Zinc in PDB 4esj: Restriction Endonuclease Dpni in Complex with Target Dna

All present enzymatic activity of Restriction Endonuclease Dpni in Complex with Target Dna:
3.1.21.4;

The structure of Restriction Endonuclease Dpni in Complex with Target Dna, PDB code: 4esj was solved by W.Siwek, H.Czapinska, M.Bochtler, J.M.Bujnicki, K.Skowronek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.518, 98.411, 83.884, 90.00, 112.21, 90.00
R / Rfree (%)	19.8 / 21.8

The binding sites of Zinc atom in the Restriction Endonuclease Dpni in Complex with Target Dna (pdb code 4esj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Restriction Endonuclease Dpni in Complex with Target Dna, PDB code: 4esj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Restriction Endonuclease Dpni in Complex with Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Restriction Endonuclease Dpni in Complex with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:41.0 occ:1.00 SG A:CYS59 2.3 43.1 1.0 SG A:CYS56 2.3 43.8 1.0 SG A:CYS37 2.3 41.8 1.0 SG A:CYS34 2.3 36.7 1.0 CB A:CYS34 3.1 37.6 1.0 CB A:CYS56 3.1 42.2 1.0 CB A:CYS59 3.4 46.6 1.0 CB A:CYS37 3.4 43.9 1.0 N A:CYS37 3.8 41.6 1.0 N A:CYS59 3.8 48.4 1.0 CA A:CYS59 4.1 47.7 1.0 CA A:CYS37 4.2 42.9 1.0 CB A:ASN39 4.3 46.0 1.0 CB A:ASN36 4.3 40.4 1.0 CA A:CYS34 4.5 36.1 1.0 CA A:CYS56 4.6 42.6 1.0 CB A:HIS58 4.6 49.8 0.5 ND2 A:ASN36 4.7 42.2 1.0 C A:CYS37 4.7 42.9 1.0 N A:GLY38 4.8 41.6 1.0 C A:CYS59 4.8 46.9 1.0 C A:ASN36 4.8 41.5 1.0 CB A:HIS58 4.8 50.8 0.5 C A:HIS58 4.8 50.6 0.5 N A:ASN39 4.9 44.3 1.0 C A:HIS58 4.9 50.3 0.5 C A:CYS34 5.0 36.5 1.0 CD2 A:HIS58 5.0 51.0 0.5

Zinc binding site 2 out of 3 in the Restriction Endonuclease Dpni in Complex with Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Restriction Endonuclease Dpni in Complex with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.0 occ:0.50 OE1 A:GLU2 1.8 22.3 1.0 ND1 A:HIS4 2.1 22.5 1.0 CD A:GLU2 2.8 29.3 1.0 CE1 A:HIS4 3.0 23.6 1.0 CG A:HIS4 3.1 24.1 1.0 OE2 A:GLU2 3.3 29.9 1.0 CB A:HIS4 3.5 24.8 1.0 N A:HIS4 4.0 25.5 1.0 NE2 A:HIS4 4.1 23.8 1.0 O A:HOH402 4.2 25.6 1.0 CG A:GLU2 4.2 29.3 1.0 CD2 A:HIS4 4.2 22.3 1.0 CA A:HIS4 4.3 24.7 1.0 N A:LEU3 4.7 27.4 1.0 O A:HOH416 4.9 37.7 1.0 C A:LEU3 5.0 26.2 1.0

Zinc binding site 3 out of 3 in the Restriction Endonuclease Dpni in Complex with Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Restriction Endonuclease Dpni in Complex with Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:33.6 occ:1.00 SG B:CYS37 2.2 39.6 1.0 SG B:CYS34 2.2 36.8 1.0 SG B:CYS59 2.3 37.1 1.0 SG B:CYS56 2.3 36.3 1.0 CB B:CYS34 3.1 39.1 1.0 CB B:CYS56 3.1 36.0 1.0 CB B:CYS59 3.4 39.7 1.0 CB B:CYS37 3.4 43.8 1.0 N B:CYS37 3.8 42.6 1.0 N B:CYS59 3.9 40.1 1.0 CA B:CYS59 4.2 40.0 1.0 CA B:CYS37 4.2 44.1 1.0 CB B:ASN36 4.4 41.2 1.0 CA B:CYS34 4.5 38.6 1.0 CA B:CYS56 4.6 35.9 1.0 CB B:HIS58 4.6 41.5 1.0 ND2 B:ASN36 4.7 43.5 1.0 C B:HIS58 4.8 41.3 1.0 C B:CYS59 4.8 39.6 1.0 C B:CYS37 4.9 45.3 1.0 N B:GLY38 4.9 45.4 1.0 C B:ASN36 4.9 43.2 1.0 N B:SER60 5.0 38.3 1.0

W.Siwek, H.Czapinska, M.Bochtler, J.M.Bujnicki, K.Skowronek. Crystal Structure and Mechanism of Action of the N6-Methyladenine-Dependent Type Iim Restriction Endonuclease R.Dpni. Nucleic Acids Res. V. 40 7563 2012.
ISSN: ISSN 0305-1048
PubMed: 22610857
DOI: 10.1093/NAR/GKS428