Atomistry » Potassium » PDB 5f6q-5g13 » 5g0i
Atomistry »
  Potassium »
    PDB 5f6q-5g13 »
      5g0i »

Potassium in PDB 5g0i: Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A, PDB code: 5g0i was solved by Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.58 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.560, 52.830, 186.420, 90.00, 108.92, 90.00
R / Rfree (%) 17.39 / 20.03

Other elements in 5g0i:

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A (pdb code 5g0i). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A, PDB code: 5g0i:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 1 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1804

b:34.8
occ:1.00
 O A:ASP612 2.5 31.0 1.0
O A:LEU634 2.6 32.7 1.0
O A:HIS614 2.7 30.3 1.0
OD1 A:ASP610 2.8 39.6 1.0
OG A:SER633 2.8 33.7 1.0
O A:ASP610 2.9 32.0 1.0
CG A:ASP610 3.3 38.9 1.0
C A:ASP610 3.5 33.3 1.0
C A:ASP612 3.6 33.2 1.0
C A:LEU634 3.7 33.5 1.0
C A:HIS614 3.7 32.1 1.0
N A:ASP612 3.8 32.9 1.0
CB A:ASP610 3.8 30.7 1.0
N A:LEU634 3.9 30.9 1.0
OD2 A:ASP610 3.9 38.7 1.0
CB A:SER633 4.0 32.2 1.0
CB A:HIS635 4.0 28.4 1.0
CA A:ASP612 4.1 32.4 1.0
C A:TRP611 4.2 35.2 1.0
N A:TRP611 4.2 31.3 1.0
CB A:ASP612 4.2 33.5 1.0
CA A:ASP610 4.3 28.9 1.0
CA A:SER633 4.3 31.6 1.0
CA A:HIS615 4.3 30.1 1.0
ND1 A:HIS635 4.4 31.6 1.0
CA A:TRP611 4.4 32.4 1.0
N A:HIS615 4.4 30.6 1.0
N A:HIS614 4.4 27.9 1.0
O A:HOH2334 4.4 33.5 1.0
C A:SER633 4.5 33.8 1.0
CA A:LEU634 4.5 32.1 1.0
CA A:HIS635 4.5 29.1 1.0
N A:HIS635 4.5 29.8 1.0
N A:GLY616 4.5 32.1 1.0
CE1 A:HIS573 4.7 38.6 1.0
N A:VAL613 4.7 31.0 1.0
CG A:HIS635 4.7 30.9 1.0
CA A:HIS614 4.7 28.6 1.0
C A:VAL613 4.7 32.0 1.0
OH A:TYR631 4.8 37.0 1.0
C A:HIS615 4.8 34.6 1.0
ND1 A:HIS573 4.8 39.2 1.0
O A:TRP611 4.9 33.7 1.0

Potassium binding site 2 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 2 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1805

b:35.6
occ:1.00
 O A:VAL629 2.6 34.0 1.0
O A:PHE623 2.7 33.8 1.0
O A:HOH2344 2.7 30.2 1.0
O A:TYR662 2.7 33.0 1.0
O A:ASP626 2.9 37.5 1.0
O A:HOH2339 3.1 33.7 1.0
C A:TYR662 3.6 34.3 1.0
C A:PHE623 3.6 36.1 1.0
CB A:TYR662 3.6 31.6 1.0
CB A:PHE623 3.7 33.8 1.0
C A:VAL629 3.8 34.2 1.0
C A:ASP626 4.0 39.3 1.0
CA A:TYR662 4.2 30.5 1.0
N A:TYR631 4.3 29.4 1.0
CA A:PHE623 4.3 33.7 1.0
N A:ASN663 4.5 32.2 1.0
N A:GLU624 4.5 34.6 1.0
CA A:LEU630 4.5 31.7 1.0
N A:ASP626 4.5 39.1 1.0
CA A:ASP626 4.6 38.4 1.0
CB A:ASP626 4.6 39.9 1.0
N A:LEU630 4.6 31.9 1.0
CA A:GLU624 4.7 36.2 1.0
CB A:TYR631 4.7 31.3 1.0
O A:GLU624 4.8 37.2 1.0
CA A:ASN663 4.8 31.7 1.0
C A:GLU624 4.8 39.6 1.0
CB A:ASN663 4.8 29.8 1.0
O A:GLY659 4.8 34.2 1.0
C A:LEU630 4.8 34.3 1.0
CA A:VAL629 4.9 30.0 1.0
CG A:TYR662 5.0 32.7 1.0
CG A:PHE623 5.0 33.0 1.0

