Zinc in PDB 3sng: X-Ray Structure of Fully Glycosylated Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato)

The structure of X-Ray Structure of Fully Glycosylated Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 3sng 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 / 2.16
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.031, 101.031, 71.529, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 22.3

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

Chlorine

(Cl)

1 atom

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

Zinc binding site 1 out of 3 in the X-Ray Structure of Fully Glycosylated 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 Fully Glycosylated Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:23.1 occ:1.00 O A:HOH701 1.8 16.4 1.0 NE2 A:HIS31 2.0 23.6 1.0 OD1 A:ASP151 2.1 19.3 1.0 O A:TRP26 2.1 23.1 1.0 N A:TRP26 2.2 22.4 1.0 C A:TRP26 2.9 28.6 1.0 CA A:TRP26 3.0 26.7 1.0 CE1 A:HIS31 3.0 26.9 1.0 CD2 A:HIS31 3.0 24.5 1.0 CG A:ASP151 3.2 18.1 1.0 ZN A:ZN402 3.3 21.1 1.0 OD2 A:ASP151 3.5 19.1 1.0 CB A:TRP26 3.6 25.3 1.0 OD2 A:ASP70 3.7 27.7 1.0 NE2 A:HIS147 3.7 23.2 1.0 CE1 A:HIS147 3.9 25.3 1.0 CE1 A:HIS157 4.0 23.4 1.0 ND1 A:HIS31 4.1 24.1 1.0 CG A:HIS31 4.1 25.1 1.0 NE2 A:HIS157 4.1 24.3 1.0 N A:SER27 4.2 28.2 1.0 CG A:TRP26 4.4 24.8 1.0 CB A:ASP151 4.5 19.9 1.0 CD1 A:TRP26 4.6 23.9 1.0 CG A:ASP70 4.6 26.8 1.0 CA A:ASP151 4.7 21.4 1.0 CD2 A:HIS147 4.7 21.8 1.0 OD1 A:ASP70 4.7 28.1 1.0 OD1 A:ASP185 4.8 31.1 1.0 ZN A:ZN403 4.8 31.8 1.0 ND1 A:HIS157 4.8 24.9 1.0 ND1 A:HIS147 4.9 22.0 1.0 CA A:SER27 4.9 29.4 1.0 N A:ASP151 4.9 20.1 1.0 O A:SER27 5.0 27.5 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of Fully Glycosylated 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 Fully Glycosylated Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:21.1 occ:1.00 O A:HOH701 1.9 16.4 1.0 OD2 A:ASP151 2.0 19.1 1.0 NE2 A:HIS147 2.0 23.2 1.0 ND1 A:HIS85 2.1 19.1 1.0 OD1 A:ASP70 2.7 28.1 1.0 CE1 A:HIS85 2.9 21.3 1.0 CG A:ASP151 2.9 18.1 1.0 CD2 A:HIS147 3.0 21.8 1.0 CE1 A:HIS147 3.1 25.3 1.0 OD1 A:ASP151 3.2 19.3 1.0 CG A:HIS85 3.2 17.8 1.0 ZN A:ZN401 3.3 23.1 1.0 CG A:ASP70 3.4 26.8 1.0 OD2 A:ASP70 3.5 27.7 1.0 CB A:HIS85 3.7 21.5 1.0 NE2 A:HIS31 4.0 23.6 1.0 NE2 A:HIS85 4.1 18.3 1.0 NH1 A:ARG73 4.1 31.8 1.0 CG A:HIS147 4.1 18.6 1.0 ND1 A:HIS147 4.2 22.0 1.0 CD2 A:HIS85 4.2 18.9 1.0 CE1 A:HIS157 4.3 23.4 1.0 CB A:ASP151 4.3 19.9 1.0 CE1 A:HIS31 4.5 26.9 1.0 CA A:HIS85 4.6 19.9 1.0 O A:TRP26 4.8 23.1 1.0 CB A:ASP70 4.8 25.4 1.0 CE1 A:PHE148 4.9 19.9 1.0 ND1 A:HIS157 4.9 24.9 1.0 O A:HIS85 5.0 20.5 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of Fully Glycosylated 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 Fully Glycosylated Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:31.8 occ:1.00 O1 A:SO4601 2.1 35.2 1.0 NE2 A:HIS181 2.1 33.8 1.0 OD2 A:ASP185 2.1 30.6 1.0 NE2 A:HIS157 2.1 24.3 1.0 OD1 A:ASP185 2.6 31.1 1.0 CG A:ASP185 2.7 29.2 1.0 CE1 A:HIS157 2.9 23.4 1.0 CD2 A:HIS181 3.0 24.6 1.0 CD2 A:HIS157 3.1 21.6 1.0 CE1 A:HIS181 3.1 28.3 1.0 S A:SO4601 3.3 38.7 1.0 O2 A:SO4601 3.6 36.6 1.0 ND1 A:HIS157 4.0 24.9 1.0 O4 A:SO4601 4.1 51.2 1.0 CG A:HIS157 4.2 21.7 1.0 CG A:HIS181 4.2 29.1 1.0 CB A:ASP185 4.2 27.9 1.0 ND1 A:HIS181 4.2 28.5 1.0 O3 A:SO4601 4.3 34.3 1.0 N A:TRP26 4.3 22.4 1.0 O A:HOH814 4.4 41.3 1.0 O A:HOH701 4.4 16.4 1.0 NE2 A:GLN154 4.6 24.1 1.0 ZN A:ZN401 4.8 23.1 1.0 O A:TRP26 4.8 23.1 1.0 C A:TRP26 4.9 28.6 1.0 CA A:TRP26 4.9 26.7 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