Zinc in PDB 3dlj: Crystal Structure of Human Carnosine Dipeptidase 1

All present enzymatic activity of Crystal Structure of Human Carnosine Dipeptidase 1:
3.4.13.20;

The structure of Crystal Structure of Human Carnosine Dipeptidase 1, PDB code: 3dlj was solved by A.Dong, E.Dobrovetsky, A.Seitova, H.He, W.Tempel, I.Kozieradzki, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.M.Edwards, A.Bochkarev, D.Cossar, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.91 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.106, 75.613, 103.716, 90.00, 109.79, 90.00
R / Rfree (%)	20 / 25.4

The binding sites of Zinc atom in the Crystal Structure of Human Carnosine Dipeptidase 1 (pdb code 3dlj). 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 Human Carnosine Dipeptidase 1, PDB code: 3dlj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Carnosine Dipeptidase 1


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 Human Carnosine Dipeptidase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:34.9 occ:1.00 NE2 A:HIS452 2.0 35.7 1.0 OE1 A:GLU174 2.1 38.3 1.0 OD2 A:ASP139 2.2 35.5 1.0 OE2 A:GLU174 2.7 40.7 1.0 CD A:GLU174 2.7 39.7 1.0 UNK A:UNX2004 2.8 2.0 0.0 CG A:ASP139 2.9 33.4 1.0 CE1 A:HIS452 3.0 33.9 1.0 OD1 A:ASP139 3.1 31.6 1.0 CD2 A:HIS452 3.1 35.1 1.0 ZN A:ZN2002 3.5 30.3 1.0 OE2 A:GLU173 3.8 39.0 1.0 O A:HOH2035 3.9 25.0 1.0 ND1 A:HIS452 4.1 33.1 1.0 CG A:GLU174 4.2 39.5 1.0 CG A:HIS452 4.2 35.3 1.0 CB A:ASP139 4.4 31.5 1.0 CE1 A:HIS106 4.4 26.0 1.0 NE2 A:HIS106 4.5 26.1 1.0 CG A:GLN110 4.6 35.3 1.0 CD A:GLU173 4.7 39.6 1.0 O A:HOH2024 4.8 24.5 1.0 OE1 A:GLU173 4.9 41.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Carnosine Dipeptidase 1


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 Human Carnosine Dipeptidase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:30.3 occ:1.00 OD2 A:ASP202 1.8 39.2 1.0 OD1 A:ASP139 2.0 31.6 1.0 NE2 A:HIS106 2.0 26.1 1.0 CG A:ASP202 2.7 38.7 1.0 UNK A:UNX2004 2.8 2.0 0.0 OD1 A:ASP202 2.8 38.2 1.0 CE1 A:HIS106 2.9 26.0 1.0 CD2 A:HIS106 3.0 26.2 1.0 CG A:ASP139 3.1 33.4 1.0 ZN A:ZN2001 3.5 34.9 1.0 OE2 A:GLU173 3.5 39.0 1.0 OD2 A:ASP139 3.7 35.5 1.0 CD A:GLU173 4.0 39.6 1.0 OE1 A:GLU174 4.0 38.3 1.0 CB A:ASN140 4.0 29.8 1.0 ND1 A:HIS106 4.0 29.5 1.0 CB A:ASP202 4.1 36.4 1.0 CG A:HIS106 4.1 29.6 1.0 OE1 A:GLU173 4.3 41.2 1.0 CB A:ASP139 4.3 31.5 1.0 O A:HOH2094 4.4 42.2 1.0 CG A:ASN140 4.4 29.5 1.0 CA A:ASP139 4.5 31.8 1.0 C A:ASP139 4.6 31.1 1.0 ND2 A:ASN140 4.8 27.8 1.0 CG A:GLU173 4.8 39.5 1.0 N A:ASN140 4.8 30.6 1.0 CD A:GLU174 4.8 39.7 1.0 CA A:ASN140 4.9 30.1 1.0 OD1 A:ASN140 5.0 29.5 1.0 O A:ASP139 5.0 31.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Carnosine Dipeptidase 1


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 Human Carnosine Dipeptidase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:26.8 occ:1.00 OD2 B:ASP139 2.0 36.4 1.0 OE1 B:GLU174 2.0 30.5 1.0 NE2 B:HIS452 2.1 30.6 1.0 OE2 B:GLU174 2.5 32.1 1.0 CD B:GLU174 2.6 31.9 1.0 CG B:ASP139 2.9 33.1 1.0 UNK B:UNX2003 3.0 2.0 0.0 CE1 B:HIS452 3.1 28.7 1.0 CD2 B:HIS452 3.1 32.2 1.0 OD1 B:ASP139 3.1 32.5 1.0 ZN B:ZN2002 3.4 29.9 1.0 O B:HOH2017 4.0 23.0 1.0 CG B:GLU174 4.1 32.2 1.0 OE1 B:GLU173 4.2 39.5 1.0 ND1 B:HIS452 4.2 26.9 1.0 CG B:HIS452 4.2 29.8 1.0 CG B:GLN110 4.2 33.4 1.0 CB B:ASP139 4.3 32.5 1.0 NE2 A:HIS235 4.4 31.9 1.0 CE1 B:HIS106 4.4 24.7 1.0 NE2 B:HIS106 4.5 25.6 1.0 NE2 B:GLN110 4.7 40.2 1.0 CD2 A:HIS235 4.7 31.8 1.0 UNK A:UNX2006 4.8 2.0 0.0 CD B:GLN110 4.9 36.0 1.0 O B:HOH2026 4.9 27.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Carnosine Dipeptidase 1


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 Human Carnosine Dipeptidase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:29.9 occ:1.00 OD1 B:ASP139 1.9 32.5 1.0 NE2 B:HIS106 2.0 25.6 1.0 OD2 B:ASP202 2.2 39.8 1.0 OD1 B:ASP202 2.3 39.9 1.0 CG B:ASP202 2.6 37.4 1.0 CE1 B:HIS106 2.9 24.7 1.0 CG B:ASP139 3.0 33.1 1.0 CD2 B:HIS106 3.1 27.9 1.0 UNK B:UNX2003 3.3 2.0 0.0 ZN B:ZN2001 3.4 26.8 1.0 OD2 B:ASP139 3.5 36.4 1.0 OE1 B:GLU173 3.6 39.5 1.0 OE1 B:GLU174 3.9 30.5 1.0 CD B:GLU173 4.0 40.1 1.0 ND1 B:HIS106 4.0 29.0 1.0 CB B:ASN140 4.1 30.2 1.0 CB B:ASP202 4.1 36.0 1.0 OE2 B:GLU173 4.1 42.9 1.0 CG B:HIS106 4.2 27.2 1.0 CB B:ASP139 4.3 32.5 1.0 CD B:GLU174 4.4 31.9 1.0 O B:HOH2074 4.5 33.9 1.0 CA B:ASP139 4.5 32.5 1.0 CG B:ASN140 4.6 30.6 1.0 OE2 B:GLU174 4.7 32.1 1.0 C B:ASP139 4.7 32.3 1.0 O B:ASP202 4.8 36.4 1.0 CG B:GLU173 4.9 35.6 1.0 N B:ASN140 4.9 31.4 1.0 CA B:ASN140 5.0 30.7 1.0 CA B:ASP202 5.0 36.0 1.0

E.Dobrovetsky, A.Dong, A.Seitova, H.He, W.Tempel, I.Kozieradzki, C.H.Arrowsmith, J.Weigelt, C.Bountra, A.M.Edwards, A.Bochkarev, D.Cossar. Crystal Structure of Human Carnosine Dipeptidase 1. To Be Published.