Zinc in PDB 7yh4: Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2)

All present enzymatic activity of Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2):
3.4.13.4;

The structure of Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2), PDB code: 7yh4 was solved by K.Chandravanshi, N.K.Gaur, A.Kumar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 2.03
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.834, 112.888, 123.217, 90, 90, 90
R / Rfree (%)	19.7 / 23.7

The binding sites of Zinc atom in the Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2) (pdb code 7yh4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2), PDB code: 7yh4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2)


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 Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.6 occ:0.44 OE2 A:GLU165 2.0 46.2 1.0 O A:HOH621 2.1 53.6 1.0 SG A:CYS124 2.3 57.0 1.0 NE2 A:HIS377 2.3 57.6 1.0 ZN A:ZN502 2.9 45.4 0.5 CD A:GLU165 2.9 44.7 1.0 CB A:CYS124 3.0 53.4 1.0 OE1 A:GLU165 3.1 48.4 1.0 CE1 A:HIS377 3.2 59.4 1.0 CD2 A:HIS377 3.3 59.8 1.0 NE2 A:HIS126 3.8 35.0 1.0 OE1 A:GLU164 4.1 44.1 1.0 CE1 A:HIS126 4.3 36.9 1.0 CG A:GLU165 4.3 39.5 1.0 ND1 A:HIS377 4.3 55.8 1.0 O A:HOH642 4.4 46.7 1.0 CG A:HIS377 4.4 57.4 1.0 CA A:CYS124 4.4 43.5 1.0 O A:HOH627 4.5 63.7 1.0 NE2 A:HIS189 4.5 57.5 1.0 CD1 A:LEU117 4.7 43.7 1.0 CD2 A:HIS126 4.7 35.5 1.0 O A:HOH604 4.8 48.2 1.0 CE1 A:HIS189 4.9 58.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2)


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 Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:45.4 occ:0.50 O A:HOH621 2.1 53.6 1.0 NE2 A:HIS189 2.2 57.5 1.0 O A:HOH604 2.2 48.2 1.0 NE2 A:HIS126 2.2 35.0 1.0 SG A:CYS124 2.8 57.0 1.0 ZN A:ZN501 2.9 44.6 0.4 CE1 A:HIS189 3.1 58.3 1.0 CE1 A:HIS126 3.2 36.9 1.0 CD2 A:HIS189 3.2 56.9 1.0 CD2 A:HIS126 3.3 35.5 1.0 OE1 A:GLU164 3.6 44.1 1.0 OE2 A:GLU165 3.6 46.2 1.0 CB A:CYS124 3.9 53.4 1.0 CD A:GLU164 4.0 41.4 1.0 OE1 A:GLU113 4.1 41.4 1.0 ND1 A:HIS189 4.2 58.0 1.0 ND1 A:HIS126 4.3 37.8 1.0 CG A:HIS189 4.3 54.7 1.0 OE2 A:GLU164 4.3 43.5 1.0 CG A:HIS126 4.4 36.1 1.0 CD A:GLU165 4.5 44.7 1.0 CD1 A:ILE129 4.5 36.3 1.0 O A:CYS124 4.6 42.5 1.0 CG A:GLU164 4.9 36.5 1.0 OE1 A:GLU165 5.0 48.4 1.0 O A:HOH609 5.0 44.9 1.0

K.Chandravanshi, N.K.Gaur, A.Kumar, R.D.Makde. Crystal Structure of Human Cytosolic Beta-Alanyl Lysine Dipeptidase (PM20D2) To Be Published.