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Iron in PDB 5exr: Crystal Structure of Human Primosome

Enzymatic activity of Crystal Structure of Human Primosome

All present enzymatic activity of Crystal Structure of Human Primosome:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Primosome, PDB code: 5exr 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) 39.94 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.096, 210.164, 172.565, 90.00, 93.56, 90.00
R / Rfree (%) 26.8 / 32.6

Other elements in 5exr:

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

Zinc (Zn) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human Primosome (pdb code 5exr). 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 Primosome, PDB code: 5exr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5exr

Go back to Iron Binding Sites List in 5exr
Iron binding site 1 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:1.1
occ:1.00
 FE1 B:SF4601 0.0 1.1 1.0
S4 B:SF4601 2.1 1.1 1.0
S2 B:SF4601 2.1 2.4 1.0
S3 B:SF4601 2.2 1.1 1.0
SG B:CYS367 2.4 7.8 1.0
FE2 B:SF4601 2.8 1.1 1.0
FE3 B:SF4601 2.9 1.1 1.0
CB B:CYS367 3.0 27.1 1.0
FE4 B:SF4601 3.1 9.2 1.0
CG B:GLN421 3.3 1.2 1.0
S1 B:SF4601 3.6 1.1 1.0
CD B:GLN421 3.7 1.1 1.0
CA B:CYS367 3.9 26.2 1.0
OE1 B:GLN421 4.1 2.8 1.0
NE2 B:GLN421 4.4 1.1 1.0
CB B:GLN421 4.4 13.8 1.0
CD B:PRO444 4.4 23.4 1.0
CG B:PRO444 4.5 18.2 1.0
C B:CYS367 4.8 22.6 1.0
N B:PRO444 4.9 21.2 1.0
N B:CYS367 5.0 25.3 1.0
CA B:GLN421 5.0 15.3 1.0

Iron binding site 2 out of 8 in 5exr

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Iron binding site 2 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:1.1
occ:1.00
 FE2 B:SF4601 0.0 1.1 1.0
S3 B:SF4601 2.1 1.1 1.0
S4 B:SF4601 2.1 1.1 1.0
S1 B:SF4601 2.2 1.1 1.0
FE1 B:SF4601 2.8 1.1 1.0
FE3 B:SF4601 2.8 1.1 1.0
FE4 B:SF4601 3.0 9.2 1.0
SG B:CYS384 3.2 56.0 1.0
CB B:CYS384 3.2 51.3 1.0
S2 B:SF4601 3.4 2.4 1.0
SG B:CYS287 3.8 1.1 1.0
CA B:CYS384 3.8 47.3 1.0
CB B:CYS287 4.1 14.2 1.0
CD B:PRO385 4.4 27.4 1.0
N B:CYS384 4.8 51.8 1.0
CG2 B:ILE370 4.8 1.1 1.0
C B:CYS384 4.8 40.9 1.0
CG1 B:ILE371 4.8 29.8 1.0
N B:PRO385 5.0 33.7 1.0
SG B:CYS367 5.0 7.8 1.0
CG B:GLN421 5.0 1.2 1.0

Iron binding site 3 out of 8 in 5exr

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Iron binding site 3 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:1.1
occ:1.00
 FE3 B:SF4601 0.0 1.1 1.0
S4 B:SF4601 2.0 1.1 1.0
S2 B:SF4601 2.1 2.4 1.0
S1 B:SF4601 2.2 1.1 1.0
FE2 B:SF4601 2.8 1.1 1.0
FE1 B:SF4601 2.9 1.1 1.0
CB B:CYS424 3.0 46.9 1.0
SG B:CYS424 3.1 55.3 1.0
FE4 B:SF4601 3.2 9.2 1.0
S3 B:SF4601 3.7 1.1 1.0
CD2 B:PHE386 3.9 46.8 1.0
CG B:GLN421 4.1 1.2 1.0
CE2 B:PHE386 4.1 43.8 1.0
CA B:GLN421 4.2 15.3 1.0
CA B:CYS424 4.3 49.6 1.0
SG B:CYS384 4.4 56.0 1.0
CB B:GLN421 4.5 13.8 1.0
CD B:PRO286 4.6 28.9 1.0
O B:TYR420 4.7 18.7 1.0
N B:CYS424 4.8 44.4 1.0
O B:GLN421 4.9 14.3 1.0
SG B:CYS287 4.9 1.1 1.0
N B:GLN421 4.9 18.3 1.0

Iron binding site 4 out of 8 in 5exr

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Iron binding site 4 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:9.2
occ:1.00
 FE4 B:SF4601 0.0 9.2 1.0
S3 B:SF4601 2.1 1.1 1.0
S1 B:SF4601 2.1 1.1 1.0
S2 B:SF4601 2.1 2.4 1.0
SG B:CYS287 2.2 1.1 1.0
FE2 B:SF4601 3.0 1.1 1.0
FE1 B:SF4601 3.1 1.1 1.0
CG B:PRO285 3.1 25.1 1.0
FE3 B:SF4601 3.2 1.1 1.0
CB B:PRO285 3.5 26.4 1.0
CG B:PRO444 3.5 18.2 1.0
CB B:CYS287 3.8 14.2 1.0
S4 B:SF4601 4.0 1.1 1.0
CB B:PRO444 4.3 15.8 1.0
CD B:PRO444 4.4 23.4 1.0
CA B:PRO444 4.4 18.8 1.0
N B:CYS287 4.4 19.6 1.0
SG B:CYS367 4.5 7.8 1.0
SG B:CYS424 4.5 55.3 1.0
CD B:PRO286 4.6 28.9 1.0
CD B:PRO285 4.6 22.5 1.0
N B:PRO444 4.7 21.2 1.0
CA B:CYS287 4.7 18.4 1.0
CA B:PRO285 4.8 23.2 1.0
N B:PRO286 4.9 29.4 1.0
CE B:MET288 5.0 19.0 1.0
C B:PRO285 5.0 27.6 1.0

