Zinc in PDB 8qud: Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5

The structure of Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5 also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5 (pdb code 8qud). 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 Human KV3.1 in Complex with Modulator AUT5, PDB code: 8qud:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


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 Human KV3.1 in Complex with Modulator AUT5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:39.8 occ:1.00 ND1 A:HIS77 2.1 15.6 1.0 SG B:CYS83 2.3 11.0 1.0 SG A:CYS104 2.3 15.5 1.0 SG A:CYS105 2.3 8.9 1.0 CE1 A:HIS77 3.0 5.7 1.0 CG A:HIS77 3.1 8.6 1.0 CB B:CYS83 3.2 4.6 1.0 CB A:HIS77 3.4 0.0 1.0 CB A:CYS104 3.6 11.1 1.0 CB A:CYS105 3.8 17.7 1.0 N A:CYS105 4.1 6.6 1.0 CA A:HIS77 4.1 7.3 1.0 C A:CYS104 4.1 15.9 1.0 NE2 A:HIS77 4.1 9.5 1.0 CD2 A:HIS77 4.2 15.0 1.0 O B:HOH714 4.4 28.7 1.0 CA A:CYS104 4.4 15.9 1.0 CB A:GLU102 4.5 21.6 1.0 O A:CYS104 4.5 27.8 1.0 CA A:CYS105 4.5 13.7 1.0 CA B:CYS83 4.6 3.0 1.0 N A:CYS78 4.7 16.7 1.0 CG B:PRO85 4.8 14.5 1.0 CD B:PRO85 4.8 7.9 1.0 N A:CYS104 4.9 18.2 1.0 CB B:PRO85 4.9 9.1 1.0 C A:HIS77 5.0 8.7 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


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 Human KV3.1 in Complex with Modulator AUT5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:39.8 occ:1.00 ND1 B:HIS77 2.1 15.6 1.0 SG C:CYS83 2.3 11.0 1.0 SG B:CYS104 2.3 15.5 1.0 SG B:CYS105 2.3 8.9 1.0 CE1 B:HIS77 3.0 5.7 1.0 CG B:HIS77 3.1 8.6 1.0 CB C:CYS83 3.1 4.6 1.0 CB B:HIS77 3.4 0.0 1.0 CB B:CYS104 3.6 11.1 1.0 CB B:CYS105 3.8 17.7 1.0 N B:CYS105 4.1 6.6 1.0 CA B:HIS77 4.1 7.3 1.0 C B:CYS104 4.1 15.9 1.0 NE2 B:HIS77 4.1 9.5 1.0 CD2 B:HIS77 4.2 15.0 1.0 O C:HOH714 4.4 28.7 1.0 CA B:CYS104 4.4 15.9 1.0 CB B:GLU102 4.5 21.6 1.0 O B:CYS104 4.5 27.8 1.0 CA B:CYS105 4.5 13.7 1.0 CA C:CYS83 4.5 3.0 1.0 N B:CYS78 4.7 16.7 1.0 CD C:PRO85 4.8 7.9 1.0 CG C:PRO85 4.8 14.5 1.0 N B:CYS104 4.9 18.2 1.0 N C:CYS83 5.0 19.3 1.0 C B:HIS77 5.0 8.7 1.0 CB C:PRO85 5.0 9.1 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


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 Human KV3.1 in Complex with Modulator AUT5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:39.8 occ:1.00 ND1 D:HIS77 2.1 15.6 1.0 SG D:CYS104 2.3 15.5 1.0 SG D:CYS105 2.3 8.9 1.0 SG A:CYS83 2.4 11.0 1.0 CE1 D:HIS77 3.0 5.7 1.0 CG D:HIS77 3.1 8.6 1.0 CB A:CYS83 3.2 4.6 1.0 CB D:HIS77 3.4 0.0 1.0 CB D:CYS104 3.6 11.1 1.0 CB D:CYS105 3.8 17.7 1.0 N D:CYS105 4.1 6.6 1.0 CA D:HIS77 4.1 7.3 1.0 C D:CYS104 4.1 15.9 1.0 NE2 D:HIS77 4.1 9.5 1.0 CD2 D:HIS77 4.2 15.0 1.0 O A:HOH716 4.4 28.7 1.0 CA D:CYS104 4.4 15.9 1.0 CB D:GLU102 4.5 21.6 1.0 O D:CYS104 4.5 27.8 1.0 CA D:CYS105 4.5 13.7 1.0 CA A:CYS83 4.7 3.0 1.0 N D:CYS78 4.7 16.7 1.0 CG A:PRO85 4.8 14.5 1.0 CD A:PRO85 4.9 7.9 1.0 N D:CYS104 4.9 18.2 1.0 CB A:PRO85 5.0 9.1 1.0 C D:HIS77 5.0 8.7 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


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 Human KV3.1 in Complex with Modulator AUT5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:39.8 occ:1.00 ND1 C:HIS77 2.1 15.6 1.0 SG C:CYS104 2.3 15.5 1.0 SG C:CYS105 2.3 8.9 1.0 SG D:CYS83 2.3 11.0 1.0 CE1 C:HIS77 3.0 5.7 1.0 CG C:HIS77 3.1 8.6 1.0 CB D:CYS83 3.2 4.6 1.0 CB C:HIS77 3.4 0.0 1.0 CB C:CYS104 3.6 11.1 1.0 CB C:CYS105 3.8 17.7 1.0 N C:CYS105 4.1 6.6 1.0 CA C:HIS77 4.1 7.3 1.0 C C:CYS104 4.1 15.9 1.0 NE2 C:HIS77 4.1 9.5 1.0 CD2 C:HIS77 4.2 15.0 1.0 O D:HOH716 4.4 28.7 1.0 CA C:CYS104 4.4 15.9 1.0 CB C:GLU102 4.5 21.6 1.0 O C:CYS104 4.5 27.8 1.0 CA C:CYS105 4.5 13.7 1.0 CA D:CYS83 4.6 3.0 1.0 N C:CYS78 4.7 16.7 1.0 N C:CYS104 4.9 18.2 1.0 CD D:PRO85 4.9 7.9 1.0 CG D:PRO85 4.9 14.5 1.0 C C:HIS77 5.0 8.7 1.0

Q.Liang, G.Chi, L.Cirqueira, L.Zhi, A.Marasco, N.Pilati, M.J.Gunthorpe, G.Alvaro, C.H.Large, D.B.Sauer, W.Treptow, M.Covarrubias. The Binding and Mechanism of A Positive Allosteric Modulator of KV3 Channels. Nat Commun V. 15 2533 2024.
ISSN: ESSN 2041-1723
PubMed: 38514618
DOI: 10.1038/S41467-024-46813-8