Zinc in PDB 6dq3: Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate

The structure of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate, PDB code: 6dq3 was solved by J.Li, N.Korotkova, K.V.Korotkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.69 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.160, 78.430, 138.070, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.6

The binding sites of Zinc atom in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate (pdb code 6dq3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate, PDB code: 6dq3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:33.1 occ:1.00 OD1 A:ASP168 2.1 31.7 1.0 NE2 A:HIS227 2.1 31.3 1.0 NE2 A:HIS223 2.2 28.8 1.0 OXT A:ACT401 2.2 30.7 1.0 O A:HOH524 2.4 30.9 1.0 O A:ACT401 2.4 30.4 1.0 C A:ACT401 2.6 29.9 1.0 CE1 A:HIS227 3.0 31.0 1.0 CG A:ASP168 3.0 36.9 1.0 CD2 A:HIS227 3.1 30.0 1.0 CD2 A:HIS223 3.1 26.1 1.0 HE1 A:HIS227 3.2 37.3 1.0 CE1 A:HIS223 3.2 27.4 1.0 HD2 A:HIS223 3.3 31.3 1.0 HD2 A:HIS227 3.3 36.1 1.0 OD2 A:ASP168 3.3 32.2 1.0 HE1 A:HIS223 3.4 32.9 1.0 HB3 A:ASP167 3.5 37.3 1.0 HA A:PRO263 3.5 25.6 1.0 H A:SER264 3.8 30.8 1.0 HD11 A:ILE193 3.9 36.5 1.0 CH3 A:ACT401 4.0 28.8 1.0 HE2 A:HIS105 4.1 50.5 1.0 ND1 A:HIS227 4.1 32.7 1.0 CG A:HIS227 4.2 29.7 1.0 ND1 A:HIS223 4.3 29.3 1.0 CG A:HIS223 4.3 26.7 1.0 HB3 A:PRO263 4.3 30.3 1.0 CB A:ASP167 4.3 31.0 1.0 H2 A:ACT401 4.3 34.6 1.0 HB2 A:ASP167 4.3 37.3 1.0 HA A:ASP168 4.3 32.1 1.0 CB A:ASP168 4.4 28.9 1.0 CA A:PRO263 4.5 21.3 1.0 H3 A:ACT401 4.5 34.6 1.0 N A:SER264 4.5 25.7 1.0 H1 A:ACT401 4.6 34.6 1.0 H A:ASP168 4.7 35.0 1.0 N A:ASP168 4.7 29.1 1.0 CA A:ASP168 4.7 26.7 1.0 CD1 A:ILE193 4.8 30.4 1.0 NE2 A:HIS105 4.8 42.1 1.0 CB A:PRO263 4.9 25.2 1.0 HB3 A:ASP168 4.9 34.7 1.0 HD1 A:HIS227 4.9 39.3 1.0 HG3 A:PRO263 4.9 30.4 1.0 HB2 A:ASP168 4.9 34.7 1.0 HD2 A:HIS105 5.0 51.1 1.0

Zinc binding site 2 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:35.2 occ:1.00 OE1 A:GLU231 1.9 36.7 1.0 OD1 B:ASP269 2.1 34.1 1.0 CD A:GLU231 2.6 39.5 1.0 OE2 A:GLU231 2.7 34.6 1.0 CG B:ASP269 2.8 33.6 1.0 OD2 B:ASP269 2.8 30.1 1.0 H B:THR270 3.7 31.2 1.0 OG1 B:THR270 3.9 30.1 1.0 HG1 B:THR270 3.9 36.1 1.0 HB2 B:ASN268 4.0 34.8 1.0 CG A:GLU231 4.0 39.3 1.0 H A:TYR267 4.0 33.3 1.0 HB3 A:ARG266 4.0 38.5 1.0 H B:ASP269 4.1 30.2 1.0 HD22 B:ASN268 4.1 46.5 1.0 HA A:ARG266 4.2 31.4 1.0 HG3 A:GLU231 4.2 47.2 1.0 HG2 A:ARG266 4.2 44.5 1.0 O A:TYR267 4.2 25.9 1.0 ND2 B:ASN268 4.3 38.7 1.0 CB B:ASP269 4.3 27.1 1.0 N B:THR270 4.4 26.0 1.0 HB2 A:GLU231 4.6 43.7 1.0 HD21 B:ASN268 4.6 46.5 1.0 HG2 A:GLU231 4.6 47.2 1.0 HB B:THR270 4.6 33.8 1.0 N B:ASP269 4.6 25.3 1.0 HD3 A:ARG266 4.6 50.5 1.0 CG B:ASN268 4.7 28.2 1.0 HB3 A:GLU231 4.7 43.7 1.0 O B:HOH594 4.7 35.2 1.0 N A:TYR267 4.7 27.7 1.0 CB A:ARG266 4.7 32.1 1.0 CB A:GLU231 4.7 36.4 1.0 HB2 B:ASP269 4.7 32.6 1.0 CB B:THR270 4.8 28.1 1.0 CB B:ASN268 4.8 28.9 1.0 HB3 B:ASP269 4.8 32.6 1.0 CG A:ARG266 4.9 37.0 1.0 CA A:ARG266 4.9 26.1 1.0 CA B:ASP269 4.9 27.9 1.0

