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Zinc in PDB 6dcr: E. Coli Pria Helicase Winged Helix Domain Deletion Protein

Protein crystallography data

The structure of E. Coli Pria Helicase Winged Helix Domain Deletion Protein, PDB code: 6dcr 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) 48.83 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.132, 56.505, 195.863, 90.00, 97.67, 90.00
R / Rfree (%) 18.6 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein (pdb code 6dcr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein, PDB code: 6dcr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dcr

Go back to Zinc Binding Sites List in 6dcr
Zinc binding site 1 out of 4 in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Pria Helicase Winged Helix Domain Deletion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:65.2
occ:1.00
SG A:CYS439 2.3 56.5 1.0
SG A:CYS476 2.3 54.6 1.0
SG A:CYS436 2.3 58.8 1.0
SG A:CYS479 2.4 57.3 1.0
HB3 A:CYS479 2.8 71.2 1.0
HB3 A:CYS476 3.0 73.6 1.0
HB3 A:CYS436 3.0 58.4 1.0
CB A:CYS476 3.0 61.3 1.0
CB A:CYS436 3.0 48.7 1.0
HB2 A:CYS436 3.1 58.4 1.0
HB2 A:CYS476 3.1 73.6 1.0
HB3 A:CYS439 3.1 69.5 1.0
CB A:CYS479 3.1 59.3 1.0
H A:CYS439 3.2 70.2 1.0
H A:CYS479 3.2 69.2 1.0
CB A:CYS439 3.3 57.9 1.0
HB3 A:SER481 3.7 81.2 1.0
HB3 A:TRP441 3.8 69.3 1.0
N A:CYS479 3.8 57.7 1.0
HB3 A:SER478 3.8 77.3 1.0
N A:CYS439 3.8 58.5 1.0
HB2 A:CYS479 3.9 71.2 1.0
CA A:CYS479 4.0 66.7 1.0
HB2 A:CYS439 4.1 69.5 1.0
HB2 A:ASP438 4.1 81.0 1.0
CA A:CYS439 4.1 60.2 1.0
H A:SER481 4.2 74.6 1.0
H A:TRP441 4.2 61.7 1.0
HB2 A:TRP441 4.3 69.3 1.0
H A:GLY480 4.5 79.9 1.0
CB A:TRP441 4.5 57.7 1.0
CB A:SER481 4.5 67.7 1.0
CA A:CYS476 4.5 64.0 1.0
H A:SER478 4.5 77.8 1.0
HB2 A:SER481 4.5 81.2 1.0
CA A:CYS436 4.6 53.3 1.0
H A:GLY440 4.6 60.8 1.0
C A:CYS479 4.7 62.5 1.0
H A:ASP438 4.7 71.7 1.0
CB A:SER478 4.7 64.4 1.0
C A:CYS439 4.8 55.1 1.0
C A:SER478 4.8 63.2 1.0
N A:GLY480 4.8 66.6 1.0
HA A:CYS479 4.8 80.0 1.0
HA A:CYS476 4.9 76.7 1.0
N A:GLY440 4.9 50.7 1.0
N A:SER481 4.9 62.1 1.0
HA A:CYS436 4.9 64.0 1.0
C A:ASP438 4.9 62.6 1.0
HA A:CYS439 4.9 72.2 1.0
N A:TRP441 5.0 51.4 1.0
HD21 A:LEU484 5.0 75.9 1.0
CB A:ASP438 5.0 67.5 1.0

