Zinc in PDB 1itq: Human Renal Dipeptidase

All present enzymatic activity of Human Renal Dipeptidase:
3.4.13.19;

The structure of Human Renal Dipeptidase, PDB code: 1itq was solved by Y.Nitanai, Y.Satow, H.Adachi, M.Tsujimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.948, 81.213, 57.164, 90.00, 96.73, 90.00
R / Rfree (%)	18.1 / 25.8

The binding sites of Zinc atom in the Human Renal Dipeptidase (pdb code 1itq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Renal Dipeptidase, PDB code: 1itq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Renal Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Renal Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.4 occ:1.00 NE2 A:HIS20 2.0 0.0 1.0 O A:HOH421 2.2 25.9 1.0 OD1 A:ASP22 2.3 31.1 1.0 OE1 A:GLU125 2.4 30.7 1.0 O A:HOH422 2.8 28.5 1.0 OD2 A:ASP22 2.8 20.0 1.0 CG A:ASP22 2.9 22.5 1.0 CE1 A:HIS20 2.9 8.0 1.0 CD A:GLU125 3.1 26.2 1.0 CD2 A:HIS20 3.2 6.8 1.0 OE2 A:GLU125 3.2 35.5 1.0 ZN A:ZN402 3.4 19.2 1.0 OG A:SER66 3.9 12.9 1.0 OD1 A:ASP288 3.9 22.9 1.0 ND1 A:HIS20 4.1 2.2 1.0 NE2 A:HIS219 4.1 0.0 1.0 CG A:HIS20 4.2 3.7 1.0 CB A:ASP22 4.3 8.8 1.0 CG A:GLU125 4.5 22.9 1.0 CB A:SER66 4.6 2.9 1.0 CE1 A:HIS219 4.6 7.1 1.0 CD2 A:HIS219 4.8 7.2 1.0 CG A:TYR68 4.9 6.4 1.0 NE2 A:HIS152 4.9 7.3 1.0 CB A:TYR68 4.9 5.5 1.0 CB A:GLU125 4.9 10.6 1.0 CG A:ASP288 5.0 18.5 1.0 CD2 A:TYR68 5.0 4.1 1.0

Zinc binding site 2 out of 4 in the Human Renal Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Renal Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:19.2 occ:1.00 NE2 A:HIS219 2.1 0.0 1.0 OE2 A:GLU125 2.3 35.5 1.0 NE2 A:HIS198 2.3 5.6 1.0 O A:HOH423 2.6 14.4 1.0 O A:HOH422 2.8 28.5 1.0 CD2 A:HIS219 2.9 7.2 1.0 CD2 A:HIS198 3.1 8.0 1.0 CE1 A:HIS219 3.2 7.1 1.0 CD A:GLU125 3.4 26.2 1.0 ZN A:ZN401 3.4 22.4 1.0 CE1 A:HIS198 3.4 8.4 1.0 OE1 A:GLU125 3.8 30.7 1.0 NE2 A:HIS20 3.9 0.0 1.0 NH1 A:ARG230 4.0 8.0 1.0 CG A:HIS219 4.1 8.7 1.0 NE2 A:HIS152 4.2 7.3 1.0 ND1 A:HIS219 4.2 3.6 1.0 O A:HOH421 4.3 25.9 1.0 O A:HOH1195 4.3 49.6 1.0 CG A:HIS198 4.3 9.7 1.0 OD2 A:ASP288 4.4 24.3 1.0 CE1 A:HIS20 4.4 8.0 1.0 ND1 A:HIS198 4.5 11.0 1.0 CD2 A:HIS20 4.5 6.8 1.0 CD2 A:HIS152 4.5 7.6 1.0 OD1 A:ASP288 4.5 22.9 1.0 CG A:GLU125 4.6 22.9 1.0 CG A:ASP288 4.8 18.5 1.0 CZ A:ARG230 4.8 10.4 1.0 NE A:ARG230 4.9 2.0 1.0

