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Iron in PDB 3l9q: Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain

Protein crystallography data

The structure of Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain, PDB code: 3l9q was solved by S.Vaithiyalingam, B.F.Eichman, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.32 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.441, 53.050, 88.844, 90.00, 115.09, 90.00
R / Rfree (%) 13 / 16.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain (pdb code 3l9q). 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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain, PDB code: 3l9q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3l9q

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Iron binding site 1 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:22.0
occ:1.00
FE1 A:SF4500 0.0 22.0 1.0
S3 A:SF4500 2.3 21.4 1.0
S2 A:SF4500 2.3 21.2 1.0
S4 A:SF4500 2.3 21.4 1.0
SG A:CYS424 2.3 22.0 1.0
FE4 A:SF4500 2.7 20.7 1.0
FE2 A:SF4500 2.7 21.7 1.0
FE3 A:SF4500 2.7 20.7 1.0
CB A:CYS424 3.1 20.9 1.0
S1 A:SF4500 3.9 21.0 1.0
CD2 A:LEU441 3.9 23.7 1.0
CB A:PRO285 4.2 18.1 1.0
CE2 A:PHE386 4.3 24.8 1.0
CD A:PRO286 4.4 17.4 1.0
CD2 A:PHE386 4.4 24.4 1.0
CA A:CYS424 4.6 21.9 1.0
SG A:CYS367 4.7 22.7 1.0
SG A:CYS287 4.7 19.3 1.0
SG A:CYS384 4.8 21.7 1.0

Iron binding site 2 out of 8 in 3l9q

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Iron binding site 2 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:21.7
occ:1.00
FE2 A:SF4500 0.0 21.7 1.0
S4 A:SF4500 2.3 21.4 1.0
S1 A:SF4500 2.3 21.0 1.0
S3 A:SF4500 2.3 21.4 1.0
SG A:CYS384 2.3 21.7 1.0
FE4 A:SF4500 2.7 20.7 1.0
FE1 A:SF4500 2.7 22.0 1.0
FE3 A:SF4500 2.7 20.7 1.0
CB A:CYS384 3.3 21.1 1.0
S2 A:SF4500 3.9 21.2 1.0
CA A:CYS384 4.1 19.6 1.0
CD2 A:PHE386 4.2 24.4 1.0
CD1 A:ILE371 4.6 24.2 1.0
CB A:CYS287 4.6 19.0 1.0
CD A:PRO385 4.7 22.4 1.0
SG A:CYS287 4.7 19.3 1.0
CG1 A:ILE371 4.7 22.8 1.0
CE2 A:PHE386 4.8 24.8 1.0
C A:CYS384 4.8 20.4 1.0
SG A:CYS424 4.8 22.0 1.0
CB A:CYS424 4.9 20.9 1.0
SG A:CYS367 5.0 22.7 1.0
N A:PRO385 5.0 20.6 1.0

Iron binding site 3 out of 8 in 3l9q

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Iron binding site 3 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:20.7
occ:1.00
FE3 A:SF4500 0.0 20.7 1.0
S1 A:SF4500 2.3 21.0 1.0
S2 A:SF4500 2.3 21.2 1.0
S4 A:SF4500 2.3 21.4 1.0
SG A:CYS367 2.3 22.7 1.0
FE4 A:SF4500 2.7 20.7 1.0
FE1 A:SF4500 2.7 22.0 1.0
FE2 A:SF4500 2.7 21.7 1.0
CB A:CYS367 3.2 21.6 1.0
CA A:CYS367 3.8 21.3 1.0
S3 A:SF4500 3.9 21.4 1.0
CD2 A:LEU441 4.3 23.7 1.0
CG A:PRO444 4.5 15.4 1.0
CD A:PRO444 4.6 15.3 1.0
CG A:GLN421 4.6 25.8 1.0
N A:CYS367 4.8 19.5 1.0
SG A:CYS424 4.8 22.0 1.0
CG A:LEU441 4.8 22.1 1.0
N A:PRO444 4.8 16.4 1.0
SG A:CYS287 4.9 19.3 1.0
SG A:CYS384 4.9 21.7 1.0
CD1 A:ILE371 4.9 24.2 1.0
C A:CYS367 4.9 22.3 1.0

Iron binding site 4 out of 8 in 3l9q

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Iron binding site 4 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:20.7
occ:1.00
FE4 A:SF4500 0.0 20.7 1.0
S2 A:SF4500 2.3 21.2 1.0
SG A:CYS287 2.3 19.3 1.0
S3 A:SF4500 2.3 21.4 1.0
S1 A:SF4500 2.3 21.0 1.0
FE2 A:SF4500 2.7 21.7 1.0
FE1 A:SF4500 2.7 22.0 1.0
FE3 A:SF4500 2.7 20.7 1.0
CB A:CYS287 3.2 19.0 1.0
S4 A:SF4500 3.9 21.4 1.0
CB A:PRO285 4.1 18.1 1.0
N A:CYS287 4.1 17.2 1.0
CG A:PRO444 4.1 15.4 1.0
CA A:CYS287 4.3 19.0 1.0
CG A:PRO285 4.4 17.3 1.0
CB A:PRO444 4.7 14.9 1.0
SG A:CYS367 4.7 22.7 1.0
SG A:CYS384 4.8 21.7 1.0
CD1 A:ILE370 4.8 20.4 1.0
SG A:CYS424 4.9 22.0 1.0

