Zinc in PDB 5jgf: Crystal Structure of MAPE1

All present enzymatic activity of Crystal Structure of MAPE1:
3.4.11.22;

The structure of Crystal Structure of MAPE1, PDB code: 5jgf was solved by N.N.Noda, W.Adachi, F.Inagaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.49 / 1.83
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	140.969, 140.969, 348.917, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 17.9

The binding sites of Zinc atom in the Crystal Structure of MAPE1 (pdb code 5jgf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of MAPE1, PDB code: 5jgf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of MAPE1


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 MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:17.2 occ:1.00 OD1 A:ASP303 2.0 12.9 1.0 OD1 A:ASP385 2.1 13.4 1.0 O A:HOH757 2.2 23.1 1.0 NE2 A:HIS132 2.2 12.1 1.0 O A:HOH947 2.3 14.6 1.0 OD2 A:ASP385 2.6 13.4 1.0 CG A:ASP385 2.7 13.6 1.0 CG A:ASP303 2.9 15.7 1.0 CE1 A:HIS132 3.1 12.9 1.0 OD2 A:ASP303 3.2 14.3 1.0 O A:HOH705 3.2 36.3 1.0 CD2 A:HIS132 3.2 13.1 1.0 ZN A:ZN602 3.3 15.7 1.0 CB A:ASP304 3.8 17.6 1.0 OE1 A:GLU339 3.8 15.5 1.0 OE2 A:GLU340 4.0 13.9 1.0 CB A:ASP385 4.2 12.6 1.0 ND1 A:HIS132 4.2 12.5 1.0 O B:HOH925 4.3 24.0 1.0 CG2 A:VAL386 4.3 13.5 1.0 CD A:GLU339 4.3 17.6 1.0 CG A:HIS132 4.3 12.6 1.0 CB A:ASP303 4.3 16.9 1.0 CG A:ASP304 4.4 17.6 1.0 CA A:ASP304 4.6 16.2 1.0 N A:ASP304 4.6 16.4 1.0 C A:ASP303 4.7 19.5 1.0 CD A:GLU340 4.7 14.8 1.0 N A:VAL386 4.7 13.9 1.0 CA A:ASP303 4.7 18.3 1.0 OE2 A:GLU339 4.8 20.7 1.0 CA A:ASP385 4.8 13.8 1.0 OD2 A:ASP304 4.9 14.7 1.0 OD1 A:ASP304 4.9 15.5 1.0 O A:VAL386 4.9 14.6 1.0 O A:HOH854 4.9 16.1 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of MAPE1


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 MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:15.7 occ:1.00 OD2 A:ASP303 1.9 14.3 1.0 O A:HOH757 2.0 23.1 1.0 OE2 A:GLU340 2.0 13.9 1.0 NE2 A:HIS479 2.1 12.9 1.0 OE1 A:GLU340 2.6 15.1 1.0 CD A:GLU340 2.6 14.8 1.0 CG A:ASP303 2.9 15.7 1.0 O B:HOH925 3.0 24.0 1.0 CD2 A:HIS479 3.0 13.7 1.0 CE1 A:HIS479 3.2 15.3 1.0 OD1 A:ASP303 3.3 12.9 1.0 ZN A:ZN601 3.3 17.2 1.0 O A:HOH947 3.7 14.6 1.0 O A:HOH996 3.9 32.2 1.0 O A:HOH818 4.0 12.3 1.0 OE1 A:GLU339 4.0 15.5 1.0 CG A:GLU340 4.1 12.9 1.0 O A:HOH705 4.2 36.3 1.0 CB A:ASP303 4.2 16.9 1.0 CG A:HIS479 4.2 12.5 1.0 ND1 A:HIS479 4.2 11.7 1.0 NE2 B:HIS210 4.4 19.2 1.0 NE2 A:HIS132 4.4 12.1 1.0 CE1 A:HIS132 4.4 12.9 1.0 SD A:MET478 4.6 19.3 1.0 O A:HOH817 4.8 19.4 1.0 CG A:MET478 4.8 13.4 1.0 CD1 A:LEU136 4.8 12.5 1.0 CE1 B:HIS210 4.9 19.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of MAPE1


