Iron in PDB 6dhw: Crystal Structure of Primase Iron-Sulfur Domain (266-457)

The structure of Crystal Structure of Primase Iron-Sulfur Domain (266-457), PDB code: 6dhw was solved by M.E.Holt, 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)	37.20 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.193, 52.560, 88.774, 90.00, 115.08, 90.00
R / Rfree (%)	18.1 / 21.1

The binding sites of Iron atom in the Crystal Structure of Primase Iron-Sulfur Domain (266-457) (pdb code 6dhw). 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 Primase Iron-Sulfur Domain (266-457), PDB code: 6dhw:
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 Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.8 occ:1.00 FE1 A:SF4501 0.0 21.8 1.0 S3 A:SF4501 2.3 21.3 1.0 S2 A:SF4501 2.3 20.2 1.0 S4 A:SF4501 2.3 20.2 1.0 SG A:CYS287 2.6 24.3 1.0 FE2 A:SF4501 2.7 20.9 1.0 FE3 A:SF4501 2.7 21.5 1.0 FE4 A:SF4501 2.7 21.3 1.0 CB A:CYS287 3.2 21.9 1.0 S1 A:SF4501 3.9 20.8 1.0 CB A:PRO285 4.0 21.2 1.0 N A:CYS287 4.1 23.7 1.0 CG A:PRO444 4.1 21.4 1.0 CA A:CYS287 4.3 23.0 1.0 CG A:PRO285 4.4 20.2 1.0 CB A:PRO444 4.6 17.6 1.0 CD1 A:ILE370 4.8 20.6 1.0 SG A:CYS367 5.0 24.5 1.0 SG A:CYS384 5.0 24.1 1.0 CB A:CYS384 5.0 25.6 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.9 occ:1.00 FE2 A:SF4501 0.0 20.9 1.0 S1 A:SF4501 2.3 20.8 1.0 S4 A:SF4501 2.3 20.2 1.0 S3 A:SF4501 2.3 21.3 1.0 SG A:CYS384 2.6 24.1 1.0 FE1 A:SF4501 2.7 21.8 1.0 FE4 A:SF4501 2.7 21.3 1.0 FE3 A:SF4501 2.7 21.5 1.0 CB A:CYS384 3.3 25.6 1.0 S2 A:SF4501 3.9 20.2 1.0 CA A:CYS384 4.1 24.6 1.0 CD2 A:PHE386 4.1 21.6 1.0 CD1 A:ILE371 4.5 30.0 1.0 CB A:CYS287 4.7 21.9 1.0 CE2 A:PHE386 4.7 29.1 1.0 CD A:PRO385 4.7 21.8 1.0 CG1 A:ILE371 4.7 24.8 1.0 C A:CYS384 4.8 22.4 1.0 SG A:CYS287 4.9 24.3 1.0 CB A:CYS424 5.0 21.9 1.0 SG A:CYS424 5.0 24.5 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) 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 S4 A:SF4501 2.3 20.2 1.0 S1 A:SF4501 2.3 20.8 1.0 S2 A:SF4501 2.3 20.2 1.0 SG A:CYS367 2.6 24.5 1.0 FE4 A:SF4501 2.7 21.3 1.0 FE1 A:SF4501 2.7 21.8 1.0 FE2 A:SF4501 2.7 20.9 1.0 CB A:CYS367 3.3 24.7 1.0 S3 A:SF4501 3.9 21.3 1.0 CA A:CYS367 3.9 27.4 1.0 CD2 A:LEU441 4.4 21.5 1.0 CG A:PRO444 4.6 21.4 1.0 CG A:GLN421 4.7 29.3 1.0 CD A:PRO444 4.7 18.5 1.0 CG A:LEU441 4.8 24.9 1.0 N A:CYS367 4.8 18.9 1.0 N A:PRO444 4.9 20.4 1.0 C A:CYS367 4.9 30.1 1.0 CD1 A:ILE371 5.0 30.0 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.3 occ:1.00 FE4 A:SF4501 0.0 21.3 1.0 S2 A:SF4501 2.3 20.2 1.0 S1 A:SF4501 2.3 20.8 1.0 S3 A:SF4501 2.3 21.3 1.0 SG A:CYS424 2.6 24.5 1.0 FE3 A:SF4501 2.7 21.5 1.0 FE1 A:SF4501 2.7 21.8 1.0 FE2 A:SF4501 2.7 20.9 1.0 CB A:CYS424 3.2 21.9 1.0 S4 A:SF4501 3.9 20.2 1.0 CD2 A:LEU441 3.9 21.5 1.0 CB A:PRO285 4.2 21.2 1.0 CE2 A:PHE386 4.2 29.1 1.0 CD A:PRO286 4.4 19.8 1.0 CD2 A:PHE386 4.5 21.6 1.0 CA A:CYS424 4.6 26.2 1.0 SG A:CYS367 4.9 24.5 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.7 occ:1.00 FE1 B:SF4501 0.0 19.7 1.0 S2 B:SF4501 2.3 20.3 1.0 S4 B:SF4501 2.3 20.3 1.0 S3 B:SF4501 2.3 20.2 1.0 SG B:CYS367 2.5 19.7 1.0 FE4 B:SF4501 2.7 18.9 1.0 FE2 B:SF4501 2.7 19.4 1.0 FE3 B:SF4501 2.7 19.8 1.0 CB B:CYS367 3.3 26.3 1.0 CA B:CYS367 3.9 24.3 1.0 S1 B:SF4501 3.9 20.6 1.0 CG B:PRO444 4.4 19.4 1.0 CD B:PRO444 4.6 18.2 1.0 CD2 B:LEU441 4.7 21.6 1.0 CG B:GLN421 4.8 22.0 1.0 N B:CYS367 4.8 21.8 1.0 N B:PRO444 4.9 15.6 1.0 CD1 B:ILE371 4.9 18.9 1.0 C B:CYS367 4.9 22.1 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.4 occ:1.00 FE2 B:SF4501 0.0 19.4 1.0 S3 B:SF4501 2.3 20.2 1.0 S4 B:SF4501 2.3 20.3 1.0 S1 B:SF4501 2.3 20.6 1.0 SG B:CYS287 2.5 20.4 1.0 FE3 B:SF4501 2.7 19.8 1.0 FE1 B:SF4501 2.7 19.7 1.0 FE4 B:SF4501 2.7 18.9 1.0 CB B:CYS287 3.2 18.9 1.0 S2 B:SF4501 3.9 20.3 1.0 CG B:PRO444 4.0 19.4 1.0 N B:CYS287 4.1 17.6 1.0 CB B:PRO285 4.1 20.6 1.0 CA B:CYS287 4.3 21.6 1.0 CG B:PRO285 4.5 26.6 1.0 CB B:PRO444 4.5 19.1 1.0 SG B:CYS367 5.0 19.7 1.0 CD1 B:ILE370 5.0 21.6 1.0 SG B:CYS384 5.0 19.9 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.8 occ:1.00 FE3 B:SF4501 0.0 19.8 1.0 S2 B:SF4501 2.3 20.3 1.0 S4 B:SF4501 2.3 20.3 1.0 S1 B:SF4501 2.3 20.6 1.0 SG B:CYS384 2.6 19.9 1.0 FE2 B:SF4501 2.7 19.4 1.0 FE4 B:SF4501 2.7 18.9 1.0 FE1 B:SF4501 2.7 19.7 1.0 CB B:CYS384 3.3 18.2 1.0 S3 B:SF4501 3.9 20.2 1.0 CA B:CYS384 4.1 18.4 1.0 CD2 B:PHE386 4.2 22.1 1.0 CD1 B:ILE371 4.5 18.9 1.0 CB B:CYS287 4.7 18.9 1.0 CD B:PRO385 4.7 19.8 1.0 CG1 B:ILE371 4.7 22.4 1.0 CE2 B:PHE386 4.7 21.5 1.0 C B:CYS384 4.8 22.2 1.0 SG B:CYS287 4.9 20.4 1.0 CB B:CYS424 5.0 16.0 1.0 N B:PRO385 5.0 23.0 1.0 SG B:CYS424 5.0 20.3 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Primase Iron-Sulfur Domain (266-457)