Iron binding site 5 out of 8 in 3l9q

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Iron binding site 5 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:16.1
occ:1.00
FE1 B:SF4500 0.0 16.1 1.0
S2 B:SF4500 2.3 15.6 1.0
S4 B:SF4500 2.3 16.0 1.0
S3 B:SF4500 2.3 16.2 1.0
SG B:CYS367 2.3 15.7 1.0
FE4 B:SF4500 2.7 15.6 1.0
FE2 B:SF4500 2.7 15.1 1.0
FE3 B:SF4500 2.8 15.4 1.0
CB B:CYS367 3.2 16.6 1.0
CA B:CYS367 3.8 16.1 1.0
S1 B:SF4500 3.9 15.1 1.0
CG B:PRO444 4.4 13.9 1.0
CD B:PRO444 4.5 15.4 1.0
CD2 B:LEU441 4.6 20.2 1.0
CG B:GLN421 4.7 18.6 1.0
N B:CYS367 4.7 15.1 1.0
SG B:CYS424 4.8 15.5 1.0
N B:PRO444 4.8 14.8 1.0
SG B:CYS384 4.9 16.0 1.0
SG B:CYS287 4.9 16.0 1.0
CD1 B:ILE371 4.9 16.3 1.0
C B:CYS367 4.9 18.2 1.0

Iron binding site 6 out of 8 in 3l9q

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Iron binding site 6 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:15.1
occ:1.00
FE2 B:SF4500 0.0 15.1 1.0
S1 B:SF4500 2.3 15.1 1.0
S3 B:SF4500 2.3 16.2 1.0
S4 B:SF4500 2.3 16.0 1.0
SG B:CYS424 2.3 15.5 1.0
FE4 B:SF4500 2.7 15.6 1.0
FE3 B:SF4500 2.7 15.4 1.0
FE1 B:SF4500 2.7 16.1 1.0
CB B:CYS424 3.2 15.1 1.0
S2 B:SF4500 3.9 15.6 1.0
CD2 B:LEU441 4.2 20.2 1.0
CB B:PRO285 4.2 15.5 1.0
CE2 B:PHE386 4.2 15.1 1.0
CD2 B:PHE386 4.4 15.8 1.0
CD B:PRO286 4.5 14.6 1.0
CA B:CYS424 4.6 15.5 1.0
SG B:CYS367 4.8 15.7 1.0
SG B:CYS287 4.8 16.0 1.0
SG B:CYS384 4.8 16.0 1.0
CD1 B:PHE447 5.0 16.2 1.0

Iron binding site 7 out of 8 in 3l9q

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Iron binding site 7 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:15.4
occ:1.00
FE3 B:SF4500 0.0 15.4 1.0
S4 B:SF4500 2.3 16.0 1.0
S2 B:SF4500 2.3 15.6 1.0
S1 B:SF4500 2.3 15.1 1.0
SG B:CYS384 2.3 16.0 1.0
FE4 B:SF4500 2.7 15.6 1.0
FE2 B:SF4500 2.7 15.1 1.0
FE1 B:SF4500 2.8 16.1 1.0
CB B:CYS384 3.3 15.6 1.0
S3 B:SF4500 3.9 16.2 1.0
CA B:CYS384 4.1 14.3 1.0
CD2 B:PHE386 4.1 15.8 1.0
CB B:CYS287 4.6 16.4 1.0
CD1 B:ILE371 4.6 16.3 1.0
SG B:CYS287 4.7 16.0 1.0
CG1 B:ILE371 4.7 15.9 1.0
CD B:PRO385 4.7 17.9 1.0
C B:CYS384 4.7 15.1 1.0
CE2 B:PHE386 4.8 15.1 1.0
SG B:CYS424 4.8 15.5 1.0
N B:PRO385 4.9 14.9 1.0
CB B:CYS424 5.0 15.1 1.0
SG B:CYS367 5.0 15.7 1.0

Iron binding site 8 out of 8 in 3l9q

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Iron binding site 8 out of 8 in the Crystal Structure of Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain


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 Human Polymerase Alpha-Primase P58 Iron-Sulfur Cluster Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:15.6
occ:1.00
FE4 B:SF4500 0.0 15.6 1.0
S3 B:SF4500 2.3 16.2 1.0
SG B:CYS287 2.3 16.0 1.0
S2 B:SF4500 2.3 15.6 1.0
S1 B:SF4500 2.3 15.1 1.0
FE3 B:SF4500 2.7 15.4 1.0
FE2 B:SF4500 2.7 15.1 1.0
FE1 B:SF4500 2.7 16.1 1.0
CB B:CYS287 3.2 16.4 1.0
S4 B:SF4500 3.9 16.0 1.0
CG B:PRO444 4.0 13.9 1.0
CB B:PRO285 4.1 15.5 1.0
N B:CYS287 4.1 15.2 1.0
CA B:CYS287 4.2 17.0 1.0
CG B:PRO285 4.4 15.7 1.0
CB B:PRO444 4.5 14.3 1.0
SG B:CYS384 4.7 16.0 1.0
SG B:CYS367 4.8 15.7 1.0
SG B:CYS424 4.9 15.5 1.0
CA B:PRO444 4.9 14.0 1.0
CD1 B:ILE370 5.0 15.8 1.0
CD B:PRO444 5.0 15.4 1.0
CB B:CYS384 5.0 15.6 1.0

Reference:

S.Vaithiyalingam, E.M.Warren, B.F.Eichman, W.J.Chazin. Insights Into Eukaryotic Dna Priming From the Structure and Functional Interactions of the 4FE-4S Cluster Domain of Human Dna Primase. Proc.Natl.Acad.Sci.Usa V. 107 13684 2010.
ISSN: ISSN 0027-8424
PubMed: 20643958
DOI: 10.1073/PNAS.1002009107
Page generated: Sun Dec 13 15:11:06 2020

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