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Zinc in PDB 4nl8: Pria Helicase Bound to Ssb C-Terminal Tail Peptide

Protein crystallography data

The structure of Pria Helicase Bound to Ssb C-Terminal Tail Peptide, PDB code: 4nl8 was solved by B.Bhattacharyya, N.P.George, T.M.Thurmes, J.L.Keck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.610, 153.248, 192.373, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 29.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide (pdb code 4nl8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide, PDB code: 4nl8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 1 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


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 Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:0.3
occ:1.00
 SG A:CYS435 2.3 95.5 1.0
SG A:CYS438 2.3 0.4 1.0
SG A:CYS475 2.3 0.0 1.0
SG A:CYS478 2.3 0.4 1.0
CB A:CYS438 3.1 0.5 1.0
CB A:CYS475 3.2 0.5 1.0
CB A:CYS435 3.3 0.2 1.0
CB A:CYS478 3.4 0.9 1.0
N A:CYS478 3.5 0.4 1.0
N A:CYS438 3.9 0.0 1.0
CA A:CYS478 4.0 0.0 1.0
CA A:CYS438 4.0 0.3 1.0
N A:GLY479 4.5 0.4 1.0
C A:CYS478 4.5 0.1 1.0
C A:SER477 4.5 0.2 1.0
CB A:SER480 4.5 0.7 1.0
N A:SER480 4.6 0.6 1.0
CB A:TRP440 4.6 96.7 1.0
C A:CYS438 4.7 0.8 1.0
CB A:SER477 4.7 0.9 1.0
CA A:CYS475 4.7 0.9 1.0
CA A:CYS435 4.7 98.5 1.0
N A:SER477 4.9 0.6 1.0
CA A:SER477 4.9 0.7 1.0
N A:GLY439 4.9 0.1 1.0
N A:TRP440 5.0 0.0 1.0

Zinc binding site 2 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 2 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


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 Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:0.0
occ:1.00
 SG A:CYS465 2.3 0.5 1.0
SG A:CYS444 2.3 0.7 1.0
SG A:CYS462 2.3 0.5 1.0
SG A:CYS447 2.4 0.8 1.0
CB A:CYS444 3.2 0.5 1.0
CB A:CYS462 3.3 0.9 1.0
CB A:CYS447 3.3 0.7 1.0
CB A:CYS465 3.4 0.9 1.0
N A:CYS447 3.7 0.6 1.0
N A:CYS465 3.7 0.4 1.0
O A:CYS447 3.8 0.1 1.0
CA A:CYS447 4.0 0.0 1.0
CA A:CYS465 4.0 1.0 1.0
OG A:SER467 4.2 0.8 1.0
C A:CYS447 4.3 0.7 1.0
C A:CYS465 4.5 0.7 1.0
CA A:CYS444 4.7 0.1 1.0
CA A:CYS462 4.8 1.0 1.0
O A:CYS465 4.8 0.5 1.0
C A:HIS464 4.8 1.0 1.0
CB A:SER449 4.9 0.0 1.0
CB A:ARG446 4.9 0.9 1.0
C A:ARG446 4.9 0.9 1.0

Zinc binding site 3 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 3 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


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 Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:0.2
occ:1.00
 SG B:CYS435 2.3 0.8 1.0
SG B:CYS438 2.3 93.5 1.0
SG B:CYS475 2.3 0.1 1.0
SG B:CYS478 2.3 0.9 1.0
CB B:CYS438 3.1 0.8 1.0
CB B:CYS475 3.2 98.4 1.0
CB B:CYS435 3.2 0.2 1.0
CB B:CYS478 3.4 0.0 1.0
N B:CYS478 3.6 0.5 1.0
N B:CYS438 3.9 0.8 1.0
CA B:CYS478 4.0 0.4 1.0
CA B:CYS438 4.0 0.7 1.0
CB B:SER480 4.5 1.0 1.0
N B:GLY479 4.5 0.1 1.0
C B:CYS478 4.5 0.7 1.0
C B:SER477 4.5 0.4 1.0
N B:SER480 4.6 0.5 1.0
CB B:TRP440 4.6 0.9 1.0
C B:CYS438 4.7 0.1 1.0
CA B:CYS475 4.7 98.5 1.0
CA B:CYS435 4.7 0.2 1.0
CB B:SER477 4.7 0.3 1.0
N B:GLY439 4.9 0.6 1.0
N B:SER477 4.9 99.2 1.0
CA B:SER477 4.9 0.5 1.0
N B:TRP440 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 4 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


