Zinc in PDB 5b2f: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition)

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition), PDB code: 5b2f was solved by T.Nakamura, M.Niiyama, K.Ida, K.Uegaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.46 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.821, 77.821, 229.230, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 27

The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition) (pdb code 5b2f). 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 Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition), PDB code: 5b2f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition)


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 Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.3 occ:1.00 O72 A:MQG302 1.9 25.8 1.0 ND1 A:HIS44 2.0 28.6 1.0 NE2 A:HIS155 2.1 18.4 1.0 OD2 A:ASP47 2.1 17.5 1.0 CG A:ASP47 2.8 24.6 1.0 CE1 A:HIS44 2.9 26.6 1.0 OD1 A:ASP47 2.9 26.0 1.0 CE1 A:HIS155 3.0 24.9 1.0 O71 A:MQG302 3.0 24.6 1.0 P7 A:MQG302 3.0 29.6 1.0 CD2 A:HIS155 3.1 22.5 1.0 CG A:HIS44 3.1 22.1 1.0 CB A:HIS44 3.6 22.5 1.0 CB A:PRO43 3.9 20.1 1.0 NE2 C:HIS264 3.9 25.6 1.0 NE2 A:HIS44 4.0 28.7 1.0 N A:HIS44 4.1 23.9 1.0 ND1 A:HIS155 4.2 21.0 1.0 CD2 A:HIS44 4.2 22.3 1.0 CG A:HIS155 4.2 25.0 1.0 CE1 C:HIS264 4.3 28.7 1.0 N2 A:MQG302 4.3 25.1 1.0 C2 A:MQG302 4.3 28.6 1.0 CB A:ASP47 4.3 22.8 1.0 C8 A:MQG302 4.4 27.0 1.0 O3 A:MQG302 4.4 26.1 1.0 CA A:HIS44 4.4 24.2 1.0 CG A:PRO43 4.5 21.9 1.0 CD A:PRO43 4.7 22.3 1.0 OD1 A:ASP46 4.7 27.9 1.0 C A:PRO43 4.8 24.3 1.0 CA A:PRO43 4.9 23.0 1.0 C3 A:MQG302 5.0 27.1 1.0

Zinc binding site 2 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition)


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 Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:28.9 occ:1.00 O72 B:MQG302 1.8 35.5 1.0 OD2 B:ASP47 2.0 25.9 1.0 ND1 B:HIS44 2.2 27.7 1.0 NE2 B:HIS155 2.2 33.1 1.0 CG B:ASP47 2.6 25.8 1.0 OD1 B:ASP47 2.7 25.8 1.0 P7 B:MQG302 2.8 29.9 1.0 O71 B:MQG302 2.8 28.6 1.0 CE1 B:HIS44 3.1 31.1 1.0 CE1 B:HIS155 3.2 23.8 1.0 CG B:HIS44 3.2 27.6 1.0 CD2 B:HIS155 3.2 30.5 1.0 CB B:HIS44 3.5 28.5 1.0 N B:HIS44 4.0 28.7 1.0 NE2 A:HIS264 4.1 33.0 1.0 CB B:PRO43 4.1 26.4 1.0 N2 B:MQG302 4.1 25.0 1.0 C8 B:MQG302 4.2 27.1 1.0 CB B:ASP47 4.2 26.8 1.0 C2 B:MQG302 4.2 29.1 1.0 NE2 B:HIS44 4.3 26.8 1.0 O3 B:MQG302 4.3 32.3 1.0 ND1 B:HIS155 4.3 32.1 1.0 CE1 A:HIS264 4.3 29.9 1.0 CD2 B:HIS44 4.3 29.2 1.0 CA B:HIS44 4.3 26.8 1.0 CG B:HIS155 4.4 29.3 1.0 CG B:PRO43 4.5 26.6 1.0 CD B:PRO43 4.7 25.2 1.0 OD1 B:ASP46 4.7 29.3 1.0 C B:PRO43 4.8 28.8 1.0 C3 B:MQG302 4.9 26.1 1.0

Zinc binding site 3 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition)


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 Horikoshii Complexed with Its Inhibitor Mpg (Phosphate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:32.2 occ:1.00 ND1 C:HIS44 1.9 26.8 1.0 NE2 C:HIS155 2.0 28.6 1.0 OD2 C:ASP47 2.0 35.1 1.0 O72 C:MQG302 2.1 28.5 1.0 O71 C:MQG302 2.7 29.0 1.0 CG C:ASP47 2.8 30.9 1.0 CE1 C:HIS44 2.9 28.4 1.0 OD1 C:ASP47 2.9 28.4 1.0 P7 C:MQG302 2.9 32.8 1.0 CD2 C:HIS155 3.0 26.8 1.0 CE1 C:HIS155 3.0 28.7 1.0 CG C:HIS44 3.0 25.7 1.0 CB C:HIS44 3.4 25.2 1.0 NE2 C:HIS44 4.0 32.0 1.0 NE2 B:HIS264 4.1 37.2 1.0 CD2 C:HIS44 4.1 26.9 1.0 N C:HIS44 4.1 25.5 1.0 ND1 C:HIS155 4.1 23.8 1.0 CG C:HIS155 4.1 25.1 1.0 O3 C:MQG302 4.2 36.2 1.0 CB C:PRO43 4.2 27.5 1.0 CB C:ASP47 4.2 30.5 1.0 C8 C:MQG302 4.2 32.3 1.0 N2 C:MQG302 4.2 33.9 1.0 C2 C:MQG302 4.3 32.7 1.0 CA C:HIS44 4.4 25.6 1.0 CE1 B:HIS264 4.4 36.2 1.0 CG C:PRO43 4.4 24.1 1.0 CD C:PRO43 4.7 27.4 1.0 OD1 C:ASP46 4.7 37.3 1.0 C C:PRO43 4.8 25.5 1.0 C3 C:MQG302 4.9 32.1 1.0 O C:HIS44 5.0 26.4 1.0

T.Nakamura, Y.Yonezawa, Y.Tsuchiya, M.Niiyama, K.Ida, M.Oshima, J.Morita, K.Uegaki. Substrate Recognition of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii J.Struct.Biol. V. 195 286 2016.
ISSN: ESSN 1095-8657
PubMed: 27456364
DOI: 10.1016/J.JSB.2016.07.015