Nickel in PDB 5y2j: Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66

The structure of Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66, PDB code: 5y2j was solved by K.Suguna, S.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.47 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.610, 69.570, 69.570, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.8

The binding sites of Nickel atom in the Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66 (pdb code 5y2j). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66, PDB code: 5y2j:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66


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 the Oligomerization Domain of NSP4 From Rotavirus Strain MF66 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:30.3 occ:1.00 O B:HOH301 2.0 44.8 1.0 O B:GLN137 2.1 52.5 1.0 NE2 A:HIS131 2.2 45.4 1.0 CE1 A:HIS131 2.9 47.8 1.0 C B:GLN137 3.2 55.4 1.0 CD2 A:HIS131 3.3 44.0 1.0 CA B:GLN137 3.9 52.3 1.0 CB B:ILE142 4.1 30.0 1.0 ND1 A:HIS131 4.1 44.3 1.0 N B:SER138 4.1 60.0 1.0 N B:GLY140 4.3 64.3 1.0 CG A:HIS131 4.3 44.0 1.0 CA B:SER138 4.3 69.1 1.0 CB B:GLN137 4.4 56.7 1.0 CE D:MET106 4.6 50.3 1.0 CA B:GLY140 4.6 63.3 1.0 C B:SER138 4.7 65.8 1.0 CE D:MET99 4.7 52.6 1.0 N B:THR139 4.8 63.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Oligomerization Domain of NSP4 From Rotavirus Strain MF66 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:84.0 occ:1.00 O D:HOH212 2.2 69.1 1.0 OD1 D:ASP114 2.2 70.9 1.0 NE2 B:HIS131 2.3 57.0 1.0 O D:HOH204 2.6 61.0 1.0 CD2 B:HIS131 3.1 57.4 1.0 CG D:ASP114 3.1 81.9 1.0 OD2 D:ASP114 3.4 85.8 1.0 CE1 B:HIS131 3.4 52.5 1.0 O D:HOH213 4.2 68.8 1.0 CG B:HIS131 4.3 52.3 1.0 ND1 B:HIS131 4.4 51.5 1.0 CB D:ASP114 4.5 61.0 1.0 CD1 D:LEU110 4.9 57.5 1.0

S.Kumar, R.Ramappa, K.Pamidimukkala, C.D.Rao, K.Suguna. New Tetrameric Forms of the Rotavirus NSP4 with Antiparallel Helices. Arch. Virol. V. 163 1531 2018.
ISSN: ISSN 1432-8798
PubMed: 29455326
DOI: 10.1007/S00705-018-3753-6