Zinc in PDB 3ldy: An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci

The structure of An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci, PDB code: 3ldy was solved by B.W.Shen, D.Heiter, S.-H.Chan, S.-Y.Xu, G.Wilson, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.908, 115.788, 114.689, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.7

The structure of An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci (pdb code 3ldy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci, PDB code: 3ldy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn143 b:10.9 occ:1.00 SG A:CYS109 2.0 27.4 1.0 SG A:CYS66 2.3 29.5 1.0 SG A:CYS63 2.4 31.2 1.0 SG A:CYS112 2.4 26.8 1.0 CB A:CYS112 3.2 22.0 1.0 CB A:CYS66 3.2 30.0 1.0 CB A:CYS63 3.3 29.6 1.0 CB A:CYS109 3.5 22.7 1.0 N A:CYS66 3.7 30.3 1.0 CA A:CYS66 4.0 30.6 1.0 N A:CYS109 4.1 22.7 1.0 N A:CYS112 4.2 20.9 1.0 CA A:CYS112 4.3 21.8 1.0 CA A:CYS109 4.4 23.6 1.0 CG2 A:ILE68 4.5 29.3 1.0 CB A:TYR65 4.6 30.2 1.0 NE1 A:TRP136 4.7 31.2 1.0 CA A:CYS63 4.7 30.7 1.0 O A:CYS109 4.8 22.5 1.0 C A:TYR65 4.8 30.6 1.0 C A:CYS66 4.8 30.6 1.0 C A:CYS109 4.9 22.6 1.0 CG2 A:ILE132 5.0 29.2 1.0 N A:GLY67 5.0 30.9 1.0

Zinc binding site 2 out of 2 in the An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of An Extraordinary Mechanism of Dna Perturbation Exhibited By the Rare- Cutting Hnh Restriction Endonuclease Paci within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn144 b:24.6 occ:1.00 SG A:CYS27 2.3 38.3 1.0 SG A:CYS4 2.3 45.3 1.0 SG A:CYS24 2.4 38.6 1.0 SG A:CYS7 2.4 42.6 1.0 CB A:CYS4 3.2 48.7 1.0 CB A:CYS27 3.2 35.6 1.0 CB A:CYS7 3.3 43.0 1.0 CB A:CYS24 3.5 36.6 1.0 N A:CYS7 3.5 44.9 1.0 N A:CYS24 3.9 38.5 1.0 CA A:CYS7 4.0 43.4 1.0 N A:CYS27 4.1 34.9 1.0 CA A:CYS24 4.2 37.2 1.0 CA A:CYS27 4.2 35.7 1.0 NH2 A:ARG9 4.3 30.8 1.0 CB A:ARG6 4.4 48.6 1.0 C A:ARG6 4.6 46.8 1.0 CA A:CYS4 4.7 48.8 1.0 CD1 A:LEU11 4.7 38.0 1.0 NE A:ARG9 4.8 34.6 1.0 C A:CYS24 4.8 36.1 1.0 O A:CYS24 4.8 36.5 1.0 CA A:ARG6 4.9 48.0 1.0 C A:CYS7 4.9 42.6 1.0 N A:ARG6 4.9 48.2 1.0 CG A:ARG6 5.0 51.4 1.0 N A:GLN8 5.0 42.0 1.0

B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, B.L.Stoddard. Unusual Target Site Disruption By the Rare-Cutting Hnh Restriction Endonuclease Paci. Structure V. 18 734 2010.
ISSN: ISSN 0969-2126
PubMed: 20541511
DOI: 10.1016/J.STR.2010.03.009