Zinc binding site 3 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:41.4 occ:1.00 OE2 A:GLU114 1.9 45.7 1.0 NE2 A:HIS108 2.1 41.9 1.0 OXT A:ACT405 2.3 51.2 1.0 O A:ACT405 2.7 50.3 1.0 CD A:GLU114 2.7 42.9 1.0 C A:ACT405 2.8 52.3 1.0 OE1 A:GLU114 2.9 42.8 1.0 CE1 A:HIS108 3.0 40.4 1.0 HD13 A:ILE121 3.1 51.9 1.0 HE1 A:HIS108 3.1 48.5 1.0 CD2 A:HIS108 3.2 40.4 1.0 HD2 A:HIS108 3.4 48.6 1.0 HD11 A:ILE121 3.5 51.9 1.0 CD1 A:ILE121 3.7 43.2 1.0 ND1 A:HIS108 4.1 39.4 1.0 CG A:GLU114 4.2 40.3 1.0 HD12 A:ILE121 4.2 51.9 1.0 CH3 A:ACT405 4.2 53.1 1.0 CG A:HIS108 4.2 39.3 1.0 H A:SER111 4.3 43.4 1.0 HG2 A:GLU114 4.4 48.4 1.0 HG3 A:GLU114 4.5 48.4 1.0 HA A:MET110 4.5 45.1 1.0 H2 A:ACT405 4.6 63.8 1.0 H1 A:ACT405 4.7 63.8 1.0 HG21 A:ILE121 4.7 37.9 1.0 HB3 A:SER111 4.8 48.9 1.0 HG12 A:ILE121 4.8 47.7 1.0 H3 A:ACT405 4.8 63.8 1.0 HD1 A:HIS108 4.9 47.3 1.0 CG1 A:ILE121 4.9 39.7 1.0 HG A:SER111 5.0 52.1 1.0

Zinc binding site 4 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:35.7 occ:1.00 OE1 B:GLU231 2.0 39.8 1.0 OD1 A:ASP269 2.1 29.7 1.0 O A:HOH628 2.2 32.1 1.0 CD B:GLU231 2.6 40.6 1.0 OE2 B:GLU231 2.6 39.4 1.0 OD2 A:ASP269 2.8 29.2 1.0 CG A:ASP269 2.8 32.0 1.0 H A:THR270 3.7 31.1 1.0 OG1 A:THR270 3.9 32.9 1.0 H B:TYR267 3.9 30.8 1.0 HG1 A:THR270 3.9 39.5 1.0 HB2 A:ASN268 4.0 33.9 1.0 HB3 B:ARG266 4.0 35.3 1.0 CG B:GLU231 4.1 42.7 1.0 HG2 B:ARG266 4.1 38.8 1.0 H A:ASP269 4.1 33.5 1.0 O B:HOH553 4.2 42.5 1.0 O B:TYR267 4.2 27.8 1.0 HA B:ARG266 4.2 27.5 1.0 HD22 A:ASN268 4.2 41.1 1.0 CB A:ASP269 4.3 27.5 1.0 ND2 A:ASN268 4.4 34.2 1.0 HG3 B:GLU231 4.4 51.2 1.0 N A:THR270 4.4 25.9 1.0 HB2 B:GLU231 4.5 45.7 1.0 HB A:THR270 4.6 37.1 1.0 HD21 A:ASN268 4.6 41.1 1.0 HG2 B:GLU231 4.6 51.2 1.0 N B:TYR267 4.6 25.6 1.0 N A:ASP269 4.6 27.9 1.0 CG A:ASN268 4.7 26.2 1.0 HB3 B:GLU231 4.7 45.7 1.0 O B:HOH564 4.7 34.1 1.0 CB B:ARG266 4.7 29.4 1.0 CB B:GLU231 4.7 38.1 1.0 HD3 B:ARG266 4.7 51.2 1.0 HB3 A:ASP269 4.7 33.0 1.0 CB A:THR270 4.7 30.9 1.0 HB2 A:ASP269 4.8 33.0 1.0 CB A:ASN268 4.8 28.2 1.0 CG B:ARG266 4.8 32.3 1.0 CA B:ARG266 4.9 23.1 1.0 CA A:ASP269 4.9 29.8 1.0

