Atomistry » Vanadium » PDB 4zi4-6raj » 5dmp
Atomistry »
  Vanadium »
    PDB 4zi4-6raj »
      5dmp »

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

Protein crystallography data

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

Other elements in 5dmp:

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

Magnesium (Mg) 1 atom

Vanadium Binding Sites:

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 5dmp

Go back to Vanadium Binding Sites List in 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

Reference:

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
Page generated: Thu Oct 29 07:05:46 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy