Iron in PDB 5i7m: Crystal Structure of Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain

The structure of Crystal Structure of Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain, PDB code: 5i7m was solved by L.E.Salay, M.K.Thompson, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.66 / 1.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.963, 52.624, 89.195, 90.00, 115.27, 90.00
R / Rfree (%)	21.1 / 25

The binding sites of Iron atom in the Crystal Structure of Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain (pdb code 5i7m). 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain, PDB code: 5i7m:
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 Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.9 occ:1.00 FE1 A:SF4501 0.0 21.9 1.0 S2 A:SF4501 2.1 27.9 1.0 S4 A:SF4501 2.1 27.8 1.0 S3 A:SF4501 2.1 26.6 1.0 SG A:CYS424 2.1 23.2 1.0 FE3 A:SF4501 3.0 21.5 1.0 FE2 A:SF4501 3.0 19.9 1.0 FE4 A:SF4501 3.0 22.0 1.0 CB A:CYS424 3.1 23.7 1.0 S1 A:SF4501 3.7 25.8 1.0 CE2 A:PHE386 4.1 25.5 1.0 CD2 A:LEU441 4.1 27.4 1.0 CD A:PRO286 4.2 22.3 1.0 CB A:PRO285 4.2 21.1 1.0 CD2 A:PHE386 4.3 23.7 1.0 CA A:CYS424 4.5 24.3 1.0 SG A:CYS367 4.8 25.8 1.0 CG A:PRO286 4.8 20.3 1.0 SG A:CYS287 4.9 21.2 1.0 CD2 A:PHE447 5.0 21.1 1.0 N A:PRO286 5.0 23.2 1.0 SG A:CYS384 5.0 21.5 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.9 occ:1.00 FE2 A:SF4501 0.0 19.9 1.0 S3 A:SF4501 2.1 26.6 1.0 S1 A:SF4501 2.1 25.8 1.0 S4 A:SF4501 2.1 27.8 1.0 SG A:CYS384 2.2 21.5 1.0 FE4 A:SF4501 3.0 22.0 1.0 FE1 A:SF4501 3.0 21.9 1.0 FE3 A:SF4501 3.0 21.5 1.0 CB A:CYS384 3.2 20.5 1.0 S2 A:SF4501 3.7 27.9 1.0 CA A:CYS384 3.9 21.6 1.0 CD2 A:PHE386 4.0 23.7 1.0 CD1 A:ILE371 4.5 33.1 1.0 CG1 A:ILE371 4.6 28.3 1.0 CD A:PRO385 4.6 22.9 1.0 CE2 A:PHE386 4.6 25.5 1.0 C A:CYS384 4.6 23.8 1.0 CB A:CYS287 4.7 19.6 1.0 SG A:CYS287 4.8 21.2 1.0 SG A:CYS424 4.9 23.2 1.0 N A:PRO385 4.9 23.5 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.5 occ:1.00 FE3 A:SF4501 0.0 21.5 1.0 SG A:CYS287 2.1 21.2 1.0 S2 A:SF4501 2.1 27.9 1.0 S4 A:SF4501 2.1 27.8 1.0 S1 A:SF4501 2.1 25.8 1.0 FE1 A:SF4501 3.0 21.9 1.0 FE4 A:SF4501 3.0 22.0 1.0 FE2 A:SF4501 3.0 19.9 1.0 CB A:CYS287 3.0 19.6 1.0 S3 A:SF4501 3.7 26.6 1.0 CB A:PRO285 4.0 21.1 1.0 N A:CYS287 4.0 20.6 1.0 CG A:PRO444 4.1 17.7 1.0 CA A:CYS287 4.1 20.3 1.0 CG A:PRO285 4.2 21.0 1.0 CB A:PRO444 4.5 18.4 1.0 CD1 A:ILE370 4.8 24.1 1.0 SG A:CYS367 4.8 25.8 1.0 SG A:CYS384 4.9 21.5 1.0 SG A:CYS424 5.0 23.2 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:22.0 occ:1.00 FE4 A:SF4501 0.0 22.0 1.0 S1 A:SF4501 2.1 25.8 1.0 S3 A:SF4501 2.1 26.6 1.0 SG A:CYS367 2.1 25.8 1.0 S2 A:SF4501 2.1 27.9 1.0 FE2 A:SF4501 3.0 19.9 1.0 FE1 A:SF4501 3.0 21.9 1.0 FE3 A:SF4501 3.0 21.5 1.0 CB A:CYS367 3.1 26.6 1.0 S4 A:SF4501 3.7 27.8 1.0 CA A:CYS367 3.7 25.1 1.0 CG A:PRO444 4.5 17.7 1.0 CD A:PRO444 4.6 18.9 1.0 CD2 A:LEU441 4.7 27.4 1.0 CG A:GLN421 4.7 25.3 1.0 N A:CYS367 4.7 22.0 1.0 N A:PRO444 4.8 17.8 1.0 C A:CYS367 