Iron in PDB 5dqo: Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain

The structure of Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain, PDB code: 5dqo 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)	44.14 / 2.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	60.398, 60.398, 246.729, 90.00, 90.00, 120.00
R / Rfree (%)	25.1 / 27.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain (pdb code 5dqo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain, PDB code: 5dqo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:62.2 occ:1.00 FE1 A:SF4501 0.0 62.2 1.0 S4 A:SF4501 2.1 51.3 1.0 S3 A:SF4501 2.1 77.4 1.0 S2 A:SF4501 2.1 57.5 1.0 SG A:CYS287 2.3 50.1 1.0 FE2 A:SF4501 3.0 62.4 1.0 FE4 A:SF4501 3.0 67.2 1.0 FE3 A:SF4501 3.0 57.8 1.0 CB A:CYS287 3.4 49.0 1.0 CB A:PRO285 3.5 29.0 1.0 S1 A:SF4501 3.7 57.5 1.0 N A:CYS287 3.8 42.6 1.0 CG A:PRO285 3.9 36.1 1.0 CG A:PRO444 4.2 29.0 1.0 CA A:CYS287 4.2 44.6 1.0 CD A:PRO286 4.3 48.6 1.0 N A:PRO286 4.3 46.4 1.0 CB A:PRO444 4.5 31.8 1.0 CA A:PRO285 4.7 33.3 1.0 C A:PRO285 4.8 41.9 1.0 C A:PRO286 4.9 41.0 1.0 CD A:PRO385 4.9 32.2 1.0 SG A:CYS367 4.9 34.5 1.0 CA A:PRO444 5.0 38.3 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:62.4 occ:1.00 FE2 A:SF4501 0.0 62.4 1.0 S4 A:SF4501 2.1 51.3 1.0 S3 A:SF4501 2.1 77.4 1.0 S1 A:SF4501 2.1 57.5 1.0 SG A:CYS367 2.3 34.5 1.0 FE1 A:SF4501 3.0 62.2 1.0 FE4 A:SF4501 3.0 67.2 1.0 FE3 A:SF4501 3.0 57.8 1.0 CB A:CYS367 3.3 43.0 1.0 S2 A:SF4501 3.7 57.5 1.0 CD2 A:LEU441 3.8 41.0 1.0 CA A:CYS367 4.0 42.9 1.0 CG A:PRO444 4.4 29.0 1.0 SG A:CYS424 4.4 44.5 1.0 CD A:PRO444 4.5 32.1 1.0 CG A:GLN421 4.7 35.9 1.0 CG A:LEU441 4.8 40.2 1.0 N A:PRO444 4.8 32.8 1.0 CA A:PRO444 5.0 38.3 1.0 CB A:CYS424 5.0 43.6 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:57.8 occ:1.00 FE3 A:SF4501 0.0 57.8 1.0 S4 A:SF4501 2.1 51.3 1.0 S1 A:SF4501 2.1 57.5 1.0 S2 A:SF4501 2.1 57.5 1.0 SG A:CYS424 2.3 44.5 1.0 CB A:CYS424 2.7 43.6 1.0 FE4 A:SF4501 3.0 67.2 1.0 FE2 A:SF4501 3.0 62.4 1.0 FE1 A:SF4501 3.0 62.2 1.0 CD A:PRO286 3.6 48.6 1.0 S3 A:SF4501 3.7 77.4 1.0 CE2 A:PHE386 3.9 32.1 1.0 CA A:CYS424 4.2 35.8 1.0 CG A:PRO286 4.2 47.9 1.0 CD2 A:LEU441 4.2 41.0 1.0 CD2 A:PHE386 4.2 31.7 1.0 CB A:PRO285 4.3 29.0 1.0 N A:PRO286 4.6 46.4 1.0 CB A:PRO286 4.9 53.0 1.0 CD2 A:PHE447 4.9 48.9 1.0 SG A:CYS384 5.0 45.6 1.0 C A:CYS424 5.0 38.9 