Iron in PDB 5f0q: Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer, PDB code: 5f0q was solved by T.H.Tahirov, A.G.Baranovskiy, N.D.Babayeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.48 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	122.507, 126.002, 83.942, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.8

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer (pdb code 5f0q). 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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer, PDB code: 5f0q:
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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:53.5 occ:1.00 FE1 A:SF4501 0.0 53.5 1.0 S4 A:SF4501 2.2 49.0 1.0 S2 A:SF4501 2.2 47.3 1.0 S3 A:SF4501 2.2 49.0 1.0 SG A:CYS367 2.3 52.4 1.0 FE2 A:SF4501 2.9 54.8 1.0 FE3 A:SF4501 3.0 54.6 1.0 FE4 A:SF4501 3.1 52.1 1.0 CB A:CYS367 3.3 51.6 1.0 S1 A:SF4501 3.6 49.2 1.0 CA A:CYS367 3.9 51.3 1.0 CG A:PRO444 4.4 45.5 1.0 CD2 A:LEU441 4.4 45.2 1.0 CD A:PRO444 4.6 49.1 1.0 CG A:GLN421 4.7 60.4 1.0 N A:CYS367 4.8 44.3 1.0 N A:PRO444 4.9 47.0 1.0 CG A:LEU441 4.9 51.6 1.0 CD1 A:ILE371 4.9 53.9 1.0

Iron binding site 2 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:54.8 occ:1.00 FE2 A:SF4501 0.0 54.8 1.0 S4 A:SF4501 2.1 49.0 1.0 S3 A:SF4501 2.2 49.0 1.0 S1 A:SF4501 2.2 49.2 1.0 SG A:CYS384 2.5 60.8 1.0 FE1 A:SF4501 2.9 53.5 1.0 FE3 A:SF4501 3.0 54.6 1.0 FE4 A:SF4501 3.1 52.1 1.0 CB A:CYS384 3.2 52.5 1.0 S2 A:SF4501 3.6 47.3 1.0 CA A:CYS384 3.9 53.0 1.0 CD2 A:PHE386 4.4 49.3 1.0 CD1 A:ILE371 4.4 53.9 1.0 CG1 A:ILE371 4.5 51.5 1.0 C A:CYS384 4.6 59.7 1.0 CD A:PRO385 4.6 59.9 1.0 N A:PRO385 4.9 59.4 1.0

Iron binding site 3 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:54.6 occ:1.00 FE3 A:SF4501 0.0 54.6 1.0 S4 A:SF4501 2.1 49.0 1.0 S1 A:SF4501 2.2 49.2 1.0 S2 A:SF4501 2.2 47.3 1.0 SG A:CYS424 2.3 51.8 1.0 FE2 A:SF4501 3.0 54.8 1.0 FE1 A:SF4501 3.0 53.5 1.0 CB A:CYS424 3.1 55.5 1.0 FE4 A:SF4501 3.2 52.1 1.0 S3 A:SF4501 3.8 49.0 1.0 CD2 A:LEU441 3.8 45.2 1.0 CB A:PRO285 4.3 44.5 1.0 CG A:PRO286 4.3 46.0 1.0 CE2 A:PHE386 4.4 49.6 1.0 CD2 A:PHE386 4.4 49.3 1.0 CD A:PRO286 4.5 47.4 1.0 CA A:CYS424 4.5 58.2 1.0

Iron binding site 4 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:52.1 occ:1.00 FE4 A:SF4501 0.0 52.1 1.0 S3 A:SF4501 2.1 49.0 1.0 S1 A:SF4501 2.1 49.2 1.0 S2 A:SF4501 2.1 47.3 1.0 SG A:CYS287 2.3 55.9 1.0 FE2 A:SF4501 3.1 54.8 1.0 CB A:CYS287 3.1 48.5 1.0 FE1 A:SF4501 3.1 53.5 1.0 FE3 A:SF4501 3.2 54.6 1.0 CG A:PRO444 3.9 45.5 1.0 S4 A:SF4501 4.0 49.0 1.0 N A:CYS287 4.1 47.9 1.0 CA A:CYS287 4.2 46.5 1.0 CG A:PRO285 4.3 50.6 1.0 CB A:PRO285 4.4 44.5 1.0 CB A:PRO444 4.5 46.2 1.0 CD1 A:ILE370 4.9 46.7 1.0

