Nickel in PDB 8jqf: Structure of Cmcbda in Complex with NI2+ and Glycerol

The structure of Structure of Cmcbda in Complex with NI2+ and Glycerol, PDB code: 8jqf was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.67 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.228, 60.017, 86.635, 90, 110.92, 90
R / Rfree (%)	16.1 / 19.6

The binding sites of Nickel atom in the Structure of Cmcbda in Complex with NI2+ and Glycerol (pdb code 8jqf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Cmcbda in Complex with NI2+ and Glycerol, PDB code: 8jqf:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Cmcbda in Complex with NI2+ and Glycerol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Cmcbda in Complex with NI2+ and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:14.2 occ:1.00 OD1 B:ASP22 2.0 14.0 1.0 O4 B:SO4403 2.0 17.6 1.0 NE2 B:HIS72 2.1 13.1 1.0 ND1 B:HIS143 2.1 15.0 1.0 O3 B:GOL401 2.2 15.2 1.0 O3 B:SO4403 2.9 19.6 1.0 CE1 B:HIS143 3.0 16.1 1.0 S B:SO4403 3.1 22.0 1.0 CG B:ASP22 3.1 14.7 1.0 CE1 B:HIS72 3.1 14.8 1.0 CD2 B:HIS72 3.1 13.1 1.0 CG B:HIS143 3.2 14.6 1.0 C3 B:GOL401 3.3 22.7 1.0 OD2 B:ASP22 3.4 14.1 1.0 CB B:HIS143 3.7 13.6 1.0 CA B:HIS143 3.7 14.7 1.0 O2 B:SO4403 4.0 21.7 1.0 O1 B:SO4403 4.0 25.5 1.0 NE2 B:HIS143 4.1 14.3 1.0 CB B:ASP21 4.2 14.5 1.0 N B:MET144 4.2 15.8 1.0 NE2 B:HIS230 4.2 17.0 1.0 ND1 B:HIS72 4.2 13.0 1.0 CG B:HIS72 4.2 12.1 1.0 CD2 B:HIS143 4.3 14.7 1.0 C2 B:GOL401 4.4 25.8 1.0 CB B:ASP22 4.4 12.9 1.0 CD2 B:HIS230 4.5 14.9 1.0 C B:HIS143 4.5 15.2 1.0 N B:ASP22 4.5 12.6 1.0 OD2 B:ASP21 4.7 18.4 1.0 CA B:ASP22 4.7 12.6 1.0 O2 B:GOL401 4.8 20.7 1.0 N B:HIS143 4.8 14.7 1.0 CG B:ASP21 4.8 19.1 1.0 SD B:MET48 4.9 17.1 1.0

Nickel binding site 2 out of 2 in the Structure of Cmcbda in Complex with NI2+ and Glycerol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Cmcbda in Complex with NI2+ and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:27.0 occ:1.00 ND1 A:HIS143 2.1 28.5 1.0 NE2 A:HIS72 2.1 27.9 1.0 OD1 A:ASP22 2.1 23.8 1.0 O2 A:SO4403 2.2 27.8 0.8 O1 A:GOL401 2.3 30.0 1.0 O1 A:SO4403 2.7 31.8 0.8 CE1 A:HIS143 2.8 29.7 1.0 S A:SO4403 3.0 33.6 0.8 CE1 A:HIS72 3.0 27.9 1.0 CG A:ASP22 3.1 22.6 1.0 CD2 A:HIS72 3.2 25.2 1.0 C1 A:GOL401 3.2 35.9 1.0 CG A:HIS143 3.3 29.5 1.0 OD2 A:ASP22 3.3 25.5 1.0 CA A:HIS143 3.8 28.7 1.0 CB A:HIS143 3.9 26.2 1.0 O3 A:SO4403 4.0 39.6 0.8 NE2 A:HIS230 4.0 29.7 1.0 NE2 A:HIS143 4.0 30.0 1.0 O4 A:SO4403 4.1 39.9 0.8 CB A:ASP21 4.1 25.4 1.0 N A:MET144 4.1 29.9 1.0 ND1 A:HIS72 4.2 28.4 1.0 CG A:HIS72 4.3 25.9 1.0 CD2 A:HIS143 4.3 28.0 1.0 CD2 A:HIS230 4.3 26.7 1.0 CB A:ASP22 4.4 20.9 1.0 C A:HIS143 4.5 31.0 1.0 N A:ASP22 4.5 23.2 1.0 C2 A:GOL401 4.5 36.2 1.0 OD2 A:ASP21 4.7 29.9 1.0 O2 A:GOL401 4.7 30.6 1.0 CA A:ASP22 4.7 21.8 1.0 CG A:ASP21 4.8 34.2 1.0 N A:HIS143 4.9 30.0 1.0 SD A:MET48 4.9 26.6 1.0 CE A:MET48 5.0 23.1 1.0

S.Hu, L.Xu, C.Xie, J.Hong. Structural Insights Into the Catalytic Activity of Cyclobacterium Marinum N -Acetylglucosamine Deacetylase. J.Agric.Food Chem. 2023.
ISSN: ESSN 1520-5118
PubMed: 38141024
DOI: 10.1021/ACS.JAFC.3C06146