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Iron in PDB 4rr2: Crystal Structure of Human Primase

Protein crystallography data

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

Other elements in 4rr2:

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

Zinc (Zn) 2 atoms

Iron Binding Sites:

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 4rr2

Go back to Iron Binding Sites List in 4rr2
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 4rr2

Go back to Iron Binding Sites List in 4rr2
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 4rr2

Go back to Iron Binding Sites List in 4rr2
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 4rr2

Go back to Iron Binding Sites List in 4rr2
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

Reference:

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
Page generated: Mon Aug 5 09:24:03 2024

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