Zinc in PDB 5b2e: N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition)

The structure of N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition), PDB code: 5b2e 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)	37.89 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.435, 77.435, 229.573, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 22.1

The binding sites of Zinc atom in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-Containing Condition) (pdb code 5b2e). 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 (Acetate-Containing Condition), PDB code: 5b2e:
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 (Acetate-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 (Acetate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:18.0 occ:1.00 O72 A:MQG302 1.9 19.9 1.0 NE2 A:HIS155 2.0 13.3 1.0 OD2 A:ASP47 2.0 13.3 1.0 ND1 A:HIS44 2.0 19.2 1.0 CG A:ASP47 2.7 19.2 1.0 CE1 A:HIS155 2.9 20.2 1.0 OD1 A:ASP47 2.9 18.6 1.0 P7 A:MQG302 3.0 18.1 1.0 CE1 A:HIS44 3.0 17.1 1.0 O71 A:MQG302 3.0 18.3 1.0 CD2 A:HIS155 3.1 16.9 1.0 CG A:HIS44 3.1 14.3 1.0 CB A:HIS44 3.5 15.7 1.0 CB A:PRO43 3.9 14.2 1.0 NE2 C:HIS264 4.0 18.7 1.0 N A:HIS44 4.0 17.3 1.0 ND1 A:HIS155 4.0 16.2 1.0 NE2 A:HIS44 4.1 17.2 1.0 CG A:HIS155 4.2 14.6 1.0 CB A:ASP47 4.2 18.1 1.0 N2 A:MQG302 4.2 16.6 1.0 CD2 A:HIS44 4.2 16.8 1.0 C2 A:MQG302 4.2 19.6 1.0 C8 A:MQG302 4.3 18.4 1.0 CE1 C:HIS264 4.4 20.5 1.0 CA A:HIS44 4.4 17.3 1.0 O3 A:MQG302 4.4 18.4 1.0 CG A:PRO43 4.5 16.3 1.0 CD A:PRO43 4.7 17.2 1.0 OD1 A:ASP46 4.7 20.3 1.0 C A:PRO43 4.8 15.9 1.0 CA A:PRO43 4.9 16.8 1.0 C3 A:MQG302 5.0 16.9 1.0

Zinc binding site 2 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-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 (Acetate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:20.4 occ:1.00 O72 B:MQG302 1.7 21.4 1.0 OD2 B:ASP47 1.9 17.9 1.0 ND1 B:HIS44 2.1 21.4 1.0 NE2 B:HIS155 2.1 21.6 1.0 CG B:ASP47 2.7 15.5 1.0 OD1 B:ASP47 2.8 18.2 1.0 P7 B:MQG302 2.8 20.8 1.0 O71 B:MQG302 2.9 18.6 1.0 CE1 B:HIS44 3.0 22.0 1.0 CE1 B:HIS155 3.1 17.6 1.0 CD2 B:HIS155 3.1 21.6 1.0 CG B:HIS44 3.2 22.5 1.0 CB B:HIS44 3.5 18.8 1.0 NE2 A:HIS264 4.0 23.5 1.0 N B:HIS44 4.0 19.9 1.0 CB B:PRO43 4.1 16.9 1.0 N2 B:MQG302 4.1 17.8 1.0 CB B:ASP47 4.2 17.6 1.0 C2 B:MQG302 4.2 22.8 1.0 NE2 B:HIS44 4.2 19.6 1.0 C8 B:MQG302 4.2 20.8 1.0 ND1 B:HIS155 4.2 22.1 1.0 CG B:HIS155 4.3 19.6 1.0 CD2 B:HIS44 4.3 22.6 1.0 CE1 A:HIS264 4.3 25.6 1.0 CG B:PRO43 4.3 20.6 1.0 CA B:HIS44 4.4 20.6 1.0 O3 B:MQG302 4.4 19.4 1.0 OD1 B:ASP46 4.8 23.5 1.0 CD B:PRO43 4.8 17.1 1.0 C B:PRO43 4.8 21.0 1.0 CA B:PRO43 5.0 19.4 1.0

Zinc binding site 3 out of 3 in the N,N'-Diacetylchitobiose Deacetylase From Pyrococcus Horikoshii Complexed with Its Inhibitor Mpg (Acetate-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 (Acetate-Containing Condition) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:22.7 occ:1.00 ND1 C:HIS44 1.9 16.1 1.0 NE2 C:HIS155 2.0 17.8 1.0 O72 C:MQG302 2.0 21.0 1.0 OD2 C:ASP47 2.1 23.1 1.0 CG C:ASP47 2.8 22.8 1.0 CE1 C:HIS44 2.9 19.9 1.0 CE1 C:HIS155 2.9 19.9 1.0 O71 C:MQG302 2.9 22.1 1.0 OD1 C:ASP47 2.9 19.1 1.0 P7 C:MQG302 3.0 23.5 1.0 CG C:HIS44 3.0 17.2 1.0 CD2 C:HIS155 3.0 22.2 1.0 CB C:HIS44 3.4 19.2 1.0 CB C:PRO43 3.9 18.0 1.0 NE2 B:HIS264 4.0 25.4 1.0 N C:HIS44 4.0 17.9 1.0 NE2 C:HIS44 4.0 19.9 1.0 ND1 C:HIS155 4.1 19.9 1.0 CD2 C:HIS44 4.1 20.0 1.0 CG C:HIS155 4.1 14.9 1.0 N2 C:MQG302 4.2 20.2 1.0 CB C:ASP47 4.2 20.4 1.0 C2 C:MQG302 4.3 23.1 1.0 CA C:HIS44 4.3 19.3 1.0 C8 C:MQG302 4.3 20.5 1.0 CE1 B:HIS264 4.4 21.4 1.0 CG C:PRO43 4.4 16.9 1.0 O3 C:MQG302 4.5 26.1 1.0 CD C:PRO43 4.7 18.0 1.0 C C:PRO43 4.7 18.0 1.0 OD1 C:ASP46 4.8 24.8 1.0 CA C:PRO43 4.9 17.9 1.0 C3 C:MQG302 4.9 21.1 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