Potassium binding site 3 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 3 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1806

b:35.4
occ:1.00
 O A:ASP230 2.6 32.8 1.0
OD1 A:ASP228 2.7 35.9 1.0
O A:VAL252 2.7 33.6 1.0
O A:HIS232 2.7 31.4 1.0
OG A:SER251 2.8 36.3 1.0
O A:ASP228 2.9 34.5 1.0
CG A:ASP228 3.2 34.6 1.0
C A:ASP228 3.5 34.8 1.0
C A:ASP230 3.6 34.4 1.0
C A:VAL252 3.7 34.3 1.0
OD2 A:ASP228 3.7 42.0 1.0
C A:HIS232 3.8 33.9 1.0
CB A:ASP228 3.8 33.4 1.0
N A:ASP230 3.8 32.1 1.0
N A:VAL252 3.9 30.0 1.0
CB A:HIS253 4.0 33.5 1.0
CB A:SER251 4.0 33.9 1.0
CA A:ASP230 4.2 32.2 1.0
C A:TRP229 4.2 34.7 1.0
N A:TRP229 4.2 32.2 1.0
CA A:ASP228 4.3 31.6 1.0
CB A:ASP230 4.3 34.4 1.0
CA A:SER251 4.3 32.3 1.0
CA A:HIS233 4.3 31.8 1.0
ND1 A:HIS253 4.4 38.9 1.0
CA A:TRP229 4.4 32.4 1.0
N A:HIS233 4.4 32.6 1.0
C A:SER251 4.4 34.7 1.0
N A:HIS253 4.5 32.1 1.0
CA A:HIS253 4.5 33.2 1.0
CA A:VAL252 4.5 29.8 1.0
N A:HIS232 4.5 33.3 1.0
N A:GLY234 4.6 34.1 1.0
CG A:HIS253 4.7 37.3 1.0
O A:HOH2129 4.7 40.0 1.0
CA A:HIS232 4.8 32.6 1.0
N A:VAL231 4.8 32.0 1.0
C A:VAL231 4.8 36.6 1.0
OH A:TYR249 4.8 37.6 1.0
CE1 A:HIS192 4.9 39.5 1.0
C A:HIS233 4.9 37.0 1.0
O A:TRP229 4.9 33.8 1.0
ND1 A:HIS192 5.0 40.0 1.0

Potassium binding site 4 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 4 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1807

b:38.4
occ:1.00
 O A:VAL247 2.7 36.3 1.0
O A:PHE241 2.8 41.6 1.0
O A:HOH2137 2.8 30.5 1.0
O A:TYR280 2.9 35.8 1.0
O A:HOH2133 2.9 35.7 1.0
O A:ASP244 3.0 40.8 1.0
C A:PHE241 3.6 41.2 1.0
C A:TYR280 3.6 38.3 1.0
CB A:PHE241 3.7 37.5 1.0
CB A:TYR280 3.7 36.4 1.0
C A:VAL247 3.9 37.6 1.0
C A:ASP244 4.1 42.8 1.0
CA A:PHE241 4.3 36.8 1.0
CA A:TYR280 4.3 35.5 1.0
N A:TYR249 4.4 32.6 1.0
N A:ASN281 4.5 35.9 1.0
N A:GLU242 4.5 39.2 1.0
N A:ASP244 4.6 43.0 1.0
CA A:LEU248 4.6 34.2 1.0
CA A:ASP244 4.7 41.7 1.0
CB A:ASP244 4.8 42.9 1.0
N A:LEU248 4.8 34.8 1.0
CA A:ASN281 4.8 35.0 1.0
CB A:ASN281 4.8 34.5 1.0
CB A:TYR249 4.8 33.1 1.0
O A:GLY277 4.8 43.9 1.0
CA A:GLU242 4.9 40.2 1.0
C A:GLU242 4.9 44.5 1.0
CA A:VAL247 4.9 34.4 1.0
O A:GLU242 4.9 43.1 1.0
CG A:PHE241 4.9 37.5 1.0
C A:LEU248 5.0 35.9 1.0

Potassium binding site 5 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 5 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1804

b:55.1
occ:1.00
 O B:ASP230 2.5 53.3 1.0
O B:VAL252 2.5 58.9 1.0
O B:HIS232 2.7 58.7 1.0
OG B:SER251 2.8 59.5 1.0
OD1 B:ASP228 2.9 57.6 1.0
O B:ASP228 3.0 58.6 1.0
CG B:ASP228 3.4 59.1 1.0
C B:VAL252 3.5 60.8 1.0
C B:ASP230 3.6 53.3 1.0
C B:ASP228 3.7 57.3 1.0
C B:HIS232 3.7 60.7 1.0
CB B:HIS253 3.8 58.5 1.0
N B:VAL252 3.8 59.0 1.0
N B:ASP230 3.8 51.7 1.0
OD2 B:ASP228 3.9 65.7 1.0
CB B:ASP228 4.0 57.7 1.0
CB B:SER251 4.0 65.8 1.0
CA B:ASP230 4.2 48.9 1.0
ND1 B:HIS253 4.2 66.8 1.0
C B:TRP229 4.2 55.3 1.0
N B:HIS253 4.2 58.8 1.0
CA B:HIS253 4.3 57.4 1.0
CA B:SER251 4.3 63.0 1.0
CA B:HIS233 4.3 62.4 1.0
CA B:VAL252 4.4 57.8 1.0
N B:TRP229 4.4 52.4 1.0
CB B:ASP230 4.4 51.1 1.0
C B:SER251 4.4 64.8 1.0
N B:HIS233 4.4 60.8 1.0
N B:HIS232 4.4 54.3 1.0
CA B:TRP229 4.5 51.9 1.0
CA B:ASP228 4.5 54.4 1.0
CG B:HIS253 4.5 64.3 1.0
O B:HOH2064 4.5 46.6 1.0
C B:VAL231 4.6 57.1 1.0
N B:VAL231 4.7 51.2 1.0
N B:GLY234 4.7 64.4 1.0
CA B:HIS232 4.7 55.3 1.0
O B:TRP229 4.9 54.8 1.0
C B:HIS233 4.9 67.4 1.0
OH B:TYR249 5.0 78.0 1.0

