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Zinc in PDB 6dgd: Pria Helicase Bound to Dsdna of A Dna Replication Fork

Protein crystallography data

The structure of Pria Helicase Bound to Dsdna of A Dna Replication Fork, PDB code: 6dgd was solved by K.A.Satyshur, T.A.Windgassen, J.L.Keck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 2.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.560, 106.760, 256.830, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Pria Helicase Bound to Dsdna of A Dna Replication Fork (pdb code 6dgd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Pria Helicase Bound to Dsdna of A Dna Replication Fork, PDB code: 6dgd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dgd

Go back to Zinc Binding Sites List in 6dgd
Zinc binding site 1 out of 4 in the Pria Helicase Bound to Dsdna of A Dna Replication Fork


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pria Helicase Bound to Dsdna of A Dna Replication Fork within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:0.5
occ:1.00
SG A:CYS465 2.3 0.5 1.0
SG A:CYS447 2.3 0.9 1.0
SG A:CYS444 2.3 0.5 1.0
SG A:CYS462 2.4 0.2 1.0
CB A:CYS465 3.2 93.0 1.0
CB A:CYS444 3.3 0.4 1.0
CB A:CYS462 3.3 1.0 1.0
N A:CYS447 3.6 0.8 1.0
CB A:CYS447 3.9 0.1 1.0
N A:CYS465 3.9 0.2 1.0
CB A:ARG446 3.9 0.3 1.0
CA A:CYS465 4.1 99.8 1.0
CA A:CYS447 4.3 0.6 1.0
O A:CYS447 4.3 0.4 1.0
C A:ARG446 4.5 0.7 1.0
CB A:SER449 4.5 0.1 1.0
CA A:ARG446 4.6 0.1 1.0
N A:ARG446 4.6 0.8 1.0
C A:HIS464 4.7 0.8 1.0
CB A:HIS464 4.7 0.2 1.0
C A:CYS447 4.7 0.3 1.0
CA A:CYS444 4.7 1.0 1.0
CA A:CYS462 4.8 0.9 1.0
C A:CYS465 4.8 0.4 1.0
OG A:SER467 4.9 1.0 1.0

Zinc binding site 2 out of 4 in 6dgd

Go back to Zinc Binding Sites List in 6dgd
Zinc binding site 2 out of 4 in the Pria Helicase Bound to Dsdna of A Dna Replication Fork


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pria Helicase Bound to Dsdna of A Dna Replication Fork within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:0.4
occ:1.00
SG A:CYS438 2.2 0.8 1.0
SG A:CYS478 2.3 0.2 1.0
SG A:CYS435 2.4 0.5 1.0
SG A:CYS475 2.4 0.0 1.0
CB A:CYS438 2.9 0.6 1.0
CB A:CYS435 3.0 0.3 1.0
CB A:CYS478 3.2 0.9 1.0
CB A:CYS475 3.4 0.3 1.0
N A:CYS438 3.7 0.0 1.0
CA A:CYS438 3.8 0.4 1.0
N A:CYS478 3.9 0.3 1.0
CA A:CYS478 4.0 0.5 1.0
CB A:TRP440 4.2 0.8 1.0
N A:GLY479 4.3 1.0 1.0
C A:CYS438 4.4 0.1 1.0
N A:TRP440 4.4 0.7 1.0
CA A:CYS435 4.5 0.9 1.0
N A:GLY439 4.5 0.7 1.0
C A:CYS478 4.6 0.2 1.0
N A:SER480 4.8 0.2 1.0
CA A:CYS475 4.8 0.0 1.0
C A:SER477 4.8 0.5 1.0
C A:ASP437 4.9 0.3 1.0
C A:CYS435 5.0 0.1 1.0
CB A:SER480 5.0 0.7 1.0
CA A:TRP440 5.0 0.8 1.0

Zinc binding site 3 out of 4 in 6dgd

Go back to Zinc Binding Sites List in 6dgd
Zinc binding site 3 out of 4 in the Pria Helicase Bound to Dsdna of A Dna Replication Fork


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pria Helicase Bound to Dsdna of A Dna Replication Fork within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:0.9
occ:1.00
SG B:CYS447 2.3 0.2 1.0
SG B:CYS444 2.4 0.7 1.0
SG B:CYS465 2.4 0.6 1.0
SG B:CYS462 2.4 0.2 1.0
CB B:CYS462 3.2 0.2 1.0
CB B:CYS444 3.2 0.9 1.0
OG B:SER467 3.3 0.1 1.0
CB B:CYS465 3.5 0.5 1.0
CB B:CYS447 3.7 0.3 1.0
N B:CYS465 3.8 0.6 1.0
N B:CYS447 4.1 0.7 1.0
CA B:CYS465 4.2 0.5 1.0
CA B:CYS447 4.5 0.6 1.0
CB B:SER467 4.5 0.3 1.0
CB B:HIS464 4.5 0.8 1.0
CA B:CYS462 4.7 1.0 1.0
C B:HIS464 4.7 0.2 1.0
CA B:CYS444 4.7 0.8 1.0
C B:CYS465 4.7 0.8 1.0
CB B:ARG446 4.8 0.8 1.0
OG B:SER449 4.8 0.9 1.0
N B:HIS464 4.9 0.6 1.0
CA B:HIS464 4.9 0.7 1.0
N B:ASP466 4.9 0.8 1.0
N B:SER467 5.0 0.9 1.0

Zinc binding site 4 out of 4 in 6dgd

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Zinc binding site 4 out of 4 in the Pria Helicase Bound to Dsdna of A Dna Replication Fork


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pria Helicase Bound to Dsdna of A Dna Replication Fork within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:99.7
occ:1.00
SG B:CYS438 2.2 67.5 1.0
SG B:CYS475 2.2 89.7 1.0
SG B:CYS478 2.2 74.4 1.0
SG B:CYS435 2.3 82.0 1.0
CB B:CYS475 2.9 93.2 1.0
CB B:CYS438 3.0 83.7 1.0
CB B:CYS435 3.1 97.2 1.0
CB B:CYS478 3.3 87.0 1.0
N B:CYS478 3.7 97.2 1.0
CA B:CYS478 4.0 93.5 1.0
CB B:SER480 4.1 94.9 1.0
CA B:CYS438 4.1 67.7 1.0
N B:CYS438 4.1 74.1 1.0
N B:SER480 4.3 0.8 1.0
N B:GLY479 4.3 87.8 1.0
CA B:CYS475 4.4 79.2 1.0
C B:CYS478 4.5 91.1 1.0
CB B:TRP440 4.5 83.8 1.0
CA B:CYS435 4.6 69.9 1.0
CB B:SER477 4.7 85.4 1.0
C B:SER477 4.7 0.6 1.0
C B:CYS438 4.7 94.7 1.0
CA B:SER480 4.8 91.0 1.0
C B:CYS475 4.9 94.9 1.0
O B:CYS475 4.9 79.9 1.0

Reference:

T.A.Windgassen, M.Leroux, K.A.Satyshur, S.J.Sandler, J.L.Keck. Structure-Specific Dna Replication-Fork Recognition Directs Helicase and Replication Restart Activities of the Pria Helicase. Proc. Natl. Acad. Sci. V. 115 E9075 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30201718
DOI: 10.1073/PNAS.1809842115
Page generated: Wed Dec 16 11:40:02 2020

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