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 Primase Iron-Sulfur Domain (266-457) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:18.9 occ:1.00 FE4 B:SF4501 0.0 18.9 1.0 S1 B:SF4501 2.3 20.6 1.0 S3 B:SF4501 2.3 20.2 1.0 S2 B:SF4501 2.3 20.3 1.0 SG B:CYS424 2.5 20.3 1.0 FE1 B:SF4501 2.7 19.7 1.0 FE3 B:SF4501 2.7 19.8 1.0 FE2 B:SF4501 2.7 19.4 1.0 CB B:CYS424 3.2 16.0 1.0 S4 B:SF4501 3.9 20.3 1.0 CD2 B:LEU441 4.1 21.6 1.0 CE2 B:PHE386 4.2 21.5 1.0 CB B:PRO285 4.3 20.6 1.0 CD2 B:PHE386 4.4 22.1 1.0 CD B:PRO286 4.5 18.8 1.0 CA B:CYS424 4.6 18.9 1.0 SG B:CYS367 4.9 19.7 1.0

M.E.Holt, L.E.Salay, E.O'brien, J.K.Barton, W.J.Chazin. Functional and Structural Similarity of Human Dna Primase [4FE4S] Cluster Domain Constructs. Plos One V. 13 09345 2018.
ISSN: ESSN 1932-6203
PubMed: 30562384
DOI: 10.1371/JOURNAL.PONE.0209345