Zinc in PDB 7vqo: Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1

All present enzymatic activity of Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1:
3.2.1.24;

The binding sites of Zinc atom in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1 (pdb code 7vqo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1, PDB code: 7vqo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:129.5 occ:1.00 OD2 A:ASP404 1.9 107.7 1.0 OD1 A:ASP294 1.9 107.6 1.0 NE2 A:HIS292 2.3 105.1 1.0 NE2 A:HIS614 2.3 103.1 1.0 OD2 A:ASP294 2.3 107.6 1.0 CG A:ASP294 2.4 107.6 1.0 CE1 A:HIS614 3.0 103.1 1.0 CG A:ASP404 3.0 107.7 1.0 CD2 A:HIS292 3.2 105.1 1.0 CE1 A:HIS292 3.3 105.1 1.0 CD2 A:HIS614 3.5 103.1 1.0 OD1 A:ASP615 3.7 106.5 1.0 CB A:ASP404 3.7 107.7 1.0 CB A:ASP294 3.9 107.6 1.0 OD1 A:ASP404 4.1 107.7 1.0 ND1 A:HIS614 4.3 103.1 1.0 CG A:HIS292 4.4 105.1 1.0 ND1 A:HIS292 4.4 105.1 1.0 OH A:TYR462 4.5 105.7 1.0 CG A:HIS614 4.5 103.1 1.0 CA A:ASP294 4.6 107.6 1.0 CZ A:PHE613 4.7 103.1 1.0 CG A:ASP615 4.8 106.5 1.0 O A:ASP404 4.9 107.7 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1701 b:130.0 occ:1.00 OD2 B:ASP404 1.9 107.9 1.0 OD1 B:ASP294 1.9 108.2 1.0 NE2 B:HIS292 2.3 105.5 1.0 NE2 B:HIS614 2.3 103.5 1.0 OD2 B:ASP294 2.3 108.2 1.0 CG B:ASP294 2.4 108.2 1.0 CE1 B:HIS614 3.0 103.5 1.0 CG B:ASP404 3.0 107.9 1.0 CD2 B:HIS292 3.2 105.5 1.0 CE1 B:HIS292 3.3 105.5 1.0 CD2 B:HIS614 3.5 103.5 1.0 OD1 B:ASP615 3.7 106.8 1.0 CB B:ASP404 3.7 107.9 1.0 CB B:ASP294 3.9 108.2 1.0 OD1 B:ASP404 4.1 107.9 1.0 ND1 B:HIS614 4.3 103.5 1.0 CG B:HIS292 4.4 105.5 1.0 ND1 B:HIS292 4.4 105.5 1.0 OH B:TYR462 4.5 106.3 1.0 CG B:HIS614 4.5 103.5 1.0 CA B:ASP294 4.6 108.2 1.0 CZ B:PHE613 4.7 103.8 1.0 CG B:ASP615 4.8 106.8 1.0 O B:ASP404 4.9 107.9 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1701 b:128.6 occ:1.00 OD2 C:ASP404 1.9 107.0 1.0 OD1 C:ASP294 1.9 107.1 1.0 NE2 C:HIS292 2.3 104.6 1.0 NE2 C:HIS614 2.3 102.7 1.0 OD2 C:ASP294 2.3 107.1 1.0 CG C:ASP294 2.4 107.1 1.0 CE1 C:HIS614 3.0 102.7 1.0 CG C:ASP404 3.0 107.0 1.0 CD2 C:HIS292 3.2 104.6 1.0 CE1 C:HIS292 3.3 104.6 1.0 CD2 C:HIS614 3.5 102.7 1.0 OD1 C:ASP615 3.7 106.3 1.0 CB C:ASP404 3.7 107.0 1.0 CB C:ASP294 3.9 107.1 1.0 OD1 C:ASP404 4.1 107.0 1.0 ND1 C:HIS614 4.3 102.7 1.0 CG C:HIS292 4.4 104.6 1.0 ND1 C:HIS292 4.4 104.6 1.0 OH C:TYR462 4.5 105.0 1.0 CG C:HIS614 4.5 102.7 1.0 CA C:ASP294 4.6 107.1 1.0 CZ C:PHE613 4.7 103.1 1.0 CG C:ASP615 4.8 106.3 1.0 O C:ASP404 4.9 107.0 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of AMS1 Bound to the Fw Domain of NBR1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1701 b:129.3 occ:1.00 OD2 D:ASP404 1.9 107.2 1.0 OD1 D:ASP294 1.9 107.6 1.0 NE2 D:HIS292 2.3 104.9 1.0 NE2 D:HIS614 2.3 102.9 1.0 OD2 D:ASP294 2.3 107.6 1.0 CG D:ASP294 2.4 107.6 1.0 CE1 D:HIS614 3.0 102.9 1.0 CG D:ASP404 3.0 107.2 1.0 CD2 D:HIS292 3.2 104.9 1.0 CE1 D:HIS292 3.3 104.9 1.0 CD2 D:HIS614 3.5 102.9 1.0 OD1 D:ASP615 3.7 106.2 1.0 CB D:ASP404 3.7 107.2 1.0 CB D:ASP294 3.9 107.6 1.0 OD1 D:ASP404 4.1 107.2 1.0 ND1 D:HIS614 4.3 102.9 1.0 CG D:HIS292 4.4 104.9 1.0 ND1 D:HIS292 4.4 104.9 1.0 OH D:TYR462 4.5 105.2 1.0 CG D:HIS614 4.5 102.9 1.0 CA D:ASP294 4.6 107.6 1.0 CZ D:PHE613 4.7 103.0 1.0 CG D:ASP615 4.8 106.2 1.0 O D:ASP404 4.9 107.2 1.0

J.Zhang, Y.Y.Wang, Z.Q.Pan, Y.Li, J.Sui, L.L.Du, K.Ye. Structural Mechanism of Protein Recognition By the Fw Domain of Autophagy Receptor NBR1 Nat Commun V. 13 3650 2022.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-022-31439-5