Iron in PDB 5f0s: Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion

The structure of Crystal Structure of C-Terminal Domain of the Human Dna Primase Large Subunit with Bound Dna Template/Rna Primer and Manganese Ion, PDB code: 5f0s 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)	19.87 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	122.753, 125.613, 83.690, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 26.9

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

Manganese

(Mn)

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 and Manganese Ion (pdb code 5f0s). 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 and Manganese Ion, PDB code: 5f0s:
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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.6 occ:1.00 FE1 A:SF4501 0.0 27.6 1.0 S3 A:SF4501 2.1 13.9 1.0 S4 A:SF4501 2.2 23.8 1.0 S2 A:SF4501 2.2 24.2 1.0 SG A:CYS367 2.4 42.1 1.0 FE2 A:SF4501 2.8 24.7 1.0 FE3 A:SF4501 3.0 28.4 1.0 FE4 A:SF4501 3.1 22.4 1.0 CB A:CYS367 3.2 28.3 1.0 S1 A:SF4501 3.6 20.2 1.0 CA A:CYS367 3.8 24.6 1.0 CD2 A:LEU441 4.5 53.0 1.0 CG A:PRO444 4.5 36.9 1.0 CG A:GLN421 4.7 53.9 1.0 CD A:PRO444 4.7 37.8 1.0 CG A:LEU441 4.7 50.0 1.0 N A:CYS367 4.7 22.9 1.0 SG A:CYS384 4.8 56.1 1.0 N A:PRO444 4.8 35.4 1.0 CD1 A:LEU441 4.9 50.5 1.0 C A:CYS367 4.9 25.0 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:24.7 occ:1.00 FE2 A:SF4501 0.0 24.7 1.0 S4 A:SF4501 2.1 23.8 1.0 S1 A:SF4501 2.2 20.2 1.0 S3 A:SF4501 2.2 13.9 1.0 SG A:CYS384 2.5 56.1 1.0 FE1 A:SF4501 2.8 27.6 1.0 FE3 A:SF4501 3.0 28.4 1.0 FE4 A:SF4501 3.1 22.4 1.0 S2 A:SF4501 3.6 24.2 1.0 CB A:CYS384 3.7 55.7 1.0 CD2 A:PHE386 3.9 41.6 1.0 CA A:CYS384 4.4 54.8 1.0 CE2 A:PHE386 4.4 39.3 1.0 CB A:CYS424 4.5 45.5 1.0 CD1 A:ILE371 4.5 39.4 1.0 SG A:CYS424 4.7 48.0 1.0 CD A:PRO385 4.7 52.8 1.0 CG1 A:ILE371 4.8 39.5 1.0 CG A:PHE386 4.9 38.1 1.0 C A:CYS384 5.0 54.8 1.0 O A:TYR420 5.0 51.0 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.4 occ:1.00 FE3 A:SF4501 0.0 28.4 1.0 S4 A:SF4501 2.1 23.8 1.0 S1 A:SF4501 2.2 20.2 1.0 S2 A:SF4501 2.2 24.2 1.0 SG A:CYS424 2.5 48.0 1.0 FE2 A:SF4501 3.0 24.7 1.0 FE1 A:SF4501 3.0 27.6 1.0 FE4 A:SF4501 3.2 22.4 1.0 CB A:CYS424 3.3 45.5 1.0 CD2 A:LEU441 3.6 53.0 1.0 S3 A:SF4501 3.8 13.9 1.0 CB A:PRO285 3.9 31.7 1.0 CG A:PRO286 4.4 42.9 1.0 CE2 A:PHE386 4.4 39.3 1.0 CD A:PRO286 4.4 40.2 1.0 CG A:LEU441 4.7 50.0 1.0 CA A:CYS424 4.7 45.9 1.0 CD2 A:PHE386 4.8 41.6 1.0 CG A:PRO285 4.8 33.2 1.0 SG A:CYS367 4.8 42.1 1.0 CD1 A:PHE447 4.9 42.5 1.0 CD1 A:LEU441 5.0 50.5 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:22.4 occ:1.00 FE4 A:SF4501 0.0 22.4 1.0 S3 A:SF4501 2.1 13.9 1.0 S2 A:SF4501 2.1 24.2 1.0 S1 A:SF4501 2.1 20.2 1.0 SG A:CYS287 2.7 38.1 1.0 CB A:CYS287 2.9 39.1 1.0 FE1 A:SF4501 3.1 27.6 1.0 FE2 A:SF4501 3.1 24.7 1.0 FE3 A:SF4501 3.2 28.4 1.0 S4 A:SF4501 3.9 23.8 1.0 N A:CYS287 4.1 38.5 1.0 CA A:CYS287 4.1 41.7 1.0 CG A:PRO444 4.3 36.9 1.0 CG A:PRO285 4.5 33.2 1.0 CB A:PRO285 4.5 31.7 1.0 CD1 A:ILE370 4.6 35.1 1.0 CB A:PRO444 4.8 32.8 1.0 SG A:CYS384 4.8 56.1 1.0 CD A:PRO385 4.9 52.8 1.0 CG2 A:ILE370 4.9 33.7 1.0 O A:GLY383 4.9 58.5 1.0 CA A:CYS384 5.0 54.8 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.7 occ:1.00 FE1 B:SF4501 0.0 24.7 1.0 S3 B:SF4501 2.1 14.6 1.0 S2 B:SF4501 2.2 15.2 1.0 S4 B:SF4501 2.2 22.1 1.0 SG B:CYS367 2.5 34.1 1.0 FE2 B:SF4501 2.9 30.2 1.0 FE3 B:SF4501 2.9 27.1 1.0 FE4 B:SF4501 3.0 22.4 1.0 CB B:CYS367 3.3 37.3 1.0 S1 B:SF4501 3.5 27.6 1.0 CA B:CYS367 3.9 38.6 1.0 CG B:PRO444 3.9 62.1 1.0 CD B:PRO444 4.3 59.3 1.0 N B:PRO444 4.7 55.6 1.0 N B:CYS367 4.8 39.2 1.0 CD1 B:ILE370 4.9 6.2 1.0 CD2 B:LEU441 4.9 38.6 1.0 SG B:CYS287 4.9 31.8 1.0 C B:CYS367 4.9 38.1 1.0 CB B:PRO444 4.9 61.4 1.0 CA B:PRO444 5.0 57.6 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:30.2 occ:1.00 FE2 B:SF4501 0.0 30.2 1.0 S4 B:SF4501 2.1 22.1 1.0 S1 B:SF4501 2.2 27.6 1.0 S3 B:SF4501 2.2 14.6 1.0 SG B:CYS384 2.6 26.5 1.0 FE1 B:SF4501 2.9 24.7 1.0 FE3 B:SF4501 3.0 27.1 1.0 FE4 B:SF4501 3.2 22.4 1.0 CB B:CYS384 3.5 35.4 1.0 S2 B:SF4501 3.7 15.2 1.0 CD2 B:PHE386 3.8 43.2 1.0 CD1 B:ILE371 4.1 29.8 1.0 CE2 B:PHE386 4.3 40.4 1.0 CA B:CYS384 4.4 38.3 1.0 CB B:CYS424 4.7 36.0 1.0 CG1 B:ILE371 4.7 23.8 1.0 CD B:PRO385 4.7 38.4 1.0 O B:TYR420 4.7 45.5 1.0 CG B:PHE386 4.8 41.1 1.0 C B:CYS384 4.9 39.7 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.1 occ:1.00 FE3 B:SF4501 0.0 27.1 1.0 S4 B:SF4501 2.1 22.1 1.0 S1 B:SF4501 2.2 27.6 1.0 S2 B:SF4501 2.2 15.2 1.0 SG B:CYS424 2.5 35.2 1.0 FE1 B:SF4501 2.9 24.7 1.0 FE2 B:SF4501 3.0 30.2 1.0 CB B:CYS424 3.2 36.0 1.0 FE4 B:SF4501 3.2 22.4 1.0 S3 B:SF4501 3.8 14.6 1.0 CD2 B:LEU441 3.8 38.6 1.0 CB B:PRO285 4.0 44.7 1.0 CE2 B:PHE386 4.2 40.4 1.0 CD B:PRO286 4.2 38.1 1.0 CG B:PRO286 4.4 36.5 1.0 CD1 B:PHE447 4.6 38.9 1.0 CD2 B:PHE386 4.6 43.2 1.0 CA B:CYS424 4.6 35.2 1.0 SG B:CYS367 4.7 34.1 1.0 CG B:LEU441 4.8 43.2 1.0 CE1 B:PHE447 4.9 42.3 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 and Manganese Ion