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 MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:19.3 occ:1.00 OD2 B:ASP303 2.0 13.5 1.0 OE2 B:GLU340 2.0 16.6 1.0 O B:HOH752 2.0 22.1 1.0 NE2 B:HIS479 2.1 14.1 1.0 OE1 B:GLU340 2.6 15.8 1.0 CD B:GLU340 2.6 17.8 1.0 O A:HOH788 2.8 28.1 1.0 CG B:ASP303 2.9 17.3 1.0 CD2 B:HIS479 3.1 14.1 1.0 CE1 B:HIS479 3.2 13.8 1.0 OD1 B:ASP303 3.3 11.3 1.0 ZN B:ZN602 3.4 18.1 1.0 O B:HOH911 3.8 12.9 1.0 O B:HOH928 3.9 30.4 1.0 OE1 B:GLU339 4.0 15.4 1.0 O B:HOH828 4.0 12.4 1.0 CG B:GLU340 4.1 14.2 1.0 CB B:ASP303 4.2 15.4 1.0 O B:HOH703 4.2 29.4 1.0 CG B:HIS479 4.2 12.1 1.0 ND1 B:HIS479 4.3 12.0 1.0 NE2 A:HIS210 4.4 17.8 1.0 NE2 B:HIS132 4.5 11.0 1.0 CE1 B:HIS132 4.5 12.6 1.0 SD B:MET478 4.6 17.1 1.0 CG B:MET478 4.8 13.9 1.0 O B:HOH888 4.8 17.1 1.0 CD1 B:LEU136 4.8 11.2 1.0 CE1 A:HIS210 4.9 18.9 1.0 CD B:GLU339 5.0 17.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of MAPE1