Zinc binding site 5 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.0 occ:1.00 OD1 B:ASP168 2.1 29.2 1.0 NE2 B:HIS227 2.1 29.4 1.0 NE2 B:HIS223 2.2 29.1 1.0 OXT B:ACT401 2.2 30.2 1.0 O B:HOH524 2.4 33.1 1.0 O B:ACT401 2.5 24.6 1.0 C B:ACT401 2.7 29.8 1.0 CG B:ASP168 3.1 31.3 1.0 CE1 B:HIS227 3.1 29.9 1.0 CD2 B:HIS227 3.1 28.8 1.0 CE1 B:HIS223 3.1 29.6 1.0 CD2 B:HIS223 3.2 27.8 1.0 HD2 B:HIS227 3.3 34.6 1.0 HE1 B:HIS223 3.3 35.6 1.0 HE1 B:HIS227 3.3 35.9 1.0 HD2 B:HIS223 3.3 33.4 1.0 OD2 B:ASP168 3.3 31.2 1.0 HB3 B:ASP167 3.5 36.5 1.0 HA B:PRO263 3.6 35.2 1.0 H B:SER264 3.8 33.5 1.0 HD11 B:ILE193 3.9 38.8 1.0 HE2 B:HIS105 4.0 70.6 1.0 CH3 B:ACT401 4.1 30.1 1.0 ND1 B:HIS227 4.2 33.5 1.0 ND1 B:HIS223 4.2 30.0 1.0 CG B:HIS227 4.3 31.3 1.0 CG B:HIS223 4.3 29.4 1.0 HA B:ASP168 4.3 31.2 1.0 HB3 B:PRO263 4.4 33.1 1.0 CB B:ASP167 4.4 30.4 1.0 H3 B:ACT401 4.4 36.1 1.0 CB B:ASP168 4.4 28.2 1.0 HB2 B:ASP167 4.5 36.5 1.0 CA B:PRO263 4.5 29.3 1.0 N B:SER264 4.6 27.9 1.0 H2 B:ACT401 4.6 36.1 1.0 H B:ASP168 4.6 31.9 1.0 H1 B:ACT401 4.7 36.1 1.0 N B:ASP168 4.7 26.5 1.0 CA B:ASP168 4.7 26.0 1.0 CD1 B:ILE193 4.8 32.3 1.0 NE2 B:HIS105 4.8 58.8 1.0 HB3 B:ASP168 4.9 33.9 1.0 HD13 B:ILE193 4.9 38.8 1.0 CB B:PRO263 4.9 27.5 1.0 HG3 B:PRO263 5.0 34.1 1.0 HB2 B:ASP168 5.0 33.9 1.0

Zinc binding site 6 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:40.5 occ:1.00 OE2 B:GLU114 2.0 47.2 1.0 O B:HOH609 2.1 36.0 1.0 NE2 B:HIS108 2.2 48.0 1.0 OXT B:ACT407 2.3 42.7 1.0 O B:ACT407 2.5 45.9 1.0 C B:ACT407 2.7 47.0 1.0 CD B:GLU114 2.7 45.4 1.0 OE1 B:GLU114 2.8 40.7 1.0 CE1 B:HIS108 3.0 47.0 1.0 HE1 B:HIS108 3.1 56.5 1.0 CD2 B:HIS108 3.2 46.9 1.0 HD13 B:ILE121 3.3 42.0 1.0 HD2 B:HIS108 3.5 56.3 1.0 HD11 B:ILE121 3.7 42.0 1.0 CD1 B:ILE121 3.9 35.0 1.0 ND1 B:HIS108 4.1 45.3 1.0 CH3 B:ACT407 4.1 48.8 1.0 CG B:GLU114 4.1 40.9 1.0 CG B:HIS108 4.3 43.5 1.0 H B:SER111 4.3 42.4 1.0 HG2 B:GLU114 4.4 49.1 1.0 HG3 B:GLU114 4.4 49.1 1.0 HD12 B:ILE121 4.5 42.0 1.0 H1 B:ACT407 4.5 58.6 1.0 HA B:MET110 4.5 41.5 1.0 H3 B:ACT407 4.7 58.6 1.0 H2 B:ACT407 4.7 58.6 1.0 HB3 B:SER111 4.7 45.8 1.0 HG12 B:ILE121 4.8 43.2 1.0 HG21 B:ILE121 4.8 37.3 1.0 HD1 B:HIS108 4.9 54.4 1.0

