Sodium 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
Zinc	(Zn)	6 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Mutant N211D of Bifunctional Nuclease TBN1 From Solanum Lycopersicum (Tomato), PDB code: 4dj4:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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 B:Na602 b:50.9 occ:1.00 O B:HOH743 2.3 44.8 1.0 O B:HOH736 2.6 44.5 1.0 NE2 B:HIS103 2.6 47.8 1.0 O B:HOH741 2.7 41.1 1.0 O B:ARG100 2.9 41.5 1.0 CE1 B:HIS103 3.4 47.2 1.0 CD2 B:HIS103 3.6 48.2 1.0 C B:ARG100 4.0 44.6 1.0 CA B:ARG100 4.5 45.1 1.0 ND1 B:HIS103 4.5 48.3 1.0 CG B:HIS103 4.7 47.3 1.0 O B:GLU99 4.8 38.8 1.0 CG B:ARG100 4.9 44.9 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