Zinc in PDB 8bgn: N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus

The structure of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus, PDB code: 8bgn was solved by W.Rypniewski, M.Bejger, K.Biniek-Antosiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.30 / 2.76
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.613, 150.613, 72.228, 90, 90, 120
R / Rfree (%)	17.6 / 22.7

The structure of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus (pdb code 8bgn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus, PDB code: 8bgn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:87.1 occ:1.00 OD2 A:ASP43 2.1 79.7 1.0 ND1 A:HIS40 2.1 63.2 1.0 NE2 A:HIS151 2.3 59.9 1.0 O A:HOH417 2.6 53.8 1.0 CG A:ASP43 2.9 61.8 1.0 CE1 A:HIS40 3.0 67.1 1.0 OD1 A:ASP43 3.1 56.4 1.0 CG A:HIS40 3.1 63.0 1.0 CD2 A:HIS151 3.2 63.5 1.0 CE1 A:HIS151 3.4 72.8 1.0 CB A:HIS40 3.5 56.6 1.0 O2 A:EDO302 3.9 103.7 1.0 NE2 B:HIS259 3.9 64.9 1.0 CE1 B:HIS259 3.9 68.2 1.0 N A:HIS40 4.1 50.1 1.0 NE2 A:HIS40 4.2 72.0 1.0 CD2 A:HIS40 4.2 71.3 1.0 C2 A:EDO302 4.2 96.1 1.0 CB A:ASP43 4.3 54.9 1.0 CA A:HIS40 4.4 50.5 1.0 CB A:PRO39 4.4 48.0 1.0 CG A:HIS151 4.4 62.4 1.0 ND1 A:HIS151 4.5 64.6 1.0 OD1 A:ASP42 4.6 59.4 1.0 CG A:PRO39 4.7 49.1 1.0 C A:PRO39 4.9 51.6 1.0 CD A:PRO39 5.0 49.3 1.0

Zinc binding site 2 out of 3 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:97.7 occ:1.00 ND1 B:HIS40 2.0 84.5 1.0 OD2 B:ASP43 2.3 74.2 1.0 NE2 B:HIS151 2.4 96.2 1.0 O B:HOH414 2.8 70.9 1.0 CE1 B:HIS40 2.9 87.2 1.0 CG B:HIS40 3.1 79.4 1.0 CG B:ASP43 3.1 81.8 1.0 CD2 B:HIS151 3.2 88.1 1.0 OD1 B:ASP43 3.3 79.9 1.0 CB B:HIS40 3.5 65.8 1.0 CE1 B:HIS151 3.5 99.8 1.0 CE1 C:HIS259 3.8 103.0 1.0 NE2 C:HIS259 3.8 108.3 1.0 NE2 B:HIS40 4.1 94.6 1.0 CD2 B:HIS40 4.2 91.7 1.0 N B:HIS40 4.2 73.2 1.0 CG B:HIS151 4.4 88.4 1.0 CA B:HIS40 4.4 67.8 1.0 CB B:PRO39 4.5 56.2 1.0 CB B:ASP43 4.5 77.4 1.0 ND1 B:HIS151 4.5 99.4 1.0 OD1 B:ASP42 4.6 70.6 1.0 CG B:PRO39 4.8 58.8 1.0 C B:PRO39 5.0 62.4 1.0

Zinc binding site 3 out of 3 in the N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of N,N-Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:109.6 occ:1.00 OD2 C:ASP43 2.2 83.5 1.0 ND1 C:HIS40 2.2 106.7 1.0 NE2 C:HIS151 2.4 80.9 1.0 CG C:ASP43 2.9 91.3 1.0 OD1 C:ASP43 3.0 108.0 1.0 O A:HOH425 3.1 71.5 1.0 CE1 C:HIS40 3.1 103.0 1.0 CG C:HIS40 3.2 100.4 1.0 CD2 C:HIS151 3.3 87.1 1.0 CE1 C:HIS151 3.4 85.3 1.0 CB C:HIS40 3.5 88.7 1.0 NE2 A:HIS259 3.8 94.2 1.0 CE1 A:HIS259 3.8 81.6 1.0 N C:HIS40 4.2 78.7 1.0 NE2 C:HIS40 4.3 101.6 1.0 CD2 C:HIS40 4.3 100.7 1.0 CB C:ASP43 4.3 86.2 1.0 CA C:HIS40 4.5 81.5 1.0 OD1 C:ASP42 4.5 88.1 1.0 CG C:HIS151 4.5 93.5 1.0 ND1 C:HIS151 4.5 88.8 1.0 CB C:PRO39 4.6 79.3 1.0 CG C:PRO39 4.9 76.5 1.0

K.Biniek-Antosiak, M.Bejger, J.Sliwiak, D.Baranowski, A.S.A.Mohammed, D.I.Svergun, W.Rypniewski. Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase From Pyrococcus Chitonophagus. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36555375
DOI: 10.3390/IJMS232415736