Zinc in PDB 3dfm: The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2

The structure of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2, PDB code: 3dfm was solved by Y.Zou, J.S.Brunzelle, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.309, 64.324, 49.875, 90.00, 98.90, 90.00
R / Rfree (%)	19.8 / 24.1

The binding sites of Zinc atom in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 (pdb code 3dfm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2, PDB code: 3dfm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.9 occ:1.00 ND1 A:HIS16 1.9 22.9 1.0 NE2 A:HIS164 2.0 24.2 1.0 OD2 A:ASP19 2.2 27.0 1.0 O3 A:SO4300 2.3 20.7 1.0 OD1 A:ASP19 2.6 31.7 1.0 CG A:ASP19 2.7 28.1 1.0 CE1 A:HIS16 2.9 25.0 1.0 CE1 A:HIS164 2.9 24.4 1.0 CG A:HIS16 3.0 23.1 1.0 O2 A:SO4300 3.0 26.1 1.0 CD2 A:HIS164 3.1 24.8 1.0 S A:SO4300 3.1 14.3 1.0 CB A:HIS16 3.4 24.1 1.0 O1 A:SO4300 3.9 26.2 1.0 NE2 A:HIS16 4.0 25.4 1.0 ND1 A:HIS164 4.1 25.4 1.0 CD2 A:HIS16 4.1 22.6 1.0 OH A:TYR190 4.1 31.1 1.0 CG A:HIS164 4.2 25.8 1.0 O4 A:SO4300 4.2 28.5 1.0 N A:HIS16 4.2 24.4 1.0 CB A:ASP19 4.2 26.4 1.0 CB A:PRO15 4.4 24.8 1.0 CA A:HIS16 4.4 24.2 1.0 OD1 A:ASP18 4.5 30.9 1.0 CE2 A:TYR190 4.6 30.0 1.0 CG A:PRO15 4.7 25.1 1.0 CZ A:TYR190 4.8 31.0 1.0 O A:HOH408 5.0 30.3 1.0 O A:HOH430 5.0 38.1 1.0

Zinc binding site 2 out of 5 in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:34.6 occ:1.00 OD2 A:ASP163 1.9 32.4 1.0 OD1 A:ASP97 1.9 30.8 1.0 NE2 A:HIS16 2.0 25.4 1.0 O2 A:SO4301 2.1 22.1 0.7 CD2 A:HIS16 2.9 22.6 1.0 CG A:ASP97 2.9 29.2 1.0 CG A:ASP163 2.9 31.2 1.0 CE1 A:HIS16 3.1 25.0 1.0 S A:SO4301 3.2 13.4 0.7 OD2 A:ASP97 3.3 29.6 1.0 CB A:ASP163 3.3 29.9 1.0 O3 A:SO4301 3.5 26.4 0.7 CE1 A:HIS161 3.6 33.9 1.0 N A:SER98 3.8 27.4 1.0 OG A:SER98 3.8 30.2 1.0 OD1 A:ASP163 4.0 31.3 1.0 CG A:HIS16 4.1 23.1 1.0 CB A:SER98 4.1 29.1 1.0 ND1 A:HIS16 4.1 22.9 1.0 O1 A:SO4301 4.1 24.4 0.7 O4 A:SO4301 4.2 23.1 0.7 CB A:ASP97 4.2 27.6 1.0 NE2 A:HIS161 4.2 31.9 1.0 ND1 A:HIS161 4.5 31.9 1.0 CA A:ASP97 4.5 27.2 1.0 CA A:SER98 4.6 29.0 1.0 C A:ASP97 4.7 26.9 1.0 CA A:ASP163 4.8 29.4 1.0 CB A:PHE44 4.9 25.5 1.0 CG A:PHE44 4.9 24.6 1.0

Zinc binding site 3 out of 5 in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:61.9 occ:1.00 NE2 A:HIS90 2.2 30.0 1.0 CE1 A:HIS90 3.1 29.5 1.0 CD2 A:HIS90 3.2 28.8 1.0 O A:HOH419 3.9 42.8 1.0 CD1 A:ILE80 4.0 29.0 1.0 ND1 A:HIS90 4.2 31.6 1.0 CG A:HIS90 4.3 29.0 1.0 CG1 A:ILE80 4.7 27.4 1.0

Zinc binding site 4 out of 5 in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:46.7 occ:1.00 OE2 A:GLU186 2.0 31.8 1.0 NE2 A:HIS250 2.1 46.4 1.0 CE1 A:HIS250 2.4 46.8 1.0 O A:HOH426 2.5 42.1 1.0 CD A:GLU186 2.8 30.4 1.0 OE1 A:GLU186 2.9 30.6 1.0 ND2 A:ASN254 3.0 62.1 1.0 CD2 A:HIS250 3.5 46.2 1.0 ND1 A:HIS250 3.7 46.2 1.0 CG A:ASN254 4.1 61.3 1.0 CG A:HIS250 4.2 46.0 1.0 CG A:GLU186 4.2 30.0 1.0 OD1 A:ASN254 4.4 60.2 1.0 OG1 A:THR263 4.5 32.2 1.0 CB A:ALA191 4.7 33.5 1.0 O A:HOH446 4.9 34.0 1.0

Zinc binding site 5 out of 5 in the The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of the Zinc Inhibited Form of Teicoplanin Deacetylase ORF2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:51.9 occ:1.00 O A:HOH489 2.1 30.7 1.0 NE2 A:HIS124 2.2 37.6 1.0 OD1 A:ASP129 2.3 36.2 1.0 O A:HOH490 2.3 22.8 1.0 OD2 A:ASP129 2.5 36.8 1.0 CG A:ASP129 2.7 35.4 1.0 CE1 A:HIS124 3.2 37.8 1.0 CD2 A:HIS124 3.2 35.1 1.0 CB A:ASP129 4.2 34.6 1.0 ND1 A:HIS124 4.3 35.6 1.0 CG A:HIS124 4.4 35.1 1.0 O A:HOH491 4.4 36.6 1.0 CA A:ASP129 5.0 34.6 1.0

Y.Zou, J.S.Brunzelle, S.K.Nair. Crystal Structures of Lipoglycopeptide Antibiotic Deacetylases: Implications For the Biosynthesis of A40926 and Teicoplanin. Chem.Biol. V. 15 533 2008.
ISSN: ISSN 1074-5521
PubMed: 18559264
DOI: 10.1016/J.CHEMBIOL.2008.05.009