Zinc in PDB 2p50: Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn

All present enzymatic activity of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn:
3.5.1.25;

The structure of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn, PDB code: 2p50 was solved by A.A.Fedorov, E.V.Fedorov, R.S.Hall, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.96 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.183, 117.992, 265.604, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.7

The binding sites of Zinc atom in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn (pdb code 2p50). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn, PDB code: 2p50:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:32.6 occ:1.00 OE1 A:GLU131 2.1 33.2 1.0 NE2 A:HIS195 2.2 22.6 1.0 NE2 A:HIS216 2.3 24.5 1.0 O A:HOH690 2.4 43.9 1.0 CD A:GLU131 2.8 28.7 1.0 CD2 A:HIS195 2.9 22.7 1.0 OE2 A:GLU131 3.0 27.4 1.0 CD2 A:HIS216 3.2 24.6 1.0 CE1 A:HIS216 3.3 23.9 1.0 CE1 A:HIS195 3.3 22.1 1.0 NE2 A:GLN59 3.8 27.7 1.0 O A:HOH624 4.0 23.1 1.0 CG A:GLU131 4.2 30.0 1.0 CE1 A:HIS143 4.2 30.6 1.0 CG A:HIS195 4.2 23.9 1.0 ND1 A:HIS195 4.3 21.7 1.0 CG A:HIS216 4.3 24.4 1.0 ND1 A:HIS216 4.4 26.3 1.0 OD1 A:ASP273 4.4 31.3 1.0 CG2 A:THR215 4.5 23.6 1.0 NE2 A:HIS143 4.7 30.4 1.0 OD2 A:ASP273 4.8 28.7 1.0 CD A:GLN59 4.9 28.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:38.1 occ:1.00 NE2 B:HIS195 2.3 22.5 1.0 OE1 B:GLU131 2.3 29.3 1.0 NE2 B:HIS216 2.3 22.8 1.0 O B:HOH696 2.3 30.9 1.0 CD B:GLU131 2.9 20.2 1.0 CD2 B:HIS195 3.0 22.0 1.0 OE2 B:GLU131 3.0 25.6 1.0 CD2 B:HIS216 3.2 22.0 1.0 CE1 B:HIS216 3.4 22.2 1.0 CE1 B:HIS195 3.4 21.0 1.0 NE2 B:GLN59 3.9 25.4 1.0 O B:HOH630 4.0 28.7 1.0 NE2 B:HIS143 4.1 34.5 1.0 CG B:HIS195 4.2 22.6 1.0 OD1 B:ASP273 4.3 24.0 1.0 CG B:GLU131 4.3 24.7 1.0 CG B:HIS216 4.4 23.1 1.0 ND1 B:HIS195 4.4 19.7 1.0 ND1 B:HIS216 4.4 25.1 1.0 CG2 B:THR215 4.5 21.0 1.0 CD2 B:HIS143 4.9 32.6 1.0 CD B:GLN59 5.0 30.0 1.0 CE1 B:HIS143 5.0 32.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:49.2 occ:1.00 OE1 C:GLU131 2.1 30.5 1.0 NE2 C:HIS195 2.3 27.1 1.0 NE2 C:HIS216 2.4 26.3 1.0 O C:HOH688 2.7 28.9 1.0 CD C:GLU131 3.0 32.2 1.0 CD2 C:HIS216 3.2 25.6 1.0 CE1 C:HIS195 3.2 26.1 1.0 OE2 C:GLU131 3.2 38.0 1.0 CD2 C:HIS195 3.3 25.8 1.0 CE1 C:HIS216 3.6 27.6 1.0 NE2 C:GLN59 4.0 28.8 1.0 CE1 C:HIS143 4.1 41.6 1.0 OD1 C:ASP273 4.3 32.5 1.0 O C:HOH684 4.3 25.2 1.0 ND1 C:HIS195 4.4 27.3 1.0 CG C:GLU131 4.4 31.1 1.0 CG C:HIS216 4.4 27.6 1.0 CG C:HIS195 4.5 27.9 1.0 ND1 C:HIS216 4.6 28.1 1.0 CG2 C:THR215 4.8 17.8 1.0 OD2 C:ASP273 4.8 32.2 1.0 NE2 C:HIS143 4.9 41.1 1.0 CG C:ASP273 4.9 31.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase Liganded with Zn within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:41.5 occ:1.00 OE1 D:GLU131 2.1 33.4 1.0 NE2 D:HIS195 2.3 19.2 1.0 NE2 D:HIS216 2.3 29.1 1.0 O D:HOH679 2.7 38.0 1.0 CD D:GLU131 3.0 33.1 1.0 CD2 D:HIS216 3.1 28.3 1.0 CD2 D:HIS195 3.2 18.1 1.0 CE1 D:HIS195 3.2 15.9 1.0 OE2 D:GLU131 3.3 35.5 1.0 O D:HOH678 3.3 44.5 1.0 CE1 D:HIS216 3.4 30.5 1.0 NE2 D:GLN59 3.9 33.4 1.0 OD1 D:ASP273 4.1 34.5 1.0 NE2 D:HIS143 4.3 39.2 1.0 CG D:HIS216 4.3 27.9 1.0 ND1 D:HIS195 4.4 17.6 1.0 CG D:HIS195 4.4 19.0 1.0 CG D:GLU131 4.4 32.2 1.0 ND1 D:HIS216 4.5 30.0 1.0 CG2 D:THR215 4.6 22.6 1.0 OD2 D:ASP273 4.7 36.7 1.0 CG D:ASP273 4.8 34.0 1.0 CD D:GLN59 4.8 32.6 1.0 CE1 D:HIS143 5.0 39.1 1.0

R.S.Hall, S.Brown, A.A.Fedorov, E.V.Fedorov, C.Xu, P.C.Babbitt, S.C.Almo, F.M.Raushel. Structural Diversity Within the Mononuclear and Binuclear Active Sites of N-Acetyl-D-Glucosamine-6-Phosphate Deacetylase. Biochemistry V. 46 7953 2007.
ISSN: ISSN 0006-2960
PubMed: 17567048
DOI: 10.1021/BI700544C