Zinc in PDB 1itu: Human Renal Dipeptidase Complexed with Cilastatin

All present enzymatic activity of Human Renal Dipeptidase Complexed with Cilastatin:
3.4.13.19;

The structure of Human Renal Dipeptidase Complexed with Cilastatin, PDB code: 1itu 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 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.179, 79.491, 56.951, 90.00, 96.34, 90.00
R / Rfree (%)	18.5 / 25.4

The binding sites of Zinc atom in the Human Renal Dipeptidase Complexed with Cilastatin (pdb code 1itu). 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 Complexed with Cilastatin, PDB code: 1itu:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 Complexed with Cilastatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.3 occ:1.00 NE2 A:HIS20 2.0 4.9 1.0 OD1 A:ASP22 2.1 11.8 1.0 OE1 A:GLU125 2.2 10.9 1.0 O A:HOH421 2.2 23.0 1.0 CG A:ASP22 2.8 13.3 1.0 OD2 A:ASP22 2.9 13.4 1.0 CD A:GLU125 3.0 13.7 1.0 CE1 A:HIS20 3.0 1.9 1.0 CD2 A:HIS20 3.1 4.3 1.0 OE2 A:GLU125 3.2 18.0 1.0 ZN A:ZN402 3.3 15.4 1.0 C1 A:CIL451 3.4 18.5 1.0 C2 A:CIL451 3.6 21.4 1.0 OG A:SER66 3.8 9.8 1.0 OD1 A:ASP288 3.8 11.6 1.0 NE2 A:HIS219 4.0 4.7 1.0 ND1 A:HIS20 4.2 6.6 1.0 C6 A:CIL451 4.2 21.5 1.0 CG A:HIS20 4.2 3.9 1.0 CB A:ASP22 4.2 8.2 1.0 CB A:SER66 4.3 7.8 1.0 CG A:GLU125 4.4 12.2 1.0 O10 A:CIL451 4.5 20.8 1.0 CE1 A:HIS219 4.6 2.3 1.0 C3 A:CIL451 4.7 20.0 1.0 CD2 A:HIS219 4.7 4.6 1.0 CB A:GLU125 4.8 10.3 1.0 CB A:TYR68 4.8 9.6 1.0 N7 A:CIL451 4.8 19.7 1.0 CG A:ASP288 4.9 12.1 1.0 O13 A:CIL451 4.9 9.1 1.0 CG A:TYR68 4.9 10.3 1.0

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


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 Complexed with Cilastatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:15.4 occ:1.00 NE2 A:HIS219 2.1 4.7 1.0 O A:HOH421 2.1 23.0 1.0 OE2 A:GLU125 2.2 18.0 1.0 NE2 A:HIS198 2.2 8.6 1.0 O13 A:CIL451 2.3 9.1 1.0 CD2 A:HIS219 3.0 4.6 1.0 CE1 A:HIS219 3.1 2.3 1.0 CD2 A:HIS198 3.1 7.3 1.0 C11 A:CIL451 3.2 10.8 1.0 O10 A:CIL451 3.2 20.8 1.0 CD A:GLU125 3.2 13.7 1.0 CE1 A:HIS198 3.3 5.0 1.0 ZN A:ZN401 3.3 13.3 1.0 C6 A:CIL451 3.5 21.5 1.0 OE1 A:GLU125 3.6 10.9 1.0 NH1 A:ARG230 3.9 9.4 1.0 N7 A:CIL451 3.9 19.7 1.0 O12 A:CIL451 3.9 12.6 1.0 NE2 A:HIS20 3.9 4.9 1.0 C8 A:CIL451 4.0 16.7 1.0 NE2 A:HIS152 4.2 3.5 1.0 C2 A:CIL451 4.2 21.4 1.0 CG A:HIS219 4.2 5.5 1.0 OD2 A:ASP288 4.2 10.9 1.0 OD1 A:ASP288 4.2 11.6 1.0 ND1 A:HIS219 4.2 7.0 1.0 CG A:HIS198 4.3 8.1 1.0 CD2 A:HIS152 4.4 5.3 1.0 ND1 A:HIS198 4.4 9.4 1.0 CD2 A:HIS20 4.4 4.3 1.0 C1 A:CIL451 4.5 18.5 1.0 CG A:GLU125 4.5 12.2 1.0 CE1 A:HIS20 4.5 1.9 1.0 CG A:ASP288 4.6 12.1 1.0 CZ A:ARG230 4.7 5.5 1.0 OD1 A:ASP22 4.9 11.8 1.0 NE A:ARG230 4.9 6.7 1.0