4.8 27.5 1.0 CG A:LEU441 4.9 24.2 1.0 SG A:CYS424 4.9 23.2 1.0 O A:CYS367 5.0 26.0 1.0 CD1 A:ILE371 5.0 33.1 1.0 SG A:CYS287 5.0 21.2 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:18.0 occ:1.00 FE1 B:SF4500 0.0 18.0 1.0 S2 B:SF4500 2.1 20.6 1.0 S3 B:SF4500 2.1 22.1 1.0 S4 B:SF4500 2.1 20.2 1.0 SG B:CYS367 2.2 19.7 1.0 FE4 B:SF4500 3.0 18.3 1.0 FE2 B:SF4500 3.0 17.7 1.0 FE3 B:SF4500 3.0 17.7 1.0 CB B:CYS367 3.2 21.3 1.0 CA B:CYS367 3.7 21.7 1.0 S1 B:SF4500 3.7 20.9 1.0 CG B:PRO444 4.4 18.2 1.0 CD B:PRO444 4.5 18.5 1.0 N B:CYS367 4.6 21.0 1.0 N B:PRO444 4.7 19.7 1.0 CG B:GLN421 4.8 22.1 1.0 C B:CYS367 4.8 21.8 1.0 SG B:CYS424 4.9 19.5 1.0 CD1 B:ILE371 4.9 26.4 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:17.7 occ:1.00 FE2 B:SF4500 0.0 17.7 1.0 S3 B:SF4500 2.1 22.1 1.0 S1 B:SF4500 2.1 20.9 1.0 S4 B:SF4500 2.1 20.2 1.0 SG B:CYS287 2.2 19.5 1.0 CB B:CYS287 3.0 18.6 1.0 FE1 B:SF4500 3.0 18.0 1.0 FE4 B:SF4500 3.0 18.3 1.0 FE3 B:SF4500 3.0 17.7 1.0 S2 B:SF4500 3.7 20.6 1.0 CB B:PRO285 3.9 16.5 1.0 CG B:PRO444 4.0 18.2 1.0 N B:CYS287 4.1 17.7 1.0 CG B:PRO285 4.2 17.5 1.0 CA B:CYS287 4.2 20.6 1.0 CB B:PRO444 4.5 20.1 1.0 CD1 B:ILE370 4.8 22.6 1.0 SG B:CYS424 4.9 19.5 1.0 SG B:CYS367 4.9 19.7 1.0 CA B:PRO444 4.9 18.3 1.0 CB B:CYS384 4.9 19.1 1.0 SG B:CYS384 5.0 20.4 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:17.7 occ:1.00 FE3 B:SF4500 0.0 17.7 1.0 S1 B:SF4500 2.1 20.9 1.0 S2 B:SF4500 2.1 20.6 1.0 S4 B:SF4500 2.1 20.2 1.0 SG B:CYS384 2.2 20.4 1.0 FE4 B:SF4500 3.0 18.3 1.0 FE2 B:SF4500 3.0 17.7 1.0 FE1 B:SF4500 3.0 18.0 1.0 CB B:CYS384 3.0 19.1 1.0 S3 B:SF4500 3.7 22.1 1.0 CA B:CYS384 4.0 19.9 1.0 CD2 B:PHE386 4.1 20.9 1.0 CD1 B:ILE371 4.6 26.4 1.0 C B:CYS384 4.6 22.0 1.0 CG1 B:ILE371 4.6 24.1 1.0 CB B:CYS287 4.7 18.6 1.0 CD B:PRO385 4.7 24.3 1.0 CE2 B:PHE386 4.8 21.2 1.0 SG B:CYS287 4.8 19.5 1.0 CB B:PHE386 4.9 20.3 1.0 N B:PRO385 4.9 20.3 1.0 SG B:CYS424 4.9 19.5 1.0 CG B:PHE386 5.0 21.1 1.0 CB B:CYS424 5.0 20.6 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Y345F Mutant of Human 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 Y345F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:18.3 occ:1.00 FE4 B:SF4500 0.0 18.3 1.0 SG B:CYS424 2.1 19.5 1.0 S2 B:SF4500 2.1 20.6 1.0 S1 B:SF4500 2.1 20.9 1.0 S3 B:SF4500 2.1 22.1 1.0 CB B:CYS424 3.0 20.6 1.0 FE1 B:SF4500 3.0 18.0 1.0 FE2 B:SF4500 3.0 17.7 1.0 FE3 B:SF4500 3.0 17.7 1.0 S4 B:SF4500 3.7 20.2 1.0 CD B:PRO286 4.1 20.0 1.0 CB B:PRO285 4.2 16.5 1.0 CE2 B:PHE386 4.2 21.2 1.0 CD2 B:LEU441 4.3 21.4 1.0 CD2 B:PHE386 4.4 20.9 1.0 CA B:CYS424 4.4 19.7 1.0 CG B:PRO286 4.8 21.1 1.0 SG B:CYS367 4.8 19.7 1.0 CD2 B:PHE447 4.9 18.5 1.0 SG B:CYS287 5.0 19.5 1.0 N B:PRO286 5.0 19.6 1.0

E.O'brien, M.E.Holt, M.K.Thompson, L.E.Salay, A.C.Ehlinger, W.J.Chazin, J.K.Barton. The [4FE4S] Cluster of Human Dna Primase Functions As A Redox Switch Using Dna Charge Transport. Science V. 355 2017.
ISSN: ESSN 1095-9203
PubMed: 28232525
DOI: 10.1126/SCIENCE.AAG1789