Iron in PDB 3q36: Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit

The structure of Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit, PDB code: 3q36 was solved by V.B.Agarkar, 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)	31.16 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.476, 83.724, 47.561, 90.00, 97.65, 90.00
R / Rfree (%)	22.8 / 25

The binding sites of Iron atom in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit (pdb code 3q36). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit, PDB code: 3q36:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe458 b:26.1 occ:1.00 FE1 A:SF4458 0.0 26.1 1.0 S4 A:SF4458 2.2 18.5 1.0 S3 A:SF4458 2.2 25.4 1.0 S2 A:SF4458 2.2 21.4 1.0 SG A:CYS367 2.3 26.6 1.0 FE2 A:SF4458 2.9 22.7 1.0 FE3 A:SF4458 3.0 23.9 1.0 FE4 A:SF4458 3.0 21.5 1.0 CB A:CYS367 3.1 30.1 1.0 S1 A:SF4458 3.6 22.2 1.0 CA A:CYS367 3.8 28.8 1.0 CD2 A:LEU441 4.2 45.2 1.0 CG A:PRO444 4.6 28.8 1.0 N A:CYS367 4.6 30.2 1.0 CD A:PRO444 4.7 31.9 1.0 CG A:GLN421 4.8 24.6 1.0 CG A:LEU441 4.9 44.4 1.0 SG A:CYS384 4.9 22.2 1.0 SG A:CYS424 4.9 26.3 1.0 C A:CYS367 4.9 30.6 1.0 N A:PRO444 4.9 31.7 1.0

Iron binding site 2 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe458 b:22.7 occ:1.00 FE2 A:SF4458 0.0 22.7 1.0 S4 A:SF4458 2.1 18.5 1.0 S1 A:SF4458 2.2 22.2 1.0 SG A:CYS384 2.2 22.2 1.0 S3 A:SF4458 2.2 25.4 1.0 FE1 A:SF4458 2.9 26.1 1.0 FE3 A:SF4458 3.0 23.9 1.0 FE4 A:SF4458 3.1 21.5 1.0 CB A:CYS384 3.3 25.8 1.0 S2 A:SF4458 3.7 21.4 1.0 CA A:CYS384 4.0 23.6 1.0 CD2 A:PHE386 4.0 15.0 1.0 CD A:PRO385 4.4 14.7 1.0 CE2 A:PHE386 4.7 13.9 1.0 C A:CYS384 4.7 20.8 1.0 N A:PRO385 4.7 19.7 1.0 CB A:CYS424 4.9 25.2 1.0 CG1 A:ILE371 4.9 22.4 1.0 SG A:CYS424 5.0 26.3 1.0 CB A:PHE386 5.0 14.4 1.0 CG A:PHE386 5.0 13.4 1.0

Iron binding site 3 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe458 b:23.9 occ:1.00 FE3 A:SF4458 0.0 23.9 1.0 S4 A:SF4458 2.1 18.5 1.0 S1 A:SF4458 2.2 22.2 1.0 S2 A:SF4458 2.2 21.4 1.0 SG A:CYS424 2.2 26.3 1.0 FE1 A:SF4458 3.0 26.1 1.0 CB A:CYS424 3.0 25.2 1.0 FE2 A:SF4458 3.0 22.7 1.0 FE4 A:SF4458 3.1 21.5 1.0 S3 A:SF4458 3.8 25.4 1.0 CD2 A:LEU441 3.9 45.2 1.0 CB A:PRO285 4.0 30.5 1.0 CE2 A:PHE386 4.2 13.9 1.0 CA A:CYS424 4.4 26.1 1.0 CD2 A:PHE386 4.4 15.0 1.0 CD A:PRO286 4.5 26.6 1.0 CG A:PRO286 4.6 28.7 1.0 CD1 A:PHE447 4.8 24.8 1.0 SG A:CYS367 4.9 26.6 1.0 CG A:PRO285 4.9 32.8 1.0 N A:PRO286 5.0 28.1 1.0

Iron binding site 4 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe458 b:21.5 occ:1.00 FE4 A:SF4458 0.0 21.5 1.0 S2 A:SF4458 2.1 21.4 1.0 S3 A:SF4458 2.1 25.4 1.0 S1 A:SF4458 2.1 22.2 1.0 SG A:CYS287 2.4 21.9 1.0 FE1 A:SF4458 3.0 26.1 1.0 FE2 A:SF4458 3.1 22.7 1.0 FE3 A:SF4458 3.1 23.9 1.0 CB A:CYS287 3.3 20.0 1.0 S4 A:SF4458 3.8 18.5 1.0 CG A:PRO444 4.1 28.8 1.0 CG A:PRO285 4.1 32.8 1.0 CB A:PRO285 4.1 30.5 1.0 N A:CYS287 4.2 24.5 1.0 CA A:CYS287 4.4 23.5 1.0 CB A:PRO444 4.5 28.8 1.0 CD1 A:ILE370 4.7 21.7 1.0 SG A:CYS367 4.9 26.6 1.0 CA A:PRO444 5.0 30.1 1.0 SG A:CYS384 5.0 22.2 1.0

