Nickel in PDB 6en3: Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide.

The structure of Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide., PDB code: 6en3 was solved by B.Trastoy, E.H.Klontz, J.Orwenyo, A.Marina, L.X.Wang, E.J.Sundberg, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.04 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.640, 90.080, 104.370, 90.00, 110.44, 90.00
R / Rfree (%)	20.9 / 24

The structure of Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide. also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide. (pdb code 6en3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide., PDB code: 6en3:

Nickel binding site 1 out of 1 in the Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Full Length Endos From Streptococcus Pyogenes in Complex with G2 Oligosaccharide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1302 b:64.9 occ:1.00 O A:PHE422 2.4 56.6 1.0 O A:HOH1407 2.5 64.9 1.0 OE1 A:GLN412 2.7 50.5 1.0 OD2 A:ASP427 2.7 49.2 1.0 O A:HOH1401 2.8 64.9 1.0 O A:HOH1402 2.9 64.9 1.0 CG A:ASP427 3.5 48.3 1.0 C A:PHE422 3.7 57.3 1.0 CD A:GLN412 3.7 50.5 1.0 OD1 A:ASP427 3.8 47.9 1.0 NE2 A:GLN412 4.2 50.7 1.0 OH A:TYR348 4.2 47.9 1.0 CA A:ASN351 4.3 51.2 1.0 CA A:LYS423 4.5 56.7 1.0 N A:LYS423 4.5 58.0 1.0 N A:ASP424 4.5 59.4 1.0 OD1 A:ASN351 4.5 51.1 1.0 CA A:PHE422 4.6 58.7 1.0 O A:GLN419 4.6 69.7 1.0 O A:LYS420 4.7 70.6 1.0 N A:PHE422 4.7 58.9 1.0 CB A:ASP427 4.7 47.7 1.0 O A:ALA352 4.7 53.9 1.0 NE2 A:GLN353 4.7 50.7 1.0 N A:ASN351 4.9 50.4 1.0 C A:ASN351 4.9 51.4 1.0 CB A:PHE422 4.9 59.4 1.0

B.Trastoy, E.Klontz, J.Orwenyo, A.Marina, L.X.Wang, E.J.Sundberg, M.E.Guerin. Structural Basis For the Recognition of Complex-Type N-Glycans By Endoglycosidase S. Nat Commun V. 9 1874 2018.
ISSN: ESSN 2041-1723
PubMed: 29760474
DOI: 10.1038/S41467-018-04300-X