Zinc in PDB 7bvp: Adhe Spirosome in Extended Conformation

All present enzymatic activity of Adhe Spirosome in Extended Conformation:
1.1.1.1; 1.2.1.10;

The binding sites of Zinc atom in the Adhe Spirosome in Extended Conformation (pdb code 7bvp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Adhe Spirosome in Extended Conformation, PDB code: 7bvp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:50.8 occ:1.00 NE2 A:HIS723 2.3 37.4 1.0 NE2 A:HIS737 2.3 41.8 1.0 NE2 A:HIS657 2.3 33.3 1.0 OD2 A:ASP653 2.3 36.9 1.0 CD2 A:HIS723 3.1 37.4 1.0 CD2 A:HIS737 3.1 41.8 1.0 CG A:ASP653 3.2 36.9 1.0 CD2 A:HIS657 3.2 33.3 1.0 CE1 A:HIS657 3.3 33.3 1.0 ND2 A:ASN741 3.3 39.6 1.0 OD1 A:ASP653 3.3 36.9 1.0 CE1 A:HIS737 3.3 41.8 1.0 CE1 A:HIS723 3.4 37.4 1.0 C5N A:NAD902 4.1 44.9 1.0 C4N A:NAD902 4.1 44.9 1.0 CG A:HIS723 4.3 37.4 1.0 CG A:HIS737 4.3 41.8 1.0 CG A:HIS657 4.3 33.3 1.0 ND1 A:HIS657 4.3 33.3 1.0 ND1 A:HIS737 4.4 41.8 1.0 ND1 A:HIS723 4.4 37.4 1.0 CG A:ASN741 4.5 39.6 1.0 CB A:ASP653 4.6 36.9 1.0 O A:ASP653 4.7 36.9 1.0 OG1 A:THR656 4.9 34.5 1.0

Zinc binding site 2 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:59.2 occ:1.00 NE2 B:HIS723 2.3 39.7 1.0 NE2 B:HIS737 2.3 45.4 1.0 NE2 B:HIS657 2.3 34.6 1.0 OD2 B:ASP653 2.3 38.8 1.0 CD2 B:HIS723 3.1 39.7 1.0 CD2 B:HIS737 3.1 45.4 1.0 CD2 B:HIS657 3.2 34.6 1.0 CG B:ASP653 3.2 38.8 1.0 CE1 B:HIS657 3.3 34.6 1.0 ND2 B:ASN741 3.3 42.4 1.0 OD1 B:ASP653 3.3 38.8 1.0 CE1 B:HIS737 3.3 45.4 1.0 C5N B:NAD902 3.3 46.0 1.0 CE1 B:HIS723 3.4 39.7 1.0 C4N B:NAD902 4.0 46.0 1.0 CG B:HIS723 4.3 39.7 1.0 C6N B:NAD902 4.3 46.0 1.0 CG B:HIS737 4.3 45.4 1.0 CG B:HIS657 4.3 34.6 1.0 ND1 B:HIS657 4.4 34.6 1.0 ND1 B:HIS737 4.4 45.4 1.0 ND1 B:HIS723 4.4 39.7 1.0 CG B:ASN741 4.5 42.4 1.0 CB B:ASP653 4.6 38.8 1.0 O B:ASP653 4.7 38.8 1.0 OG1 B:THR656 4.9 36.0 1.0

Zinc binding site 3 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn903 b:50.8 occ:1.00 NE2 C:HIS723 2.3 37.4 1.0 NE2 C:HIS737 2.3 41.8 1.0 NE2 C:HIS657 2.3 33.3 1.0 OD2 C:ASP653 2.3 36.9 1.0 CD2 C:HIS723 3.1 37.4 1.0 CD2 C:HIS737 3.1 41.8 1.0 CD2 C:HIS657 3.2 33.3 1.0 CG C:ASP653 3.2 36.9 1.0 CE1 C:HIS657 3.3 33.3 1.0 ND2 C:ASN741 3.3 39.6 1.0 OD1 C:ASP653 3.3 36.9 1.0 CE1 C:HIS737 3.3 41.8 1.0 CE1 C:HIS723 3.4 37.4 1.0 C5N C:NAD902 3.8 44.9 1.0 CG C:HIS723 4.3 37.4 1.0 CG C:HIS737 4.3 41.8 1.0 CG C:HIS657 4.3 33.3 1.0 ND1 C:HIS657 4.3 33.3 1.0 ND1 C:HIS737 4.4 41.8 1.0 ND1 C:HIS723 4.4 37.4 1.0 C6N C:NAD902 4.5 44.9 1.0 CG C:ASN741 4.5 39.6 1.0 CB C:ASP653 4.6 36.9 1.0 O C:ASP653 4.7 36.9 1.0 C4N C:NAD902 4.8 44.9 1.0 OG1 C:THR656 4.9 34.5 1.0