Iron binding site 5 out of 8 in 5exr

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Iron binding site 5 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:18.3
occ:1.00
 FE1 F:SF4601 0.0 18.3 1.0
S4 F:SF4601 2.1 1.1 1.0
S2 F:SF4601 2.1 4.5 1.0
S3 F:SF4601 2.2 1.1 1.0
SG F:CYS367 2.4 9.6 1.0
FE2 F:SF4601 2.8 1.1 1.0
CB F:CYS367 2.9 23.4 1.0
FE3 F:SF4601 2.9 8.8 1.0
FE4 F:SF4601 3.2 1.1 1.0
CA F:CYS367 3.6 22.1 1.0
S1 F:SF4601 3.7 8.0 1.0
NE2 F:GLN421 4.1 16.1 1.0
CG F:GLN421 4.4 15.2 1.0
C F:CYS367 4.5 21.9 1.0
CD F:PRO444 4.5 16.7 1.0
CB F:GLN421 4.6 22.7 1.0
CG F:PRO444 4.6 9.2 1.0
CD F:GLN421 4.6 10.3 1.0
O F:CYS367 4.7 25.7 1.0
N F:CYS367 4.8 20.2 1.0
SG F:CYS287 4.9 1.1 1.0
CG1 F:ILE371 5.0 7.6 1.0

Iron binding site 6 out of 8 in 5exr

Go back to Iron Binding Sites List in 5exr
Iron binding site 6 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:1.1
occ:1.00
 FE2 F:SF4601 0.0 1.1 1.0
S3 F:SF4601 2.2 1.1 1.0
S4 F:SF4601 2.2 1.1 1.0
S1 F:SF4601 2.2 8.0 1.0
FE1 F:SF4601 2.8 18.3 1.0
FE3 F:SF4601 2.9 8.8 1.0
FE4 F:SF4601 3.1 1.1 1.0
CB F:CYS384 3.3 51.3 1.0
SG F:CYS384 3.4 54.4 1.0
S2 F:SF4601 3.4 4.5 1.0
SG F:CYS287 3.6 1.1 1.0
CA F:CYS384 3.9 41.7 1.0
CD F:PRO385 3.9 1.1 1.0
CB F:CYS287 3.9 27.9 1.0
CG F:PRO385 4.7 9.4 1.0
N F:PRO385 4.7 17.7 1.0
N F:CYS287 4.7 35.0 1.0
C F:CYS384 4.7 26.1 1.0
CD2 F:PHE386 4.8 37.3 1.0
CA F:CYS287 4.9 32.3 1.0
N F:CYS384 5.0 44.2 1.0

Iron binding site 7 out of 8 in 5exr

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Iron binding site 7 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:8.8
occ:1.00
 FE3 F:SF4601 0.0 8.8 1.0
S4 F:SF4601 2.0 1.1 1.0
S2 F:SF4601 2.2 4.5 1.0
S1 F:SF4601 2.2 8.0 1.0
CB F:CYS424 2.8 48.1 1.0
FE2 F:SF4601 2.9 1.1 1.0
SG F:CYS424 2.9 43.8 1.0
FE1 F:SF4601 2.9 18.3 1.0
FE4 F:SF4601 3.3 1.1 1.0
S3 F:SF4601 3.7 1.1 1.0
CA F:GLN421 4.2 22.6 1.0
CA F:CYS424 4.2 49.8 1.0
CD2 F:PHE386 4.3 37.3 1.0
CE2 F:PHE386 4.4 34.5 1.0
CB F:GLN421 4.4 22.7 1.0
SG F:CYS367 4.5 9.6 1.0
O F:GLN421 4.7 31.4 1.0
CD F:PRO286 4.8 44.2 1.0
N F:CYS424 4.9 52.7 1.0
CB F:PRO285 4.9 35.6 1.0
CD2 F:LEU441 4.9 41.3 1.0
SG F:CYS287 4.9 1.1 1.0
C F:GLN421 5.0 31.6 1.0

Iron binding site 8 out of 8 in 5exr

Go back to Iron Binding Sites List in 5exr
Iron binding site 8 out of 8 in the Crystal Structure of Human Primosome


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 Primosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe601

b:1.1
occ:1.00
 FE4 F:SF4601 0.0 1.1 1.0
S3 F:SF4601 2.1 1.1 1.0
S1 F:SF4601 2.1 8.0 1.0
S2 F:SF4601 2.2 4.5 1.0
SG F:CYS287 2.2 1.1 1.0
FE2 F:SF4601 3.1 1.1 1.0
CG F:PRO444 3.1 9.2 1.0
FE1 F:SF4601 3.2 18.3 1.0
CG F:PRO285 3.3 38.7 1.0
FE3 F:SF4601 3.3 8.8 1.0
CB F:PRO285 3.7 35.6 1.0
CB F:CYS287 3.8 27.9 1.0
CD F:PRO444 3.9 16.7 1.0
CB F:PRO444 4.0 18.1 1.0
S4 F:SF4601 4.0 1.1 1.0
SG F:CYS367 4.1 9.6 1.0
CA F:PRO444 4.1 32.7 1.0
N F:PRO444 4.4 20.9 1.0
N F:CYS287 4.7 35.0 1.0
CD F:PRO285 4.7 37.6 1.0
CE F:MET288 4.8 21.2 1.0
SG F:CYS424 4.9 43.8 1.0
CA F:CYS287 4.9 32.3 1.0

Reference:

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
Page generated: Tue Aug 6 00:37:03 2024

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