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:67.2 occ:1.00 FE4 A:SF4501 0.0 67.2 1.0 S2 A:SF4501 2.1 57.5 1.0 S1 A:SF4501 2.1 57.5 1.0 S3 A:SF4501 2.1 77.4 1.0 SG A:CYS384 2.3 45.6 1.0 FE3 A:SF4501 3.0 57.8 1.0 FE2 A:SF4501 3.0 62.4 1.0 FE1 A:SF4501 3.0 62.2 1.0 CB A:CYS384 3.1 39.4 1.0 S4 A:SF4501 3.7 51.3 1.0 CA A:CYS384 3.8 45.5 1.0 CD2 A:PHE386 4.0 31.7 1.0 CD A:PRO385 4.3 32.2 1.0 CE2 A:PHE386 4.5 32.1 1.0 CD1 A:ILE371 4.6 26.7 1.0 N A:PRO385 4.6 46.8 1.0 C A:CYS384 4.6 43.2 1.0 CG1 A:ILE371 4.7 36.0 1.0 CB A:CYS424 4.8 43.6 1.0 SG A:CYS287 4.8 50.1 1.0 CB A:CYS287 5.0 49.0 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:63.7 occ:1.00 FE1 B:SF4501 0.0 63.7 1.0 S4 B:SF4501 2.1 55.4 1.0 S2 B:SF4501 2.1 52.2 1.0 S3 B:SF4501 2.1 51.5 1.0 SG B:CYS287 2.3 42.7 1.0 FE2 B:SF4501 3.0 59.6 1.0 FE4 B:SF4501 3.0 63.5 1.0 FE3 B:SF4501 3.0 62.4 1.0 CB B:CYS287 3.2 46.1 1.0 CB B:PRO285 3.5 30.6 1.0 S1 B:SF4501 3.7 59.8 1.0 CG B:PRO444 4.0 26.3 1.0 N B:CYS287 4.1 51.1 1.0 CD B:PRO286 4.3 46.2 1.0 CA B:CYS287 4.3 49.3 1.0 CB B:PRO444 4.3 30.5 1.0 CG B:PRO285 4.4 35.6 1.0 N B:PRO286 4.7 45.2 1.0 CA B:PRO285 4.8 34.8 1.0 SG B:CYS367 4.9 40.8 1.0 CB B:CYS384 5.0 61.3 1.0 CA B:PRO444 5.0 36.7 1.0 C B:PRO285 5.0 46.2 1.0 SG B:CYS384 5.0 48.8 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:59.6 occ:1.00 FE2 B:SF4501 0.0 59.6 1.0 S4 B:SF4501 2.1 55.4 1.0 S3 B:SF4501 2.1 51.5 1.0 S1 B:SF4501 2.1 59.8 1.0 SG B:CYS384 2.3 48.8 1.0 FE4 B:SF4501 3.0 63.5 1.0 FE1 B:SF4501 3.0 63.7 1.0 FE3 B:SF4501 3.0 62.4 1.0 CB B:CYS384 3.2 61.3 1.0 S2 B:SF4501 3.7 52.2 1.0 CD2 B:PHE386 3.8 35.7 1.0 CA B:CYS384 4.1 60.9 1.0 CD B:PRO385 4.4 51.4 1.0 CE2 B:PHE386 4.6 34.1 1.0 CB B:CYS287 4.6 46.1 1.0 CD1 B:ILE371 4.6 34.1 1.0 CB B:PHE386 4.7 52.3 1.0 C B:CYS384 4.7 67.2 1.0 CG B:PHE386 4.8 44.0 1.0 N B:PRO385 4.8 53.3 1.0 N B:PHE386 4.8 64.1 1.0 SG B:CYS287 4.8 42.7 1.0 CB B:CYS424 4.9 51.9 1.0 CG1 B:ILE371 5.0 35.1 1.0

Iron binding site 7 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:62.4 occ:1.00 FE3 B:SF4501 0.0 62.4 1.0 S2 B:SF4501 2.1 52.2 1.0 S4 B:SF4501 2.1 55.4 1.0 S1 B:SF4501 2.1 59.8 1.0 SG B:CYS367 2.4 40.8 1.0 FE4 B:SF4501 3.0 63.5 1.0 FE1 B:SF4501 3.0 63.7 1.0 FE2 B:SF4501 3.0 59.6 1.0 CB B:CYS367 3.1 39.7 1.0 S3 B:SF4501 3.7 51.5 1.0 CA B:CYS367 3.8 41.1 1.0 CG B:PRO444 4.5 26.3 1.0 CD1 B:ILE371 4.6 34.1 1.0 SG B:CYS424 4.6 