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


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 Complexed with Cilastatin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn411 b:16.6 occ:1.00 NE2 B:HIS20 2.0 9.2 1.0 OD1 B:ASP22 2.1 18.0 1.0 OE1 B:GLU125 2.1 17.8 1.0 O B:HOH422 2.2 26.7 1.0 CG B:ASP22 2.9 14.2 1.0 CD2 B:HIS20 3.0 11.2 1.0 OD2 B:ASP22 3.0 10.5 1.0 CD B:GLU125 3.0 19.1 1.0 CE1 B:HIS20 3.0 8.8 1.0 OE2 B:GLU125 3.2 20.0 1.0 ZN B:ZN412 3.3 19.3 1.0 C1 B:CIL452 3.4 24.4 1.0 C2 B:CIL452 3.7 25.4 1.0 OG B:SER66 3.7 5.8 1.0 OD1 B:ASP288 3.8 13.3 1.0 NE2 B:HIS219 3.9 6.3 1.0 CG B:HIS20 4.1 6.3 1.0 ND1 B:HIS20 4.1 8.2 1.0 C6 B:CIL452 4.2 28.0 1.0 CB B:ASP22 4.3 6.5 1.0 CB B:SER66 4.3 7.2 1.0 CG B:GLU125 4.4 18.0 1.0 O10 B:CIL452 4.4 30.3 1.0 CE1 B:HIS219 4.6 7.0 1.0 CD2 B:HIS219 4.6 9.0 1.0 C3 B:CIL452 4.7 24.2 1.0 CB B:GLU125 4.7 16.3 1.0 CB B:TYR68 4.8 12.0 1.0 CG B:TYR68 4.9 13.7 1.0 N7 B:CIL452 5.0 29.1 1.0 CG B:ASP288 5.0 12.9 1.0 O13 B:CIL452 5.0 23.6 1.0

Zinc binding site 4 out of 4 in the Human Renal Dipeptidase Complexed with Cilastatin


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 Complexed with Cilastatin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn412 b:19.3 occ:1.00 NE2 B:HIS219 2.1 6.3 1.0 OE2 B:GLU125 2.2 20.0 1.0 O B:HOH422 2.2 26.7 1.0 NE2 B:HIS198 2.2 7.3 1.0 O13 B:CIL452 2.4 23.6 1.0 CD2 B:HIS219 3.0 9.0 1.0 CD2 B:HIS198 3.1 8.2 1.0 O10 B:CIL452 3.1 30.3 1.0 CE1 B:HIS219 3.2 7.0 1.0 CD B:GLU125 3.2 19.1 1.0 C11 B:CIL452 3.3 29.4 1.0 CE1 B:HIS198 3.3 7.0 1.0 ZN B:ZN411 3.3 16.6 1.0 OE1 B:GLU125 3.6 17.8 1.0 C6 B:CIL452 3.6 28.0 1.0 NH1 B:ARG230 3.9 16.5 1.0 O12 B:CIL452 3.9 30.4 1.0 NE2 B:HIS20 3.9 9.2 1.0 N7 B:CIL452 4.1 29.1 1.0 NE2 B:HIS152 4.1 5.5 1.0 C8 B:CIL452 4.2 30.1 1.0 OD1 B:ASP288 4.2 13.3 1.0 CG B:HIS219 4.2 10.8 1.0 CD2 B:HIS152 4.2 6.2 1.0 ND1 B:HIS219 4.3 10.1 1.0 OD2 B:ASP288 4.3 10.0 1.0 CG B:HIS198 4.3 8.4 1.0 C2 B:CIL452 4.3 25.4 1.0 ND1 B:HIS198 4.4 8.8 1.0 CD2 B:HIS20 4.4 11.2 1.0 C1 B:CIL452 4.5 24.4 1.0 CG B:GLU125 4.5 18.0 1.0 CE1 B:HIS20 4.6 8.8 1.0 CG B:ASP288 4.6 12.9 1.0 CZ B:ARG230 4.8 12.9 1.0 NE B:ARG230 4.9 13.2 1.0 OD1 B:ASP22 5.0 18.0 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