Zinc in PDB 4dj4: X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)

The structure of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 4dj4 was solved by T.Koval, A.Stepankova, P.Lipovova, T.Podzimek, J.Matousek, J.Duskova, T.Skalova, J.Hasek, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	113.322, 113.322, 138.322, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 20.7

The structure of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) (pdb code 4dj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 4dj4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:27.1 occ:1.00 NE2 A:HIS31 2.0 21.7 1.0 N A:TRP26 2.0 25.0 1.0 O A:HOH701 2.1 37.9 1.0 OD1 A:ASP151 2.1 21.4 1.0 O A:TRP26 2.3 24.7 1.0 CA A:TRP26 2.9 26.3 1.0 C A:TRP26 2.9 27.6 1.0 CE1 A:HIS31 2.9 21.6 1.0 CD2 A:HIS31 3.0 22.8 1.0 CG A:ASP151 3.2 24.9 1.0 O A:HOH702 3.2 38.1 1.0 ZN A:ZN402 3.4 35.4 1.0 CB A:TRP26 3.5 26.5 1.0 OD2 A:ASP151 3.7 28.7 1.0 NE2 A:HIS147 3.8 27.0 1.0 CE1 A:HIS147 3.9 28.8 1.0 OD2 A:ASP70 3.9 30.1 1.0 ND1 A:HIS31 4.0 20.9 1.0 CG A:HIS31 4.1 23.4 1.0 N A:SER27 4.2 27.0 1.0 NE2 A:HIS157 4.3 30.1 1.0 CE1 A:HIS157 4.3 32.2 1.0 CG A:TRP26 4.3 26.1 1.0 CB A:ASP151 4.5 25.1 1.0 CD1 A:TRP26 4.6 27.6 1.0 O A:HOH703 4.6 34.0 1.0 CA A:ASP151 4.7 25.7 1.0 CD2 A:HIS147 4.7 28.7 1.0 OD1 A:ASP185 4.7 31.0 1.0 OD1 A:ASP70 4.7 32.4 1.0 CG A:ASP70 4.8 34.0 1.0 ND1 A:HIS147 4.8 28.0 1.0 ZN A:ZN403 4.9 31.6 1.0 N A:ASP151 4.9 25.8 1.0 O A:SER27 4.9 33.5 1.0

Zinc binding site 2 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:35.4 occ:1.00 O A:HOH701 1.9 37.9 1.0 NE2 A:HIS147 2.1 27.0 1.0 OD2 A:ASP151 2.2 28.7 1.0 ND1 A:HIS85 2.2 38.4 1.0 O A:HOH703 2.5 34.0 1.0 OD1 A:ASP70 2.5 32.4 1.0 CE1 A:HIS85 3.0 35.1 1.0 CD2 A:HIS147 3.0 28.7 1.0 CG A:ASP151 3.1 24.9 1.0 CE1 A:HIS147 3.1 28.8 1.0 OD1 A:ASP151 3.3 21.4 1.0 CG A:ASP70 3.3 34.0 1.0 ZN A:ZN401 3.4 27.1 1.0 CG A:HIS85 3.4 34.9 1.0 OD2 A:ASP70 3.5 30.1 1.0 CB A:HIS85 3.9 34.1 1.0 CE1 A:HIS157 4.1 32.2 1.0 NE2 A:HIS31 4.2 21.7 1.0 NE2 A:HIS85 4.2 39.0 1.0 CG A:HIS147 4.2 29.3 1.0 ND1 A:HIS147 4.2 28.0 1.0 O A:HOH702 4.3 38.1 1.0 CD2 A:HIS85 4.4 36.8 1.0 CB A:ASP151 4.5 25.1 1.0 O A:HOH704 4.6 39.6 1.0 CE1 A:HIS31 4.7 21.6 1.0 CB A:ASP70 4.7 36.0 1.0 CA A:HIS85 4.7 34.9 1.0 O A:TRP26 4.8 24.7 1.0 NE2 A:HIS157 4.9 30.1 1.0 ND1 A:HIS157 4.9 31.0 1.0

Zinc binding site 3 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:31.6 occ:1.00 OD2 A:ASP185 2.0 25.4 1.0 NE2 A:HIS181 2.0 28.5 1.0 NE2 A:HIS157 2.2 30.1 1.0 O A:HOH702 2.3 38.1 1.0 CG A:ASP185 2.7 29.7 1.0 OD1 A:ASP185 2.7 31.0 1.0 CD2 A:HIS181 3.0 34.0 1.0 CD2 A:HIS157 3.1 30.2 1.0 CE1 A:HIS181 3.1 30.3 1.0 CE1 A:HIS157 3.2 32.2 1.0 CB A:ASP185 4.1 29.4 1.0 CG A:HIS181 4.2 32.1 1.0 ND1 A:HIS181 4.2 32.5 1.0 N A:TRP26 4.2 25.0 1.0 CG A:HIS157 4.2 31.6 1.0 ND1 A:HIS157 4.3 31.0 1.0 O A:HOH701 4.4 37.9 1.0 O A:HOH751 4.4 29.6 1.0 O A:HOH704 4.5 39.6 1.0 O A:HOH703 4.5 34.0 1.0 NE2 A:GLN154 4.6 22.9 1.0 CA A:TRP26 4.8 26.3 1.0 ZN A:ZN401 4.9 27.1 1.0 C A:TRP26 4.9 27.6 1.0 O A:TRP26 5.0 24.7 1.0