Zinc binding site 3 out of 4 in the Human Renal Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Renal Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn411 b:23.1 occ:1.00 NE2 B:HIS20 2.0 0.0 1.0 O B:HOH431 2.1 10.4 1.0 OD1 B:ASP22 2.2 29.0 1.0 OE1 B:GLU125 2.4 26.0 1.0 O B:HOH432 2.7 25.7 1.0 CE1 B:HIS20 2.8 2.2 1.0 OD2 B:ASP22 2.8 23.9 1.0 CG B:ASP22 2.9 24.3 1.0 CD2 B:HIS20 3.2 6.8 1.0 CD B:GLU125 3.2 24.4 1.0 OE2 B:GLU125 3.4 34.9 1.0 ZN B:ZN412 3.4 20.0 1.0 OD1 B:ASP288 3.8 21.9 1.0 OG B:SER66 3.9 9.2 1.0 ND1 B:HIS20 4.0 0.0 1.0 NE2 B:HIS219 4.1 0.0 1.0 CG B:HIS20 4.2 0.0 1.0 CB B:ASP22 4.4 16.5 1.0 CB B:SER66 4.5 5.9 1.0 CG B:GLU125 4.6 24.3 1.0 CE1 B:HIS219 4.7 5.5 1.0 CD2 B:HIS219 4.7 7.2 1.0 O B:HOH1061 4.8 19.0 1.0 CG B:ASP288 4.8 14.6 1.0 CG B:TYR68 4.9 6.5 1.0 CB B:TYR68 4.9 4.2 1.0 O B:HOH1137 4.9 32.1 1.0 NE2 B:HIS152 5.0 12.9 1.0

Zinc binding site 4 out of 4 in the Human Renal Dipeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Renal Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn412 b:20.0 occ:1.00 NE2 B:HIS219 2.0 0.0 1.0 OE2 B:GLU125 2.2 34.9 1.0 NE2 B:HIS198 2.3 7.3 1.0 O B:HOH433 2.8 11.0 1.0 CD2 B:HIS219 3.0 7.2 1.0 O B:HOH432 3.0 25.7 1.0 CE1 B:HIS219 3.0 5.5 1.0 CD2 B:HIS198 3.0 4.8 1.0 CD B:GLU125 3.3 24.4 1.0 ZN B:ZN411 3.4 23.1 1.0 CE1 B:HIS198 3.4 9.0 1.0 OE1 B:GLU125 3.8 26.0 1.0 NE2 B:HIS152 4.0 12.9 1.0 NE2 B:HIS20 4.0 0.0 1.0 NH1 B:ARG230 4.0 5.9 1.0 ND1 B:HIS219 4.1 6.2 1.0 CG B:HIS219 4.1 3.6 1.0 CD2 B:HIS152 4.3 16.3 1.0 O B:HOH1061 4.3 19.0 1.0 CG B:HIS198 4.3 7.2 1.0 CE1 B:HIS20 4.4 2.2 1.0 OD2 B:ASP288 4.4 18.5 1.0 ND1 B:HIS198 4.5 8.4 1.0 O B:HOH431 4.5 10.4 1.0 OD1 B:ASP288 4.6 21.9 1.0 CG B:GLU125 4.6 24.3 1.0 CD2 B:HIS20 4.6 6.8 1.0 CG B:ASP288 4.8 14.6 1.0 CZ B:ARG230 4.8 10.1 1.0 NE B:ARG230 4.8 2.7 1.0

Y.Nitanai, Y.Satow, H.Adachi, M.Tsujimoto. Crystal Structure of Human Renal Dipeptidase Involved in Beta-Lactam Hydrolysis J.Mol.Biol. V. 321 177 2002.
ISSN: ISSN 0022-2836
PubMed: 12144777
DOI: 10.1016/S0022-2836(02)00632-0