40.4 1.0 CD2 B:LEU441 4.6 33.1 1.0 N B:CYS367 4.6 43.5 1.0 O B:CYS367 4.7 50.0 1.0 C B:CYS367 4.8 42.6 1.0 CD B:PRO444 4.8 33.8 1.0 CG B:GLN421 4.9 35.8 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Y347F 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 Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:63.5 occ:1.00 FE4 B:SF4501 0.0 63.5 1.0 S3 B:SF4501 2.1 51.5 1.0 S2 B:SF4501 2.1 52.2 1.0 S1 B:SF4501 2.1 59.8 1.0 SG B:CYS424 2.2 40.4 1.0 CB B:CYS424 2.9 51.9 1.0 FE3 B:SF4501 3.0 62.4 1.0 FE2 B:SF4501 3.0 59.6 1.0 FE1 B:SF4501 3.0 63.7 1.0 S4 B:SF4501 3.7 55.4 1.0 CD B:PRO286 3.8 46.2 1.0 CA B:CYS424 4.2 53.2 1.0 CE2 B:PHE386 4.2 34.1 1.0 CD2 B:LEU441 4.3 33.1 1.0 CB B:PRO285 4.3 30.6 1.0 CD2 B:PHE386 4.4 35.7 1.0 CG B:PRO286 4.5 45.0 1.0 CD2 B:PHE447 4.5 30.6 1.0 CE2 B:PHE447 4.7 31.4 1.0 N B:PRO286 4.9 45.2 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Y347F 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 9 of Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:58.7 occ:1.00 FE1 C:SF4501 0.0 58.7 1.0 S2 C:SF4501 2.1 46.7 1.0 S3 C:SF4501 2.1 47.1 1.0 S4 C:SF4501 2.1 57.1 1.0 SG C:CYS367 2.2 41.0 1.0 FE4 C:SF4501 3.0 60.4 1.0 FE3 C:SF4501 3.0 57.5 1.0 FE2 C:SF4501 3.0 57.1 1.0 CB C:CYS367 3.3 43.1 1.0 S1 C:SF4501 3.7 44.4 1.0 CD2 C:LEU441 3.8 24.4 1.0 CA C:CYS367 3.8 36.3 1.0 CG C:PRO444 4.5 24.6 1.0 CD C:PRO444 4.5 27.4 1.0 N C:CYS367 4.6 37.4 1.0 CD1 C:ILE371 4.7 27.0 1.0 N C:PRO444 4.7 32.7 1.0 SG C:CYS424 4.7 41.1 1.0 CG C:GLN421 4.8 35.1 1.0 C C:HIS443 4.9 32.1 1.0 CA C:PRO444 5.0 25.4 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Y347F 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 10 of Crystal Structure of Y347F Mutant of Human Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:57.1 occ:1.00 FE2 C:SF4501 0.0 57.1 1.0 S3 C:SF4501 2.1 47.1 1.0 S1 C:SF4501 2.1 44.4 1.0 S4 C:SF4501 2.1 57.1 1.0 SG C:CYS384 2.3 41.1 1.0 CB C:CYS384 3.0 40.5 1.0 FE3 C:SF4501 3.0 57.5 1.0 FE4 C:SF4501 3.0 60.4 1.0 FE1 C:SF4501 3.0 58.7 1.0 S2 C:SF4501 3.7 46.7 1.0 CA C:CYS384 3.8 45.0 1.0 CD1 C:ILE371 4.2 27.0 1.0 CD C:PRO385 4.4 43.7 1.0 CG1 C:ILE371 4.4 33.7 1.0 CD1 C:PHE386 4.4 26.2 1.0 CB C:CYS287 4.6 49.6 1.0 C C:CYS384 4.6 48.0 1.0 N C:PRO385 4.8 50.7 1.0 CE1 C:PHE386 4.8 25.1 1.0 SG C:CYS287 4.9 45.2 1.0 SG C:CYS367 5.0 41.0 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