Iron binding site 5 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe458 b:32.9 occ:1.00 FE1 B:SF4458 0.0 32.9 1.0 S4 B:SF4458 2.2 30.0 1.0 S2 B:SF4458 2.2 29.3 1.0 S3 B:SF4458 2.2 28.1 1.0 SG B:CYS367 2.5 37.0 1.0 FE2 B:SF4458 2.9 30.9 1.0 FE3 B:SF4458 3.0 31.0 1.0 FE4 B:SF4458 3.1 28.8 1.0 CB B:CYS367 3.3 32.3 1.0 S1 B:SF4458 3.6 29.8 1.0 CA B:CYS367 3.9 32.4 1.0 CG B:PRO444 4.4 25.9 1.0 CD2 B:LEU441 4.4 22.4 1.0 CG B:GLN421 4.6 26.9 1.0 N B:CYS367 4.7 33.1 1.0 SG B:CYS384 4.8 24.6 1.0 CG B:LEU441 4.9 25.3 1.0 CD B:PRO444 4.9 27.7 1.0 SG B:CYS424 4.9 24.8 1.0 C B:CYS367 4.9 32.5 1.0 CD1 B:ILE371 4.9 26.9 1.0 N B:PRO444 4.9 27.0 1.0 CD1 B:LEU441 5.0 22.8 1.0

Iron binding site 6 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe458 b:30.9 occ:1.00 FE2 B:SF4458 0.0 30.9 1.0 S4 B:SF4458 2.1 30.0 1.0 S1 B:SF4458 2.2 29.8 1.0 S3 B:SF4458 2.2 28.1 1.0 SG B:CYS384 2.3 24.6 1.0 FE1 B:SF4458 2.9 32.9 1.0 FE3 B:SF4458 3.0 31.0 1.0 FE4 B:SF4458 3.1 28.8 1.0 CB B:CYS384 3.2 27.6 1.0 S2 B:SF4458 3.7 29.3 1.0 CA B:CYS384 4.0 27.1 1.0 CD2 B:PHE386 4.1 22.9 1.0 CD B:PRO385 4.4 27.2 1.0 CD1 B:ILE371 4.7 26.9 1.0 C B:CYS384 4.7 28.2 1.0 CE2 B:PHE386 4.7 23.7 1.0 CG1 B:ILE371 4.7 28.5 1.0 CB B:CYS287 4.7 29.8 1.0 SG B:CYS424 4.9 24.8 1.0 N B:PRO385 4.9 27.9 1.0 SG B:CYS287 5.0 32.3 1.0

Iron binding site 7 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe458 b:31.0 occ:1.00 FE3 B:SF4458 0.0 31.0 1.0 S4 B:SF4458 2.1 30.0 1.0 SG B:CYS424 2.1 24.8 1.0 S2 B:SF4458 2.2 29.3 1.0 S1 B:SF4458 2.2 29.8 1.0 CB B:CYS424 2.9 28.1 1.0 FE1 B:SF4458 3.0 32.9 1.0 FE2 B:SF4458 3.0 30.9 1.0 FE4 B:SF4458 3.2 28.8 1.0 S3 B:SF4458 3.8 28.1 1.0 CD2 B:LEU441 4.0 22.4 1.0 CE2 B:PHE386 4.2 23.7 1.0 CB B:PRO285 4.2 26.4 1.0 CA B:CYS424 4.3 28.4 1.0 CD B:PRO286 4.3 28.6 1.0 CD2 B:PHE386 4.4 22.9 1.0 CD1 B:PHE447 4.8 26.7 1.0 SG B:CYS367 5.0 37.0 1.0 CG B:PRO286 5.0 27.8 1.0

Iron binding site 8 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe458 b:28.8 occ:1.00 FE4 B:SF4458 0.0 28.8 1.0 S3 B:SF4458 2.1 28.1 1.0 S2 B:SF4458 2.2 29.3 1.0 S1 B:SF4458 2.2 29.8 1.0 SG B:CYS287 2.3 32.3 1.0 FE1 B:SF4458 3.1 32.9 1.0 CB B:CYS287 3.1 29.8 1.0 FE2 B:SF4458 3.1 30.9 1.0 FE3 B:SF4458 3.2 31.0 1.0 N B:CYS287 3.9 28.1 1.0 S4 B:SF4458 3.9 30.0 1.0 CG B:PRO444 4.1 25.9 1.0 CG B:PRO285 4.1 24.8 1.0 CA B:CYS287 4.1 28.7 1.0 CB B:PRO285 4.1 26.4 1.0 CB B:PRO444 4.3 29.1 1.0 CD1 B:ILE370 4.8 28.0 1.0 N B:MET288 4.9 30.4 1.0 C B:PRO285 5.0 28.9 1.0 CA B:PRO444 5.0 27.2 1.0

Iron binding site 9 out of 9 in the Crystal Structure of the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit


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 the 4FE-4S Cluster Domain of Human Dna Primase Large Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1 b:51.6 occ:1.00 CD B:ARG302 4.6 50.5 1.0

V.B.Agarkar, N.D.Babayeva, Y.I.Pavlov, T.H.Tahirov. Crystal Structure of the C-Terminal Domain of Human Dna Primase Large Subunit: Implications For the Mechanism of the Primase - Polymerase Alpha Switch. Cell Cycle V. 10 926 2011.
ISSN: ISSN 1538-4101
PubMed: 21346410