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 MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:18.1 occ:1.00 OD1 B:ASP303 2.0 11.3 1.0 O B:HOH752 2.1 22.1 1.0 OD1 B:ASP385 2.1 13.3 1.0 NE2 B:HIS132 2.2 11.0 1.0 O B:HOH911 2.4 12.9 1.0 OD2 B:ASP385 2.5 12.6 1.0 CG B:ASP385 2.6 14.4 1.0 CG B:ASP303 3.0 17.3 1.0 CE1 B:HIS132 3.1 12.6 1.0 CD2 B:HIS132 3.2 11.9 1.0 O B:HOH703 3.2 29.4 1.0 OD2 B:ASP303 3.2 13.5 1.0 ZN B:ZN601 3.4 19.3 1.0 CB B:ASP304 3.8 16.7 1.0 OE1 B:GLU339 3.8 15.4 1.0 OE2 B:GLU340 4.0 16.6 1.0 CB B:ASP385 4.1 13.9 1.0 ND1 B:HIS132 4.2 12.1 1.0 CD B:GLU339 4.3 17.4 1.0 CG2 B:VAL386 4.3 14.1 1.0 CG B:HIS132 4.3 11.6 1.0 CB B:ASP303 4.3 15.4 1.0 O A:HOH788 4.4 28.1 1.0 CG B:ASP304 4.4 17.4 1.0 OE2 B:GLU339 4.6 18.9 1.0 N B:ASP304 4.6 16.3 1.0 CA B:ASP304 4.7 14.2 1.0 CA B:ASP303 4.7 17.4 1.0 CD B:GLU340 4.7 17.8 1.0 C B:ASP303 4.7 18.9 1.0 N B:VAL386 4.7 12.8 1.0 CA B:ASP385 4.8 13.9 1.0 OD2 B:ASP304 4.9 14.7 1.0 O B:HOH922 4.9 17.0 1.0 OD1 B:ASP304 4.9 14.8 1.0 O B:VAL386 4.9 14.0 1.0 CG B:GLU339 5.0 13.9 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:14.2 occ:1.00 OD1 C:ASP303 2.0 10.9 1.0 O C:HOH752 2.1 22.5 1.0 OD1 C:ASP385 2.1 11.4 1.0 NE2 C:HIS132 2.2 10.2 1.0 O C:HOH955 2.4 11.7 1.0 OD2 C:ASP385 2.6 13.0 1.0 CG C:ASP385 2.7 12.2 1.0 CG C:ASP303 2.9 14.5 1.0 CE1 C:HIS132 3.1 12.6 1.0 O C:HOH703 3.1 29.9 1.0 OD2 C:ASP303 3.2 13.2 1.0 CD2 C:HIS132 3.2 10.1 1.0 ZN C:ZN602 3.3 15.5 1.0 OE1 C:GLU339 3.8 17.0 1.0 CB C:ASP304 3.8 15.7 1.0 OE2 C:GLU340 4.0 13.5 1.0 CB C:ASP385 4.2 12.7 1.0 ND1 C:HIS132 4.3 11.5 1.0 CD C:GLU339 4.3 17.8 1.0 CB C:ASP303 4.3 14.6 1.0 CG2 C:VAL386 4.3 13.0 1.0 O D:HOH885 4.3 26.4 1.0 CG C:HIS132 4.3 12.0 1.0 CG C:ASP304 4.4 16.1 1.0 OE2 C:GLU339 4.6 19.7 1.0 CD C:GLU340 4.7 14.8 1.0 N C:ASP304 4.7 15.2 1.0 CA C:ASP304 4.7 14.9 1.0 C C:ASP303 4.7 16.9 1.0 CA C:ASP303 4.7 17.0 1.0 N C:VAL386 4.7 12.0 1.0 O C:HOH800 4.8 13.8 1.0 CA C:ASP385 4.8 12.7 1.0 OD2 C:ASP304 4.9 14.1 1.0 OD1 C:ASP304 4.9 13.2 1.0 O C:VAL386 4.9 13.5 1.0 OE1 C:GLU340 5.0 13.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:15.5 occ:1.00 OD2 C:ASP303 2.0 13.2 1.0 OE2 C:GLU340 2.1 13.5 1.0 O C:HOH752 2.1 22.5 1.0 NE2 C:HIS479 2.2 12.2 1.0 OE1 C:GLU340 2.6 13.1 1.0 CD C:GLU340 2.6 14.8 1.0 CG C:ASP303 2.9 14.5 1.0 O D:HOH885 3.0 26.4 1.0 CD2 C:HIS479 3.1 11.5 1.0 CE1 C:HIS479 3.2 11.8 1.0 OD1 C:ASP303 3.3 10.9 1.0 ZN C:ZN601 3.3 14.2 1.0 O C:HOH955 3.8 11.7 1.0 O C:HOH758 4.0 9.3 1.0 OE1 C:GLU339 4.0 17.0 1.0 O C:HOH1030 4.1 37.7 1.0 CG C:GLU340 4.1 12.2 1.0 CB C:ASP303 4.2 14.6 1.0 CG C:HIS479 4.2 11.1 1.0 O C:HOH703 4.3 29.9 1.0 ND1 C:HIS479 4.3 10.1 1.0 NE2 D:HIS210 4.4 20.8 1.0 NE2 C:HIS132 4.4 10.2 1.0 CE1 C:HIS132 4.5 12.6 1.0 SD C:MET478 4.6 18.1 1.0 CG C:MET478 4.7 11.4 1.0 O C:HOH879 4.8 18.2 1.0 CD1 C:LEU136 4.8 11.1 1.0 CE1 D:HIS210 4.9 20.2 1.0 CD C:GLU339 5.0 17.