Nickel in PDB 6zdc: Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel

Enzymatic activity of Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel

All present enzymatic activity of Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel:
3.2.1.130;

Protein crystallography data

The structure of Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel, PDB code: 6zdc was solved by L.F.Sobala, P.Z.Fernandes, Z.Hakki, A.J.Thompson, J.D.Howe, M.Hill, N.Zitzmann, S.Davies, Z.Stamataki, T.D.Butters, D.S.Alonzi, S.J.Williams, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.10 / 2.25
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.467, 86.535, 135.916, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel (pdb code 6zdc). 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 Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel, PDB code: 6zdc:

Nickel binding site 1 out of 1 in 6zdc

Go back to Nickel Binding Sites List in 6zdc
Nickel binding site 1 out of 1 in the Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Catalytic Domain of Human Endo-Alpha-Mannosidase Manea in Complex with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:88.3
occ:1.00
 ND1 A:HIS96 2.4 88.6 1.0
CG A:HIS96 3.2 89.8 1.0
CB A:HIS96 3.3 95.1 1.0
O A:HOH770 3.4 57.1 1.0
CE1 A:HIS96 3.4 86.1 1.0
N A:HIS96 4.0 0.2 1.0
CA A:HIS96 4.2 0.2 1.0
CD2 A:HIS96 4.4 83.5 1.0
NE2 A:HIS96 4.5 78.8 1.0
N A:MET97 4.7 0.7 1.0
C A:HIS96 4.8 0.8 1.0

Reference:

L.F.Sobala, P.Z.Fernandes, Z.Hakki, A.J.Thompson, J.D.Howe, M.Hill, N.Zitzmann, S.Davies, Z.Stamataki, T.D.Butters, D.S.Alonzi, S.J.Williams, G.J.Davies. Structure of Human Endo-Alpha-1,2-Mannosidase (Manea), An Antiviral Host-Glycosylation Target. Proc.Natl.Acad.Sci.Usa V. 117 29595 2020.
ISSN: ESSN 1091-6490
PubMed: 33154157
DOI: 10.1073/PNAS.2013620117
Page generated: Wed Dec 16 01:59:06 2020

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