Zinc binding site 7 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:42.1 occ:1.00 N1 B:IMD408 1.8 40.2 1.0 OE2 B:GLU312 1.9 49.4 1.0 OE2 B:GLU137 2.0 49.4 1.0 CD B:GLU137 2.8 45.8 1.0 C2 B:IMD408 2.9 44.2 1.0 CD B:GLU312 2.9 46.8 1.0 C5 B:IMD408 2.9 42.1 1.0 HE3 B:LYS133 2.9 65.2 1.0 OE1 B:GLU137 3.0 47.1 1.0 H2 B:IMD408 3.1 53.1 1.0 H5 B:IMD408 3.1 50.5 1.0 OE1 B:GLU312 3.2 49.4 1.0 HD22 B:LEU315 3.4 53.1 1.0 HZ1 B:LYS133 3.6 72.5 1.0 CE B:LYS133 3.8 54.3 1.0 HD23 B:LEU315 3.9 53.1 1.0 C4 B:IMD408 4.0 43.1 1.0 N3 B:IMD408 4.0 40.6 1.0 NZ B:LYS133 4.0 60.4 1.0 HE2 B:LYS133 4.0 65.2 1.0 HZ2 B:LYS133 4.1 72.5 1.0 CD2 B:LEU315 4.1 44.2 1.0 CG B:GLU137 4.2 41.3 1.0 CG B:GLU312 4.2 44.4 1.0 HG2 B:GLU312 4.3 53.3 1.0 HA B:GLU312 4.4 46.0 1.0 HG3 B:GLU137 4.4 49.6 1.0 HB2 B:LEU315 4.5 44.8 1.0 HB3 B:LEU315 4.6 44.8 1.0 HG2 B:GLU137 4.6 49.6 1.0 HG3 B:LYS133 4.6 48.3 1.0 O B:HOH512 4.6 34.9 1.0 HD21 B:LEU315 4.7 53.1 1.0 HG3 B:GLU312 4.8 53.3 1.0 HZ3 B:LYS133 4.9 72.5 1.0 CD B:LYS133 4.9 49.3 1.0 CB B:LEU315 5.0 37.3 1.0

Zinc binding site 8 out of 8 in the Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:39.7 occ:1.00 N3 B:IMD408 2.1 40.6 1.0 OE2 B:GLU319 2.2 54.6 1.0 O B:ACT406 2.3 49.1 1.0 OE1 B:GLU319 2.7 48.0 1.0 CD B:GLU319 2.8 47.9 1.0 C B:ACT406 2.9 47.6 1.0 OXT B:ACT406 2.9 47.5 1.0 C2 B:IMD408 3.1 44.2 1.0 C4 B:IMD408 3.1 43.1 1.0 H4 B:IMD408 3.3 51.8 1.0 H2 B:IMD408 3.3 53.1 1.0 HZ1 B:LYS160 3.5 56.9 1.0 O B:HOH532 3.8 43.8 1.0 O B:HOH512 3.8 34.9 1.0 O B:HOH501 3.9 32.8 1.0 HZ2 B:LYS160 4.0 56.9 1.0 NZ B:LYS160 4.2 47.4 1.0 CG B:GLU319 4.3 37.6 1.0 N1 B:IMD408 4.3 40.2 1.0 CH3 B:ACT406 4.3 48.1 1.0 C5 B:IMD408 4.3 42.1 1.0 HG2 B:GLU319 4.5 45.1 1.0 HE3 B:LYS160 4.5 53.6 1.0 HG3 B:GLU319 4.7 45.1 1.0 H1 B:ACT406 4.7 57.8 1.0 H2 B:ACT406 4.7 57.8 1.0 HZ3 B:LYS160 4.8 56.9 1.0 CE B:LYS160 4.9 44.6 1.0 H3 B:ACT406 5.0 57.8 1.0

J.Li, N.Korotkova, K.V.Korotkov. Streptococcus Pyogenes Deacetylase Pdi in Complex with Acetate To Be Published.