Zinc binding site 2 out of 4 in 6dcr

Go back to Zinc Binding Sites List in 6dcr
Zinc binding site 2 out of 4 in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Pria Helicase Winged Helix Domain Deletion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:64.4
occ:1.00
SG A:CYS466 2.4 55.4 1.0
SG A:CYS448 2.4 58.3 1.0
SG A:CYS463 2.4 57.2 1.0
SG A:CYS445 2.5 53.7 1.0
HB3 A:CYS466 3.0 71.0 1.0
HB3 A:CYS445 3.1 58.1 1.0
CB A:CYS445 3.1 48.4 1.0
HB2 A:CYS445 3.2 58.1 1.0
HB3 A:CYS448 3.2 74.3 1.0
CB A:CYS466 3.2 59.2 1.0
H A:CYS466 3.2 75.4 1.0
HB3 A:CYS463 3.3 65.9 1.0
CB A:CYS463 3.3 54.9 1.0
CB A:CYS448 3.4 61.9 1.0
H A:CYS448 3.4 67.1 1.0
HB2 A:CYS463 3.4 65.9 1.0
HB3 A:HIS465 3.7 69.2 1.0
HB2 A:ARG447 3.7 81.9 1.0
N A:CYS466 3.8 62.8 1.0
N A:CYS448 3.9 55.9 1.0
HG A:SER468 4.0 75.7 1.0
HB2 A:HIS450 4.0 60.2 1.0
H A:SER468 4.0 82.0 1.0
HB2 A:CYS466 4.0 71.0 1.0
CA A:CYS466 4.0 67.0 1.0
OG A:SER468 4.1 63.1 1.0
HB2 A:CYS448 4.2 74.3 1.0
CA A:CYS448 4.2 61.4 1.0
H A:HIS450 4.2 65.0 1.0
HB3 A:SER468 4.3 77.2 1.0
H A:HIS465 4.5 60.7 1.0
HD2 A:HIS465 4.5 71.6 1.0
H A:ASP467 4.6 72.4 1.0
H A:ARG447 4.6 73.4 1.0
C A:CYS466 4.6 66.6 1.0
CB A:ARG447 4.6 68.3 1.0
CA A:CYS445 4.6 53.3 1.0
CB A:HIS465 4.6 57.7 1.0
H A:ASP449 4.6 68.8 1.0
C A:CYS448 4.7 55.6 1.0
C A:HIS465 4.8 59.0 1.0
CA A:CYS463 4.8 59.9 1.0
CB A:SER468 4.8 64.3 1.0
N A:ASP467 4.8 60.3 1.0
N A:SER468 4.9 68.3 1.0
C A:ARG447 4.9 64.7 1.0
HA A:CYS466 4.9 80.4 1.0
HB3 A:ARG447 4.9 81.9 1.0
N A:ASP449 4.9 57.3 1.0
CB A:HIS450 5.0 50.2 1.0
HA A:CYS445 5.0 63.9 1.0
N A:HIS450 5.0 54.1 1.0

Zinc binding site 3 out of 4 in 6dcr

Go back to Zinc Binding Sites List in 6dcr
Zinc binding site 3 out of 4 in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Pria Helicase Winged Helix Domain Deletion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:77.0
occ:1.00
SG B:CYS463 2.1 77.8 1.0
SG B:CYS448 2.2 80.2 1.0
SG B:CYS466 2.4 80.5 1.0
SG B:CYS445 2.4 73.0 1.0
CB B:CYS463 3.0 82.4 1.0
HB3 B:CYS463 3.0 98.9 1.0
HB2 B:CYS463 3.1 98.9 1.0
HB3 B:CYS445 3.1 90.1 1.0
H B:CYS466 3.1 0.7 1.0
HB3 B:CYS466 3.2 0.2 1.0
H B:CYS448 3.2 0.9 1.0
CB B:CYS445 3.3 75.1 1.0
CB B:CYS466 3.3 86.8 1.0
HB2 B:CYS445 3.4 90.1 1.0
CB B:CYS448 3.6 79.5 1.0
HB3 B:CYS448 3.7 95.4 1.0
N B:CYS466 3.8 83.9 1.0
N B:CYS448 3.9 85.8 1.0
HG B:SER468 3.9 0.7 1.0
HB3 B:SER468 3.9 0.8 1.0
H B:SER468 4.0 0.9 1.0
HB3 B:HIS465 4.0 0.7 1.0
CA B:CYS466 4.1 88.5 1.0
OG B:SER468 4.1 88.9 1.0
HB2 B:CYS466 4.2 0.2 1.0
HB2 B:HIS450 4.2 0.7 1.0
CA B:CYS448 4.3 84.5 1.0
HB2 B:CYS448 4.3 95.4 1.0
H B:HIS450 4.3 0.3 1.0
H B:ARG447 4.4 0.8 1.0
CA B:CYS463 4.5 82.1 1.0
CB B:ARG447 4.5 96.7 1.0
CB B:SER468 4.5 95.7 1.0
H B:HIS465 4.5 0.7 1.0
H B:ASP467 4.6 0.4 1.0
C B:CYS466 4.6 89.7 1.0
HD2 B:HIS465 4.6 0.4 1.0
CA B:CYS445 4.7 70.7 1.0
HA B:CYS463 4.7 98.6 1.0
H B:ASP449 4.7 0.4 1.0
N B:SER468 4.8 98.3 1.0
N B:ASP467 4.8 88.7 1.0
C B:HIS465 4.8 92.9 1.0
C B:ARG447 4.8 93.4 1.0
CB B:HIS465 4.9 87.2 1.0
C B:CYS448 4.9 82.5 1.0
HA B:CYS466 4.9 0.2 1.0
N B:ARG447 5.0 93.2 1.0

