Zinc in PDB 4jdg: Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D

The structure of Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D, PDB code: 4jdg was solved by J.Stransky, J.Dohnalek, T.Koval, T.Podzimek, P.Lipovova, J.Matousek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.71 / 2.74
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.944, 115.944, 74.713, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 26.4

The binding sites of Zinc atom in the Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D (pdb code 4jdg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D, PDB code: 4jdg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:52.1 occ:1.00 NE2 A:HIS31 1.9 42.3 1.0 O A:TRP26 2.1 57.1 1.0 OD1 A:ASP151 2.1 50.2 1.0 O1 A:PO4601 2.2 38.3 1.0 O3 A:PO4601 2.3 49.7 1.0 N A:TRP26 2.3 49.8 1.0 P A:PO4601 2.7 57.1 1.0 CE1 A:HIS31 2.7 46.4 1.0 C A:TRP26 2.9 53.2 1.0 CD2 A:HIS31 3.0 41.8 1.0 CA A:TRP26 3.0 51.6 1.0 CG A:ASP151 3.2 54.9 1.0 ZN A:ZN402 3.4 52.6 1.0 CB A:TRP26 3.6 59.7 1.0 O4 A:PO4601 3.6 46.8 1.0 OD2 A:ASP151 3.6 56.6 1.0 CE1 A:HIS147 3.8 43.0 1.0 NE2 A:HIS147 3.8 38.1 1.0 ND1 A:HIS31 3.9 48.5 1.0 OD2 A:ASP70 4.0 85.7 1.0 CG A:HIS31 4.0 45.3 1.0 O2 A:PO4601 4.0 49.1 1.0 N A:SER27 4.1 49.8 1.0 OD1 A:ASP185 4.2 69.1 1.0 CE1 A:HIS157 4.4 64.3 1.0 CB A:ASP151 4.5 55.1 1.0 NE2 A:HIS157 4.6 60.1 1.0 CG A:TRP26 4.6 62.3 1.0 CA A:ASP151 4.7 53.9 1.0 ND1 A:HIS147 4.7 39.7 1.0 CD2 A:HIS147 4.8 39.5 1.0 ZN A:ZN403 4.8 50.2 1.0 CA A:SER27 4.9 43.9 1.0 CG A:ASP70 4.9 73.4 1.0 CD1 A:TRP26 5.0 65.8 1.0

Zinc binding site 2 out of 3 in the Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:52.6 occ:1.00 NE2 A:HIS147 2.2 38.1 1.0 OD2 A:ASP151 2.2 56.6 1.0 ND1 A:HIS85 2.2 59.5 1.0 O4 A:PO4601 2.2 46.8 1.0 O3 A:PO4601 2.6 49.7 1.0 CE1 A:HIS85 2.8 61.5 1.0 P A:PO4601 3.0 57.1 1.0 CG A:ASP151 3.0 54.9 1.0 CE1 A:HIS147 3.1 43.0 1.0 OD1 A:ASP70 3.1 84.4 1.0 CD2 A:HIS147 3.2 39.5 1.0 OD1 A:ASP151 3.2 50.2 1.0 ZN A:ZN401 3.4 52.1 1.0 CG A:HIS85 3.4 59.4 1.0 CG A:ASP70 3.6 73.4 1.0 OD2 A:ASP70 3.7 85.7 1.0 O1 A:PO4601 3.8 38.3 1.0 CB A:HIS85 4.0 54.6 1.0 NE2 A:HIS85 4.0 58.3 1.0 ND1 A:HIS147 4.2 39.7 1.0 NE2 A:HIS31 4.2 42.3 1.0 O2 A:PO4601 4.3 49.1 1.0 CG A:HIS147 4.3 38.2 1.0 CD2 A:HIS85 4.3 59.7 1.0 CE1 A:HIS157 4.5 64.3 1.0 CB A:ASP151 4.5 55.1 1.0 CE1 A:HIS31 4.6 46.4 1.0 CB A:ASP70 4.9 67.2 1.0 O A:TRP26 4.9 57.1 1.0 CA A:HIS85 4.9 53.2 1.0 NE A:ARG73 4.9 61.9 1.0

Zinc binding site 3 out of 3 in the Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Tomato Bifunctional Nuclease TBN1, Variant N211D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:50.2 occ:1.00 OD2 A:ASP185 2.3 58.5 1.0 NE2 A:HIS181 2.3 47.8 1.0 NE2 A:HIS157 2.4 60.1 1.0 OD1 A:ASP185 2.5 69.1 1.0 O1 A:PO4601 2.6 38.3 1.0 CG A:ASP185 2.7 63.0 1.0 O2 A:PO4601 2.8 49.1 1.0 P A:PO4601 3.1 57.1 1.0 CE1 A:HIS157 3.1 64.3 1.0 CD2 A:HIS181 3.2 49.3 1.0 CE1 A:HIS181 3.4 53.4 1.0 CD2 A:HIS157 3.4 61.6 1.0 O4 A:PO4601 3.7 46.8 1.0 CB A:ASP185 4.2 62.0 1.0 N A:TRP26 4.2 49.8 1.0 ND1 A:HIS157 4.3 61.9 1.0 NE2 A:GLN154 4.3 54.8 1.0 CG A:HIS181 4.4 51.3 1.0 ND1 A:HIS181 4.4 54.0 1.0 CG A:HIS157 4.5 60.2 1.0 O3 A:PO4601 4.5 49.7 1.0 O A:HOH717 4.7 60.8 1.0 ZN A:ZN401 4.8 52.1 1.0 O A:TRP26 4.9 57.1 1.0 CA A:TRP26 5.0 51.6 1.0

J.Stransky, T.Koval, T.Podzimek, P.Lipovova, J.Matousek, J.Dohnalek. Plant Nuclease TBN1 Involved in Apoptotic Processes Blocks Its Active Site By A Surface Loop To Be Published.