Iron binding site 5 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:50.4 occ:1.00 FE1 B:SF4501 0.0 50.4 1.0 S4 B:SF4501 2.2 47.6 1.0 S3 B:SF4501 2.2 44.7 1.0 S2 B:SF4501 2.2 46.0 1.0 SG B:CYS367 2.2 50.1 1.0 FE2 B:SF4501 2.9 49.0 1.0 FE3 B:SF4501 3.0 50.9 1.0 CB B:CYS367 3.1 51.1 1.0 FE4 B:SF4501 3.1 46.3 1.0 S1 B:SF4501 3.7 49.9 1.0 CA B:CYS367 3.8 49.3 1.0 CD2 B:LEU441 4.3 50.8 1.0 CG B:PRO444 4.3 51.4 1.0 CD B:PRO444 4.5 49.5 1.0 N B:CYS367 4.7 50.8 1.0 N B:PRO444 4.8 55.1 1.0 CG B:LEU441 4.8 49.4 1.0 CG B:GLN421 4.8 51.8 1.0 C B:CYS367 4.9 48.5 1.0 SG B:CYS384 5.0 46.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:49.0 occ:1.00 FE2 B:SF4501 0.0 49.0 1.0 S4 B:SF4501 2.2 47.6 1.0 S1 B:SF4501 2.2 49.9 1.0 S3 B:SF4501 2.2 44.7 1.0 SG B:CYS384 2.3 46.0 1.0 FE1 B:SF4501 2.9 50.4 1.0 FE3 B:SF4501 2.9 50.9 1.0 FE4 B:SF4501 3.1 46.3 1.0 CB B:CYS384 3.3 45.2 1.0 S2 B:SF4501 3.6 46.0 1.0 CA B:CYS384 4.1 43.4 1.0 CD2 B:PHE386 4.2 46.9 1.0 CD1 B:ILE371 4.5 41.2 1.0 CG1 B:ILE371 4.6 43.3 1.0 CD B:PRO385 4.6 41.7 1.0 C B:CYS384 4.7 44.8 1.0 CE2 B:PHE386 4.8 55.2 1.0 CB B:CYS287 4.9 48.6 1.0 SG B:CYS367 5.0 50.1 1.0 N B:PRO385 5.0 42.7 1.0

Iron binding site 7 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:50.9 occ:1.00 FE3 B:SF4501 0.0 50.9 1.0 S4 B:SF4501 2.1 47.6 1.0 S1 B:SF4501 2.2 49.9 1.0 S2 B:SF4501 2.2 46.0 1.0 SG B:CYS424 2.5 58.4 1.0 FE2 B:SF4501 2.9 49.0 1.0 FE1 B:SF4501 3.0 50.4 1.0 CB B:CYS424 3.1 51.3 1.0 FE4 B:SF4501 3.2 46.3 1.0 S3 B:SF4501 3.8 44.7 1.0 CD2 B:LEU441 3.8 50.8 1.0 CB B:PRO285 4.2 56.4 1.0 CE2 B:PHE386 4.2 55.2 1.0 CD B:PRO286 4.4 46.4 1.0 CD2 B:PHE386 4.5 46.9 1.0 CA B:CYS424 4.5 59.0 1.0 CG B:PRO286 4.6 43.8 1.0 SG B:CYS367 4.9 50.1 1.0 N B:PRO286 5.0 46.7 1.0 CD1 B:PHE447 5.0 46.5 1.0

Iron binding site 8 out of 8 in the Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer


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 C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:46.3 occ:1.00 FE4 B:SF4501 0.0 46.3 1.0 S3 B:SF4501 2.1 44.7 1.0 S1 B:SF4501 2.1 49.9 1.0 S2 B:SF4501 2.2 46.0 1.0 SG B:CYS287 2.2 51.0 1.0 CB B:CYS287 3.0 48.6 1.0 FE2 B:SF4501 3.1 49.0 1.0 FE1 B:SF4501 3.1 50.4 1.0 FE3 B:SF4501 3.2 50.9 1.0 N B:CYS287 3.9 47.9 1.0 S4 B:SF4501 4.0 47.6 1.0 CA B:CYS287 4.1 47.5 1.0 CG B:PRO444 4.1 51.4 1.0 CB B:PRO285 4.1 56.4 1.0 CG B:PRO285 4.2 58.5 1.0 CB B:PRO444 4.6 46.1 1.0 N B:MET288 4.9 44.0 1.0 SG B:CYS384 5.0 46.0 1.0

A.G.Baranovskiy, N.D.Babayeva, Y.Zhang, J.Gu, Y.Suwa, Y.I.Pavlov, T.H.Tahirov. Mechanism of Concerted Rna-Dna Primer Synthesis By the Human Primosome. J.Biol.Chem. V. 291 10006 2016.
ISSN: ESSN 1083-351X
PubMed: 26975377
DOI: 10.1074/JBC.M116.717405