Zinc binding site 4 out of 4 in 6dcr

Go back to Zinc Binding Sites List in 6dcr
Zinc binding site 4 out of 4 in the E. Coli Pria Helicase Winged Helix Domain Deletion Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Pria Helicase Winged Helix Domain Deletion Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:66.2
occ:1.00
SG B:CYS436 2.2 70.9 1.0
SG B:CYS439 2.2 69.4 1.0
SG B:CYS479 2.4 70.2 1.0
SG B:CYS476 2.5 72.2 1.0
HB3 B:CYS436 2.9 84.4 1.0
CB B:CYS436 3.0 70.3 1.0
H B:CYS439 3.1 87.1 1.0
H B:CYS479 3.1 88.7 1.0
HB3 B:CYS439 3.1 85.0 1.0
HB2 B:CYS436 3.1 84.4 1.0
HB3 B:CYS476 3.2 91.8 1.0
CB B:CYS476 3.2 76.5 1.0
CB B:CYS439 3.3 70.8 1.0
HB2 B:CYS476 3.3 91.8 1.0
HB3 B:CYS479 3.3 83.2 1.0
CB B:CYS479 3.5 69.4 1.0
HB3 B:SER478 3.5 82.3 1.0
HB3 B:SER481 3.7 96.3 1.0
HB3 B:TRP441 3.7 76.0 1.0
N B:CYS439 3.7 72.6 1.0
N B:CYS479 3.8 73.9 1.0
HB2 B:ASP438 4.0 89.7 1.0
H B:TRP441 4.0 74.4 1.0
CA B:CYS439 4.0 72.0 1.0
HB2 B:CYS439 4.0 85.0 1.0
H B:SER481 4.1 96.3 1.0
CA B:CYS479 4.2 73.5 1.0
HB2 B:CYS479 4.3 83.2 1.0
HB2 B:TRP441 4.3 76.0 1.0
H B:GLY440 4.3 81.1 1.0
H B:GLY480 4.4 80.8 1.0
H B:ASP438 4.4 95.2 1.0
CB B:SER478 4.4 68.6 1.0
CB B:TRP441 4.5 63.4 1.0
CA B:CYS436 4.5 73.3 1.0
H B:SER478 4.5 84.8 1.0
C B:CYS439 4.6 69.1 1.0
CB B:SER481 4.6 80.3 1.0
N B:GLY440 4.7 67.6 1.0
HG B:SER478 4.7 85.9 1.0
CA B:CYS476 4.7 74.9 1.0
OG B:SER478 4.7 71.6 1.0
N B:GLY480 4.8 67.4 1.0
N B:TRP441 4.8 62.0 1.0
C B:ASP438 4.8 76.1 1.0
C B:SER478 4.8 73.2 1.0
N B:SER481 4.8 80.2 1.0
CB B:ASP438 4.8 74.8 1.0
HA B:CYS436 4.9 87.9 1.0
C B:CYS479 4.9 74.1 1.0
HA B:CYS439 4.9 86.4 1.0
HB2 B:SER481 5.0 96.3 1.0
C B:CYS436 5.0 70.6 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 11:39:49 2020

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