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 Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:0.1
occ:1.00
 SG B:CYS447 2.3 0.9 1.0
SG B:CYS462 2.3 0.7 1.0
SG B:CYS444 2.3 0.8 1.0
SG B:CYS465 2.4 0.5 1.0
CB B:CYS444 3.2 0.8 1.0
CB B:CYS465 3.4 0.3 1.0
CB B:CYS462 3.4 1.0 1.0
CB B:CYS447 3.5 0.3 1.0
N B:CYS465 3.7 0.9 1.0
N B:CYS447 3.7 0.7 1.0
O B:CYS447 3.9 0.0 1.0
CA B:CYS465 4.0 0.8 1.0
CA B:CYS447 4.1 0.8 1.0
C B:CYS447 4.4 0.2 1.0
OG B:SER467 4.4 0.2 1.0
C B:CYS465 4.5 0.7 1.0
CB B:SER449 4.6 0.5 1.0
CA B:CYS444 4.7 0.8 1.0
C B:HIS464 4.7 0.2 1.0
O B:CYS465 4.8 1.0 1.0
CA B:CYS462 4.9 0.3 1.0
OG B:SER449 4.9 0.6 1.0
CB B:ARG446 4.9 0.5 1.0
C B:ARG446 4.9 0.8 1.0

Zinc binding site 5 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 5 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pria Helicase Bound to Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn801

b:0.6
occ:1.00
 SG E:CYS462 2.3 0.8 1.0
SG E:CYS444 2.3 0.4 1.0
SG E:CYS447 2.3 0.9 1.0
SG E:CYS465 2.4 0.9 1.0
CB E:CYS465 3.3 0.6 1.0
CB E:CYS462 3.5 0.4 1.0
CB E:CYS444 3.5 0.3 1.0
N E:CYS465 3.5 0.4 1.0
CB E:CYS447 3.7 0.6 1.0
N E:CYS447 3.9 0.5 1.0
CA E:CYS465 3.9 0.1 1.0
O E:CYS447 4.0 0.5 1.0
CA E:CYS447 4.2 0.2 1.0
CB E:SER449 4.4 0.1 1.0
C E:CYS465 4.5 0.2 1.0
C E:CYS447 4.5 0.8 1.0
O E:CYS444 4.5 95.9 1.0
C E:HIS464 4.6 0.6 1.0
OG E:SER467 4.6 98.7 1.0
CB E:ARG446 4.7 0.1 1.0
O E:CYS465 4.8 0.4 1.0
CA E:CYS444 4.8 0.9 1.0
OG E:SER449 4.8 0.7 1.0
CA E:CYS462 4.9 0.6 1.0
CB E:HIS464 4.9 0.5 1.0
C E:CYS444 4.9 0.8 1.0

Zinc binding site 6 out of 6 in 4nl8

Go back to Zinc Binding Sites List in 4nl8
Zinc binding site 6 out of 6 in the Pria Helicase Bound to Ssb C-Terminal Tail Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pria Helicase Bound to Ssb C-Terminal Tail Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn802

b:0.7
occ:1.00
 SG E:CYS435 2.3 1.0 1.0
SG E:CYS438 2.3 85.9 1.0
SG E:CYS478 2.3 0.1 1.0
SG E:CYS475 2.3 0.0 1.0
CB E:CYS438 3.1 89.3 1.0
CB E:CYS475 3.2 0.5 1.0
CB E:CYS435 3.3 0.6 1.0
CB E:CYS478 3.4 0.2 1.0
N E:CYS478 3.6 0.9 1.0
N E:CYS438 3.9 84.6 1.0
CA E:CYS478 4.0 0.1 1.0
CA E:CYS438 4.0 91.4 1.0
N E:GLY479 4.5 0.4 1.0
CB E:SER480 4.5 0.0 1.0
C E:CYS478 4.5 0.7 1.0
N E:SER480 4.5 0.5 1.0
C E:SER477 4.5 0.3 1.0
CB E:TRP440 4.6 0.6 1.0
C E:CYS438 4.6 96.1 1.0
CA E:CYS475 4.7 0.7 1.0
CA E:CYS435 4.7 0.4 1.0
CB E:SER477 4.7 0.5 1.0
N E:GLY439 4.9 93.6 1.0
N E:SER477 4.9 0.1 1.0
CA E:SER477 4.9 0.4 1.0
N E:TRP440 5.0 0.5 1.0

Reference:

B.Bhattacharyya, N.P.George, T.M.Thurmes, R.Zhou, N.Jani, S.R.Wessel, S.J.Sandler, T.Ha, J.L.Keck. Structural Mechanisms of Pria-Mediated Dna Replication Restart. Proc.Natl.Acad.Sci.Usa V. 111 1373 2014.
ISSN: ISSN 0027-8424
PubMed: 24379377
DOI: 10.1073/PNAS.1318001111
Page generated: Sun Oct 27 03:13:15 2024

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