Iron in PDB 4rr2: Crystal Structure of Human Primase

The structure of Crystal Structure of Human Primase, PDB code: 4rr2 was solved by A.G.Baranovskiy, J.Gu, Y.Suwa, N.D.Babayeva, T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	86.195, 88.899, 94.682, 93.82, 96.57, 111.72
R / Rfree (%)	22.9 / 27.1

The structure of Crystal Structure of Human Primase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Human Primase (pdb code 4rr2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Human Primase, PDB code: 4rr2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Human Primase


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 Human Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1000 b:30.9 occ:1.00 FE1 D:SF41000 0.0 30.9 1.0 S3 D:SF41000 2.1 27.6 1.0 S2 D:SF41000 2.2 19.2 1.0 S4 D:SF41000 2.2 26.5 1.0 SG D:CYS367 2.4 40.2 1.0 FE2 D:SF41000 2.9 25.4 1.0 FE3 D:SF41000 3.0 38.4 1.0 FE4 D:SF41000 3.1 32.3 1.0 CB D:CYS367 3.1 36.6 1.0 CA D:CYS367 3.6 41.5 1.0 S1 D:SF41000 3.6 17.7 1.0 CG D:PRO444 4.3 22.6 1.0 CD D:PRO444 4.4 18.1 1.0 N D:CYS367 4.5 39.2 1.0 C D:CYS367 4.7 38.8 1.0 CD2 D:LEU441 4.7 24.1 1.0 N D:PRO444 4.8 25.2 1.0 CG D:GLN421 4.9 38.7 1.0 O D:CYS367 4.9 30.6 1.0 SG D:CYS384 5.0 44.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human Primase


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 Human Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1000 b:25.4 occ:1.00 FE2 D:SF41000 0.0 25.4 1.0 S4 D:SF41000 2.1 26.5 1.0 S1 D:SF41000 2.2 17.7 1.0 S3 D:SF41000 2.2 27.6 1.0 SG D:CYS384 2.3 44.8 1.0 FE1 D:SF41000 2.9 30.9 1.0 FE3 D:SF41000 2.9 38.4 1.0 FE4 D:SF41000 3.1 32.3 1.0 CB D:CYS384 3.1 38.5 1.0 S2 D:SF41000 3.6 19.2 1.0 CA D:CYS384 4.0 38.7 1.0 CD2 D:PHE386 4.4 49.0 1.0 CD D:PRO385 4.6 26.4 1.0 SG D:CYS424 4.7 36.1 1.0 C D:CYS384 4.8 34.7 1.0 CB D:CYS287 4.9 32.5 1.0 CG1 D:ILE371 4.9 46.0 1.0 N D:PRO385 4.9 31.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human Primase


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 Human Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1000 b:38.4 occ:1.00 FE3 D:SF41000 0.0 38.4 1.0 S4 D:SF41000 2.1 26.5 1.0 S1 D:SF41000 2.2 17.7 1.0 S2 D:SF41000 2.2 19.2 1.0 SG D:CYS424 2.3 36.1 1.0 FE2 D:SF41000 2.9 25.4 1.0 FE1 D:SF41000 3.0 30.9 1.0 FE4 D:SF41000 3.3 32.3 1.0 CB D:CYS424 3.3 35.2 1.0 CD2 D:LEU441 3.6 24.1 1.0 S3 D:SF41000 3.8 27.6 1.0 CB D:PRO285 4.2 30.2 1.0 CE2 D:PHE386 4.5 46.7 1.0 CD D:PRO286 4.5 24.8 1.0 CD2 D:PHE386 4.6 49.0 1.0 SG D:CYS367 4.6 40.2 1.0 CA D:CYS424 4.6 30.5 1.0 CG D:PRO286 4.7 34.0 1.0 CG D:LEU441 4.8 17.9 1.0 CD1 D:PHE447 4.9 41.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human Primase


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 Human Primase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1000 b:32.3 occ:1.00 FE4 D:SF41000 0.0 32.3 1.0 S3 D:SF41000 2.1 27.6 1.0 S2 D:SF41000 2.1 19.2 1.0 S1 D:SF41000 2.2 17.7 1.0 SG D:CYS287 2.4 38.4 1.0 FE1 D:SF41000 3.1 30.9 1.0 FE2 D:SF41000 3.1 25.4 1.0 CB D:CYS287 3.1 32.5 1.0 FE3 D:SF41000 3.3 38.4 1.0 CG D:PRO444 3.9 22.6 1.0 S4 D:SF41000 3.9 26.5 1.0 CB D:PRO285 4.0 30.2 1.0 N D:CYS287 4.0 33.4 1.0 CG D:PRO285 4.2 35.3 1.0 CA D:CYS287 4.2 38.2 1.0 CB D:PRO444 4.5 20.2 1.0 N D:MET288 4.9 37.3 1.0 CA D:PRO444 5.0 27.2 1.0 CB D:CYS384 5.0 38.5 1.0 SG D:CYS384 5.0 44.8 1.0 CD D:PRO444 5.0 18.1 1.0

A.G.Baranovskiy, Y.Zhang, Y.Suwa, N.D.Babayeva, J.Gu, Y.I.Pavlov, T.H.Tahirov. Crystal Structure of the Human Primase. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25550159
DOI: 10.1074/JBC.M114.624742