG A:CYS384 4.8 21.7 1.0 CD1 A:ILE370 4.8 20.4 1.0 SG A:CYS424 4.9 22.0 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:16.1 occ:1.00 FE1 B:SF4500 0.0 16.1 1.0 S2 B:SF4500 2.3 15.6 1.0 S4 B:SF4500 2.3 16.0 1.0 S3 B:SF4500 2.3 16.2 1.0 SG B:CYS367 2.3 15.7 1.0 FE4 B:SF4500 2.7 15.6 1.0 FE2 B:SF4500 2.7 15.1 1.0 FE3 B:SF4500 2.8 15.4 1.0 CB B:CYS367 3.2 16.6 1.0 CA B:CYS367 3.8 16.1 1.0 S1 B:SF4500 3.9 15.1 1.0 CG B:PRO444 4.4 13.9 1.0 CD B:PRO444 4.5 15.4 1.0 CD2 B:LEU441 4.6 20.2 1.0 CG B:GLN421 4.7 18.6 1.0 N B:CYS367 4.7 15.1 1.0 SG B:CYS424 4.8 15.5 1.0 N B:PRO444 4.8 14.8 1.0 SG B:CYS384 4.9 16.0 1.0 SG B:CYS287 4.9 16.0 1.0 CD1 B:ILE371 4.9 16.3 1.0 C B:CYS367 4.9 18.2 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:15.1 occ:1.00 FE2 B:SF4500 0.0 15.1 1.0 S1 B:SF4500 2.3 15.1 1.0 S3 B:SF4500 2.3 16.2 1.0 S4 B:SF4500 2.3 16.0 1.0 SG B:CYS424 2.3 15.5 1.0 FE4 B:SF4500 2.7 15.6 1.0 FE3 B:SF4500 2.7 15.4 1.0 FE1 B:SF4500 2.7 16.1 1.0 CB B:CYS424 3.2 15.1 1.0 S2 B:SF4500 3.9 15.6 1.0 CD2 B:LEU441 4.2 20.2 1.0 CB B:PRO285 4.2 15.5 1.0 CE2 B:PHE386 4.2 15.1 1.0 CD2 B:PHE386 4.4 15.8 1.0 CD B:PRO286 4.5 14.6 1.0 CA B:CYS424 4.6 15.5 1.0 SG B:CYS367 4.8 15.7 1.0 SG B:CYS287 4.8 16.0 1.0 SG B:CYS384 4.8 16.0 1.0 CD1 B:PHE447 5.0 16.2 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:15.4 occ:1.00 FE3 B:SF4500 0.0 15.4 1.0 S4 B:SF4500 2.3 16.0 1.0 S2 B:SF4500 2.3 15.6 1.0 S1 B:SF4500 2.3 15.1 1.0 SG B:CYS384 2.3 16.0 1.0 FE4 B:SF4500 2.7 15.6 1.0 FE2 B:SF4500 2.7 15.1 1.0 FE1 B:SF4500 2.8 16.1 1.0 CB B:CYS384 3.3 15.6 1.0 S3 B:SF4500 3.9 16.2 1.0 CA B:CYS384 4.1 14.3 1.0 CD2 B:PHE386 4.1 15.8 1.0 CB B:CYS287 4.6 16.4 1.0 CD1 B:ILE371 4.6 16.3 1.0 SG B:CYS287 4.7 16.0 1.0 CG1 B:ILE371 4.7 15.9 1.0 CD B:PRO385 4.7 17.9 1.0 C B:CYS384 4.7 15.1 1.0 CE2 B:PHE386 4.8 15.1 1.0 SG B:CYS424 4.8 15.5 1.0 N B:PRO385 4.9 14.9 1.0 CB B:CYS424 5.0 15.1 1.0 SG B:CYS367 5.0 15.7 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:15.6 occ:1.00 FE4 B:SF4500 0.0 15.6 1.0 S3 B:SF4500 2.3 16.2 1.0 SG B:CYS287 2.3 16.0 1.0 S2 B:SF4500 2.3 15.6 1.0 S1 B:SF4500 2.3 15.1 1.0 FE3 B:SF4500 2.7 15.4 1.0 FE2 B:SF4500 2.7 15.1 1.0 FE1 B:SF4500 2.7 16.1 1.0 CB B:CYS287 3.2 16.4 1.0 S4 B:SF4500 3.9 16.0 1.0 CG B:PRO444 4.0 13.9 1.0 CB B:PRO285 4.1 15.5 1.0 N B:CYS287 4.1 15.2 1.0 CA B:CYS287 4.2 17.0 1.0 CG B:PRO285 4.4 15.7 1.0 CB B:PRO444 4.5 14.3 1.0 SG B:CYS384 4.7 16.0 1.0 SG B:CYS367 4.8 15.7 1.0 SG B:CYS424 4.9 15.5 1.0 CA B:PRO444 4.9 14.0 1.0 CD1 B:ILE370 5.0 15.8 1.0 CD B:PRO444 5.0 15.4 1.0 CB B:CYS384 5.0 15.6 1.0

S.Vaithiyalingam, E.M.Warren, B.F.Eichman, W.J.Chazin. Insights Into Eukaryotic Dna Priming From the Structure and Functional Interactions of the 4FE-4S Cluster Domain of Human Dna Primase. Proc.Natl.Acad.Sci.Usa V. 107 13684 2010.
ISSN: ISSN 0027-8424
PubMed: 20643958
DOI: 10.1073/PNAS.1002009107