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:15.7 occ:1.00 OD1 D:ASP303 2.0 14.5 1.0 O D:HOH728 2.0 22.3 1.0 OD1 D:ASP385 2.1 12.5 1.0 NE2 D:HIS132 2.1 8.3 1.0 O D:HOH946 2.4 13.4 1.0 OD2 D:ASP385 2.6 12.4 1.0 CG D:ASP385 2.7 12.9 1.0 CG D:ASP303 2.9 17.8 1.0 CE1 D:HIS132 3.1 11.1 1.0 OD2 D:ASP303 3.2 13.8 1.0 CD2 D:HIS132 3.2 11.0 1.0 O D:HOH703 3.2 32.1 1.0 ZN D:ZN602 3.4 16.2 1.0 OE1 D:GLU339 3.8 16.0 1.0 CB D:ASP304 3.8 17.2 1.0 OE2 D:GLU340 4.0 14.9 1.0 CB D:ASP385 4.2 12.5 1.0 ND1 D:HIS132 4.2 9.8 1.0 CD D:GLU339 4.2 17.4 1.0 CG2 D:VAL386 4.3 12.6 1.0 CG D:HIS132 4.3 10.3 1.0 CB D:ASP303 4.3 16.6 1.0 O C:HOH831 4.3 29.1 1.0 CG D:ASP304 4.4 18.6 1.0 OE2 D:GLU339 4.6 20.3 1.0 N D:ASP304 4.7 17.0 1.0 CA D:ASP304 4.7 16.0 1.0 C D:ASP303 4.7 19.1 1.0 CD D:GLU340 4.7 14.7 1.0 CA D:ASP303 4.7 18.6 1.0 N D:VAL386 4.8 13.2 1.0 O D:HOH860 4.8 16.1 1.0 CA D:ASP385 4.8 12.7 1.0 OD2 D:ASP304 4.9 16.2 1.0 OD1 D:ASP304 4.9 15.1 1.0 O D:VAL386 5.0 14.1 1.0 OE1 D:GLU340 5.0 15.1 1.0 CG D:GLU339 5.0 14.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of MAPE1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of MAPE1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:16.2 occ:1.00 OD2 D:ASP303 2.0 13.8 1.0 OE2 D:GLU340 2.0 14.9 1.0 O D:HOH728 2.1 22.3 1.0 NE2 D:HIS479 2.1 11.7 1.0 OE1 D:GLU340 2.6 15.1 1.0 CD D:GLU340 2.6 14.7 1.0 O C:HOH831 2.9 29.1 1.0 CG D:ASP303 2.9 17.8 1.0 CD2 D:HIS479 3.0 12.4 1.0 CE1 D:HIS479 3.2 13.4 1.0 OD1 D:ASP303 3.3 14.5 1.0 ZN D:ZN601 3.4 15.7 1.0 O D:HOH946 3.8 13.4 1.0 O D:HOH950 4.0 33.5 1.0 O D:HOH842 4.0 10.1 1.0 OE1 D:GLU339 4.0 16.0 1.0 CG D:GLU340 4.1 13.0 1.0 CB D:ASP303 4.2 16.6 1.0 CG D:HIS479 4.2 11.5 1.0 O D:HOH703 4.2 32.1 1.0 ND1 D:HIS479 4.3 10.8 1.0 NE2 C:HIS210 4.4 18.1 1.0 NE2 D:HIS132 4.4 8.3 1.0 CE1 D:HIS132 4.4 11.1 1.0 SD D:MET478 4.6 19.7 1.0 O D:HOH887 4.8 16.5 1.0 CD1 D:LEU136 4.8 11.8 1.0 CG D:MET478 4.8 14.3 1.0 CE1 C:HIS210 4.9 18.0 1.0 CD D:GLU339 5.0 17.4 1.0

A.Yamasaki, Y.Watanabe, W.Adachi, K.Suzuki, K.Matoba, H.Kirisako, H.Kumeta, H.Nakatogawa, Y.Ohsumi, F.Inagaki, N.N.Noda. Structural Basis For Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates Cell Rep V. 16 19 2016.
ISSN: ESSN 2211-1247
PubMed: 27320913
DOI: 10.1016/J.CELREP.2016.05.066