Zinc binding site 4 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn903 b:59.2 occ:1.00 NE2 D:HIS723 2.3 39.7 1.0 NE2 D:HIS737 2.3 45.4 1.0 NE2 D:HIS657 2.3 34.6 1.0 OD2 D:ASP653 2.3 38.8 1.0 CD2 D:HIS723 3.1 39.7 1.0 CD2 D:HIS737 3.1 45.4 1.0 CD2 D:HIS657 3.2 34.6 1.0 CG D:ASP653 3.2 38.8 1.0 CE1 D:HIS657 3.3 34.6 1.0 ND2 D:ASN741 3.3 42.4 1.0 OD1 D:ASP653 3.3 38.8 1.0 CE1 D:HIS737 3.3 45.4 1.0 CE1 D:HIS723 3.4 39.7 1.0 C5N D:NAD902 3.5 46.0 1.0 CG D:HIS723 4.3 39.7 1.0 C6N D:NAD902 4.3 46.0 1.0 CG D:HIS737 4.3 45.4 1.0 CG D:HIS657 4.3 34.6 1.0 ND1 D:HIS657 4.4 34.6 1.0 ND1 D:HIS737 4.4 45.4 1.0 ND1 D:HIS723 4.4 39.7 1.0 C4N D:NAD902 4.4 46.0 1.0 CG D:ASN741 4.5 42.4 1.0 CB D:ASP653 4.6 38.8 1.0 O D:ASP653 4.7 38.8 1.0 OG1 D:THR656 4.9 36.0 1.0

Zinc binding site 5 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn903 b:50.8 occ:1.00 NE2 E:HIS723 2.3 37.4 1.0 NE2 E:HIS737 2.3 41.8 1.0 NE2 E:HIS657 2.3 33.3 1.0 OD2 E:ASP653 2.3 36.9 1.0 CD2 E:HIS723 3.1 37.4 1.0 CD2 E:HIS737 3.1 41.8 1.0 CD2 E:HIS657 3.2 33.3 1.0 CG E:ASP653 3.2 36.9 1.0 CE1 E:HIS657 3.3 33.3 1.0 ND2 E:ASN741 3.3 39.6 1.0 OD1 E:ASP653 3.3 36.9 1.0 CE1 E:HIS737 3.3 41.8 1.0 CE1 E:HIS723 3.4 37.4 1.0 C5N E:NAD902 3.8 44.9 1.0 CG E:HIS723 4.3 37.4 1.0 C6N E:NAD902 4.3 44.9 1.0 CG E:HIS657 4.3 33.3 1.0 CG E:HIS737 4.3 41.8 1.0 ND1 E:HIS657 4.3 33.3 1.0 ND1 E:HIS737 4.4 41.8 1.0 ND1 E:HIS723 4.4 37.4 1.0 CG E:ASN741 4.5 39.6 1.0 CB E:ASP653 4.6 36.9 1.0 O E:ASP653 4.7 36.9 1.0 C4N E:NAD902 4.8 44.9 1.0 OG1 E:THR656 4.9 34.5 1.0

Zinc binding site 6 out of 6 in the Adhe Spirosome in Extended Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Adhe Spirosome in Extended Conformation within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn903 b:59.2 occ:1.00 NE2 F:HIS723 2.3 39.7 1.0 NE2 F:HIS737 2.3 45.4 1.0 NE2 F:HIS657 2.3 34.6 1.0 OD2 F:ASP653 2.3 38.8 1.0 CD2 F:HIS723 3.1 39.7 1.0 CD2 F:HIS737 3.1 45.4 1.0 CD2 F:HIS657 3.2 34.6 1.0 CG F:ASP653 3.2 38.8 1.0 CE1 F:HIS657 3.3 34.6 1.0 ND2 F:ASN741 3.3 42.4 1.0 OD1 F:ASP653 3.3 38.8 1.0 CE1 F:HIS737 3.3 45.4 1.0 CE1 F:HIS723 3.4 39.7 1.0 C5N F:NAD902 3.5 46.0 1.0 C4N F:NAD902 3.7 46.0 1.0 CG F:HIS723 4.3 39.7 1.0 CG F:HIS657 4.3 34.6 1.0 CG F:HIS737 4.3 45.4 1.0 ND1 F:HIS657 4.3 34.6 1.0 ND1 F:HIS737 4.4 45.4 1.0 ND1 F:HIS723 4.4 39.7 1.0 CG F:ASN741 4.5 42.4 1.0 CB F:ASP653 4.6 38.8 1.0 O F:ASP653 4.7 38.8 1.0 C6N F:NAD902 4.7 46.0 1.0 OG1 F:THR656 4.9 36.0 1.0

G.Kim, J.Yang, J.Jang, J.S.Choi, A.J.Roe, O.Byron, C.Seok, J.J.Song. Aldehyde-Alcohol Dehydrogenase Undergoes Structural Transition to Form Extended Spirosomes For Substrate Channeling. Commun Biol V. 3 298 2020.
ISSN: ESSN 2399-3642
PubMed: 32523125
DOI: 10.1038/S42003-020-1030-1