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

Other elements in 8qud:

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

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 6 binding sites of Potassium where determined in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5, PDB code: 8qud:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 8qud

Go back to Potassium Binding Sites List in 8qud
Potassium binding site 1 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K605

b:9.1
occ:1.00
 O C:THR400 2.8 13.5 1.0
O D:THR400 2.8 13.5 1.0
O B:THR400 2.9 13.5 1.0
O A:THR400 2.9 13.5 1.0
K C:K605 3.0 38.2 1.0
O D:LEU401 3.0 11.8 1.0
O C:LEU401 3.0 11.8 1.0
O A:LEU401 3.1 11.8 1.0
O B:LEU401 3.1 11.8 1.0
K C:K606 3.7 23.2 1.0
C C:LEU401 3.7 0.0 1.0
C D:LEU401 3.7 0.0 1.0
C B:LEU401 3.7 0.0 1.0
C A:LEU401 3.7 0.0 1.0
C C:THR400 3.9 0.0 1.0
C D:THR400 4.0 0.0 1.0
C B:THR400 4.0 0.0 1.0
C A:THR400 4.1 0.0 1.0
CA D:LEU401 4.2 0.0 1.0
CA C:LEU401 4.2 0.0 1.0
CA B:LEU401 4.2 0.0 1.0
CA A:LEU401 4.2 0.0 1.0
N C:GLY402 4.5 4.3 1.0
N C:LEU401 4.5 0.5 1.0
N D:GLY402 4.5 4.3 1.0
N D:LEU401 4.5 0.5 1.0
N B:GLY402 4.6 4.3 1.0
N B:LEU401 4.6 0.5 1.0
N A:GLY402 4.6 4.3 1.0
N A:LEU401 4.6 0.5 1.0
CA C:GLY402 4.8 0.0 1.0
CA D:GLY402 4.8 0.0 1.0
CA B:GLY402 4.9 0.0 1.0
CA A:GLY402 4.9 0.0 1.0
O C:GLY402 4.9 21.5 1.0
O D:GLY402 4.9 21.5 1.0
O A:GLY402 4.9 21.5 1.0
O B:GLY402 4.9 21.5 1.0

Potassium binding site 2 out of 6 in 8qud

Go back to Potassium Binding Sites List in 8qud
Potassium binding site 2 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
A:K606

b:30.0
occ:1.00
 K C:K606 4.0 23.2 1.0
O B:HOH725 4.0 30.0 1.0
O A:HOH725 4.1 30.0 1.0
OG1 A:THR400 4.2 16.2 1.0
OG1 B:THR400 4.3 16.2 1.0
O C:HOH725 4.3 30.0 1.0
O D:HOH725 4.3 30.0 1.0
OG1 D:THR400 4.5 16.2 1.0
OG1 C:THR400 4.5 16.2 1.0

Potassium binding site 3 out of 6 in 8qud

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Potassium binding site 3 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
A:K607

b:30.0
occ:1.00
 O D:HOH717 2.8 30.0 1.0
O A:HOH719 2.9 30.0 1.0
O C:HOH718 3.2 30.0 1.0
O B:HOH718 3.4 30.0 1.0
O A:TYR403 3.5 7.0 1.0
O B:TYR403 3.7 7.0 1.0
K B:K605 3.7 4.9 1.0
O D:TYR403 3.7 7.0 1.0
O C:TYR403 3.9 7.0 1.0
CA A:GLY404 4.4 0.0 1.0
O D:HOH726 4.4 30.0 1.0
CA D:GLY404 4.4 0.0 1.0
C A:TYR403 4.6 0.0 1.0
C A:GLY404 4.6 0.0 1.0
O A:GLY404 4.6 6.1 1.0
O A:HOH726 4.7 30.0 1.0
O C:HOH726 4.7 30.0 1.0
O D:GLY404 4.7 6.1 1.0
C D:GLY404 4.7 0.0 1.0
CA B:GLY404 4.8 0.0 1.0
C D:TYR403 4.8 0.0 1.0
C B:TYR403 4.8 0.0 1.0
CA C:GLY404 4.8 0.0 1.0
O B:HOH726 4.9 30.0 1.0
N A:GLY404 5.0 7.0 1.0

