Vanadium in PDB 5dmp: Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola.

The structure of Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola., PDB code: 5dmp was solved by N.C.Brissett, E.J.Bartlett, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.42 / 1.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.070, 57.070, 105.041, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.5

The structure of Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Vanadium atom in the Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola. (pdb code 5dmp). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total only one binding site of Vanadium was determined in the Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola., PDB code: 5dmp:

Vanadium binding site 1 out of 1 in the Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola.


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola. within 5.0Å range: probe atom residue distance (Å) B Occ A:V209 b:64.3 occ:1.00 V A:VN4209 0.0 64.3 1.0 O3 A:VN4209 1.9 58.9 1.0 O1 A:VN4209 1.9 56.1 1.0 O2 A:VN4209 1.9 46.0 1.0 MG A:MG208 3.2 76.7 1.0 NE2 A:HIS82 3.4 37.6 1.0 NH2 A:ARG50 3.6 28.6 1.0 OH A:TYR86 3.7 35.4 1.0 O A:HOH313 3.8 44.9 1.0 CE1 A:HIS40 4.0 48.6 1.0 CE1 A:HIS82 4.1 34.3 1.0 CA A:GLY99 4.1 44.9 1.0 ND1 A:HIS40 4.2 47.8 1.0 CE2 A:TYR86 4.2 29.2 1.0 CZ A:TYR86 4.2 34.1 1.0 O A:HOH310 4.3 43.9 1.0 CD2 A:HIS82 4.4 37.4 1.0 CZ A:ARG50 4.5 26.0 1.0 OD2 A:ASP48 4.6 40.3 1.0 NH1 A:ARG50 4.6 29.8 1.0 O A:HOH302 4.9 48.8 1.0 N A:GLY99 5.0 47.7 1.0

E.J.Bartlett, N.C.Brissett, P.Plocinski, T.Carlberg, A.J.Doherty. Molecular Basis For Dna Strand Displacement By Nhej Repair Polymerases. Nucleic Acids Res. V. 44 2173 2016.
ISSN: ESSN 1362-4962
PubMed: 26405198
DOI: 10.1093/NAR/GKV965