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 and Manganese Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:22.4 occ:1.00 FE4 B:SF4501 0.0 22.4 1.0 S3 B:SF4501 2.1 14.6 1.0 S2 B:SF4501 2.1 15.2 1.0 S1 B:SF4501 2.2 27.6 1.0 SG B:CYS287 2.5 31.8 1.0 CB B:CYS287 2.7 36.6 1.0 FE1 B:SF4501 3.0 24.7 1.0 FE2 B:SF4501 3.2 30.2 1.0 FE3 B:SF4501 3.2 27.1 1.0 N B:CYS287 3.6 39.5 1.0 CA B:CYS287 3.7 37.1 1.0 S4 B:SF4501 3.9 22.1 1.0 CB B:PRO285 4.2 44.7 1.0 CG B:PRO285 4.4 43.6 1.0 CD B:PRO385 4.4 38.4 1.0 CG B:PRO444 4.5 62.1 1.0 SG B:CYS384 4.8 26.5 1.0 CB B:CYS384 4.8 35.4 1.0 CG B:PRO286 4.8 36.5 1.0 C B:CYS287 4.8 38.1 1.0 C B:PRO286 4.9 40.0 1.0 CA B:CYS384 4.9 38.3 1.0 N B:MET288 4.9 35.6 1.0 O B:GLY383 4.9 39.5 1.0 N B:PRO286 4.9 37.4 1.0 CD B:PRO286 5.0 38.1 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