Potassium binding site 4 out of 6 in 8qud

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Potassium binding site 4 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
B:K605

b:4.9
occ:1.00
 O C:TYR403 2.8 7.0 1.0
O B:TYR403 2.8 7.0 1.0
O D:TYR403 2.8 7.0 1.0
O A:TYR403 2.8 7.0 1.0
O C:GLY402 3.0 21.5 1.0
O B:GLY402 3.0 21.5 1.0
O D:GLY402 3.1 21.5 1.0
O A:GLY402 3.1 21.5 1.0
C C:TYR403 3.5 0.0 1.0
C B:TYR403 3.5 0.0 1.0
C D:TYR403 3.5 0.0 1.0
C A:TYR403 3.6 0.0 1.0
K C:K605 3.6 38.2 1.0
K A:K607 3.7 30.0 1.0
C C:GLY402 4.1 0.0 1.0
CA C:TYR403 4.2 0.0 1.0
C B:GLY402 4.2 0.0 1.0
CA B:TYR403 4.2 0.0 1.0
C D:GLY402 4.2 0.0 1.0
CA D:TYR403 4.2 0.0 1.0
N C:GLY404 4.2 7.0 1.0
N B:GLY404 4.2 7.0 1.0
C A:GLY402 4.2 0.0 1.0
CA A:TYR403 4.3 0.0 1.0
N D:GLY404 4.3 7.0 1.0
N A:GLY404 4.3 7.0 1.0
CA C:GLY404 4.4 0.0 1.0
CA B:GLY404 4.4 0.0 1.0
CA D:GLY404 4.5 0.0 1.0
CA A:GLY404 4.5 0.0 1.0
N C:TYR403 4.7 6.0 1.0
N B:TYR403 4.7 6.0 1.0
N D:TYR403 4.7 6.0 1.0
N A:TYR403 4.8 6.0 1.0

Potassium binding site 5 out of 6 in 8qud

Go back to Potassium Binding Sites List in 8qud
Potassium binding site 5 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 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:K605

b:38.2
occ:1.00
 O D:GLY402 2.6 21.5 1.0
O C:GLY402 2.6 21.5 1.0
O A:GLY402 2.6 21.5 1.0
O B:GLY402 2.6 21.5 1.0
O D:LEU401 2.9 11.8 1.0
O B:LEU401 2.9 11.8 1.0
O C:LEU401 2.9 11.8 1.0
O A:LEU401 2.9 11.8 1.0
K A:K605 3.0 9.1 1.0
C D:GLY402 3.5 0.0 1.0
C C:GLY402 3.5 0.0 1.0
C A:GLY402 3.5 0.0 1.0
C B:GLY402 3.5 0.0 1.0
K B:K605 3.6 4.9 1.0
CA D:GLY402 3.9 0.0 1.0
CA C:GLY402 3.9 0.0 1.0
C D:LEU401 3.9 0.0 1.0
CA A:GLY402 3.9 0.0 1.0
CA B:GLY402 4.0 0.0 1.0
C C:LEU401 4.0 0.0 1.0
C B:LEU401 4.0 0.0 1.0
C A:LEU401 4.0 0.0 1.0
N D:GLY402 4.4 4.3 1.0
N C:GLY402 4.4 4.3 1.0
N B:GLY402 4.4 4.3 1.0
N A:GLY402 4.4 4.3 1.0
N D:TYR403 4.6 6.0 1.0
N C:TYR403 4.6 6.0 1.0
N A:TYR403 4.6 6.0 1.0
N B:TYR403 4.6 6.0 1.0
CA D:TYR403 5.0 0.0 1.0
CA A:TYR403 5.0 0.0 1.0

Potassium binding site 6 out of 6 in 8qud

Go back to Potassium Binding Sites List in 8qud
Potassium binding site 6 out of 6 in the Cryo-Em Structure of Human KV3.1 in Complex with Modulator AUT5


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 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:K606

b:23.2
occ:1.00
 O D:THR400 3.1 13.5 1.0
O C:THR400 3.2 13.5 1.0
O A:THR400 3.2 13.5 1.0
O B:THR400 3.2 13.5 1.0
OG1 D:THR400 3.4 16.2 1.0
OG1 C:THR400 3.5 16.2 1.0
OG1 A:THR400 3.5 16.2 1.0
OG1 B:THR400 3.5 16.2 1.0
CB D:THR400 3.6 7.2 1.0
CB C:THR400 3.6 7.2 1.0
K A:K605 3.7 9.1 1.0
CB A:THR400 3.7 7.2 1.0
CB B:THR400 3.7 7.2 1.0
K A:K606 4.0 30.0 1.0
C D:THR400 4.0 0.0 1.0
C C:THR400 4.1 0.0 1.0
C A:THR400 4.1 0.0 1.0
C B:THR400 4.1 0.0 1.0
CA D:THR400 4.5 0.0 1.0
CA C:THR400 4.5 0.0 1.0
CA A:THR400 4.5 0.0 1.0
CA B:THR400 4.6 0.0 1.0
CG2 C:THR400 4.7 0.0 1.0
CG2 D:THR400 4.7 0.0 1.0
CG2 B:THR400 4.8 0.0 1.0
CG2 A:THR400 4.8 0.0 1.0
O D:THR399 4.9 16.6 1.0
O C:THR399 5.0 16.6 1.0
O A:THR399 5.0 16.6 1.0

Reference:

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
Page generated: Tue Aug 13 00:30:37 2024

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