Zinc binding site 4 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:34.6 occ:1.00 NE2 B:HIS31 1.8 24.8 1.0 O B:HOH701 1.8 37.3 1.0 OD1 B:ASP151 2.0 38.6 1.0 N B:TRP26 2.2 32.3 1.0 O B:TRP26 2.3 35.4 1.0 CE1 B:HIS31 2.7 30.7 1.0 C B:TRP26 3.0 35.8 1.0 CD2 B:HIS31 3.0 26.9 1.0 CA B:TRP26 3.0 34.3 1.0 CG B:ASP151 3.0 38.1 1.0 O B:HOH702 3.2 29.3 1.0 ZN B:ZN402 3.3 38.0 1.0 OD2 B:ASP151 3.4 33.2 1.0 CB B:TRP26 3.6 37.5 1.0 OD2 B:ASP70 3.7 39.8 1.0 NE2 B:HIS147 3.7 27.8 1.0 CE1 B:HIS157 3.9 45.5 1.0 ND1 B:HIS31 3.9 29.2 1.0 CE1 B:HIS147 4.0 31.3 1.0 CG B:HIS31 4.0 30.0 1.0 O B:HOH703 4.1 32.4 1.0 NE2 B:HIS157 4.1 48.7 1.0 N B:SER27 4.3 40.1 1.0 CB B:ASP151 4.4 39.5 1.0 OD1 B:ASP185 4.4 34.0 1.0 CG B:TRP26 4.5 41.1 1.0 CA B:ASP151 4.6 36.2 1.0 CD2 B:HIS147 4.7 30.6 1.0 CG B:ASP70 4.7 43.1 1.0 ND1 B:HIS157 4.7 46.4 1.0 CD1 B:TRP26 4.8 41.1 1.0 OD1 B:ASP70 4.9 43.8 1.0 ZN B:ZN403 4.9 36.3 1.0 O B:SER27 5.0 39.7 1.0 CA B:SER27 5.0 35.4 1.0

Zinc binding site 5 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:38.0 occ:1.00 NE2 B:HIS147 2.1 27.8 1.0 O B:HOH703 2.1 32.4 1.0 OD2 B:ASP151 2.2 33.2 1.0 O B:HOH701 2.3 37.3 1.0 ND1 B:HIS85 2.3 31.4 1.0 OD1 B:ASP70 2.7 43.8 1.0 CD2 B:HIS147 3.0 30.6 1.0 CE1 B:HIS85 3.1 32.4 1.0 CG B:ASP151 3.2 38.1 1.0 CE1 B:HIS147 3.2 31.3 1.0 OD2 B:ASP70 3.2 39.8 1.0 CG B:ASP70 3.3 43.1 1.0 ZN B:ZN401 3.3 34.6 1.0 CG B:HIS85 3.4 32.1 1.0 OD1 B:ASP151 3.4 38.6 1.0 CB B:HIS85 3.8 33.2 1.0 NE2 B:HIS31 4.0 24.8 1.0 CE1 B:HIS157 4.1 45.5 1.0 CG B:HIS147 4.2 33.9 1.0 ND1 B:HIS147 4.3 30.4 1.0 NE2 B:HIS85 4.3 32.1 1.0 CE1 B:HIS31 4.3 30.7 1.0 CD2 B:HIS85 4.5 32.1 1.0 CB B:ASP151 4.5 39.5 1.0 O B:HOH702 4.6 29.3 1.0 NH1 B:ARG73 4.6 84.0 1.0 CA B:HIS85 4.7 37.1 1.0 CB B:ASP70 4.7 38.4 1.0 O B:TRP26 4.9 35.4 1.0 ND1 B:HIS157 4.9 46.4 1.0

Zinc binding site 6 out of 6 in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:36.3 occ:1.00 NE2 B:HIS181 2.1 25.7 1.0 O B:HOH702 2.1 29.3 1.0 OD2 B:ASP185 2.1 37.4 1.0 NE2 B:HIS157 2.2 48.7 1.0 OD2 A:ASP133 2.3 58.9 1.0 OD1 B:ASP185 2.6 34.0 1.0 CG B:ASP185 2.7 39.2 1.0 CG A:ASP133 2.8 63.9 1.0 OD1 A:ASP133 2.9 57.7 1.0 CD2 B:HIS157 3.0 44.6 1.0 CE1 B:HIS181 3.0 28.0 1.0 CD2 B:HIS181 3.1 28.3 1.0 CE1 B:HIS157 3.2 45.5 1.0 CB A:ASP133 4.1 71.4 1.0 CG B:HIS157 4.2 46.5 1.0 ND1 B:HIS181 4.2 29.2 1.0 CG B:HIS181 4.2 29.1 1.0 CB B:ASP185 4.2 37.5 1.0 ND1 B:HIS157 4.2 46.4 1.0 N B:TRP26 4.3 32.3 1.0 O B:HOH701 4.4 37.3 1.0 NE2 B:GLN154 4.5 37.5 1.0 O B:HOH717 4.6 31.9 1.0 O B:HOH703 4.6 32.4 1.0 O B:TRP26 4.8 35.4 1.0 ZN B:ZN401 4.9 34.6 1.0 C B:TRP26 4.9 35.8 1.0 CA B:TRP26 5.0 34.3 1.0

T.Koval, P.Lipovova, T.Podzimek, J.Matousek, J.Duskova, T.Skalova, A.Stepankova, J.Hasek, J.Dohnalek. Plant Multifunctional Nuclease TBN1 with Unexpected Phospholipase Activity: Structural Study and Reaction-Mechanism Analysis. Acta Crystallogr.,Sect.D V. 69 213 2013.
ISSN: ISSN 0907-4449
PubMed: 23385457
DOI: 10.1107/S0907444912043697