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Magnesium 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:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of the Archaeal Nhej Phosphoesterase From Methanocella Paludicola., PDB code: 5dmp:

Magnesium binding site 1 out of 1 in 5dmp

Go back to Magnesium Binding Sites List in 5dmp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg208

b:76.7
occ:1.00
O A:HOH302 2.3 48.8 1.0
O3 A:VN4209 2.6 58.9 1.0
ND1 A:HIS40 2.9 47.8 1.0
CE1 A:HIS40 3.0 48.6 1.0
V A:VN4209 3.2 64.3 1.0
NE2 A:HIS46 3.4 39.5 1.0
OD2 A:ASP48 3.5 40.3 1.0
O2 A:VN4209 3.8 46.0 1.0
CE1 A:HIS46 3.9 38.1 1.0
OD1 A:ASP48 4.0 40.6 1.0
CA A:GLY99 4.0 44.9 1.0
CG A:HIS40 4.1 37.9 1.0
CG A:ASP48 4.1 38.6 1.0
NE2 A:HIS40 4.1 44.4 1.0
O A:HOH310 4.3 43.9 1.0
N A:GLY99 4.6 47.7 1.0
O A:HOH313 4.6 44.9 1.0
CD2 A:HIS46 4.6 32.2 1.0
CD2 A:HIS40 4.6 43.9 1.0
O1 A:VN4209 4.8 56.1 1.0
CB A:HIS40 4.9 35.5 1.0
C A:GLY99 4.9 41.6 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: Mon Dec 14 20:12:03 2020

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