Potassium binding site 6 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 6 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1805

b:53.0
occ:1.00
 O B:ASP612 2.6 56.4 1.0
O B:LEU634 2.6 55.3 1.0
OG B:SER633 2.7 55.0 1.0
O B:HIS614 2.7 53.3 1.0
OD1 B:ASP610 2.8 52.9 1.0
O B:ASP610 2.8 47.0 1.0
CG B:ASP610 3.3 51.2 1.0
C B:ASP610 3.5 47.2 1.0
C B:LEU634 3.7 58.5 1.0
C B:ASP612 3.7 55.7 1.0
C B:HIS614 3.7 55.1 1.0
CB B:ASP610 3.8 43.6 1.0
N B:LEU634 3.8 51.7 1.0
N B:ASP612 3.9 49.4 1.0
CB B:SER633 3.9 52.7 1.0
OD2 B:ASP610 3.9 53.0 1.0
CB B:HIS635 4.0 58.0 1.0
CA B:SER633 4.2 50.6 1.0
CA B:ASP612 4.2 48.7 1.0
CA B:ASP610 4.3 42.4 1.0
N B:TRP611 4.3 46.0 1.0
C B:TRP611 4.3 53.9 1.0
CA B:HIS615 4.3 49.9 1.0
CB B:ASP612 4.3 47.5 1.0
ND1 B:HIS635 4.4 62.0 1.0
N B:HIS615 4.4 52.0 1.0
C B:SER633 4.4 55.3 1.0
O B:HOH2184 4.4 52.6 1.0
CA B:LEU634 4.5 53.8 1.0
N B:HIS614 4.5 54.7 1.0
CA B:TRP611 4.5 49.0 1.0
N B:HIS635 4.5 57.9 1.0
N B:GLY616 4.5 47.8 1.0
CA B:HIS635 4.5 58.3 1.0
CG B:HIS635 4.7 61.9 1.0
OH B:TYR631 4.7 57.3 1.0
CE1 B:HIS573 4.7 54.5 1.0
CA B:HIS614 4.7 54.1 1.0
C B:HIS615 4.8 51.5 1.0
N B:VAL613 4.8 54.4 1.0
C B:VAL613 4.8 60.4 1.0
ND1 B:HIS573 4.8 53.2 1.0
O B:TRP611 5.0 55.5 1.0

Potassium binding site 7 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 7 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1806

b:49.9
occ:1.00
 O B:PHE623 2.6 55.4 1.0
O B:HOH2189 2.7 39.8 1.0
O B:VAL629 2.7 48.8 1.0
O B:ASP626 2.8 55.7 1.0
O B:TYR662 2.8 53.4 1.0
O B:HOH2187 2.9 41.5 1.0
C B:PHE623 3.5 53.8 1.0
CB B:TYR662 3.6 51.3 1.0
C B:TYR662 3.6 54.6 1.0
CB B:PHE623 3.7 44.8 1.0
C B:ASP626 3.9 55.6 1.0
C B:VAL629 3.9 48.8 1.0
CA B:TYR662 4.2 51.5 1.0
CA B:PHE623 4.2 45.6 1.0
N B:GLU624 4.4 53.2 1.0
N B:ASP626 4.4 53.9 1.0
N B:TYR631 4.5 47.3 1.0
CA B:ASP626 4.5 52.2 1.0
N B:ASN663 4.5 53.0 1.0
CB B:ASP626 4.5 51.9 1.0
CA B:GLU624 4.6 54.8 1.0
CA B:LEU630 4.6 45.4 1.0
O B:GLU624 4.7 63.1 1.0
C B:GLU624 4.7 60.6 1.0
O B:GLY659 4.7 61.6 1.0
N B:LEU630 4.8 45.2 1.0
CB B:ASN663 4.8 51.5 1.0
CG B:TYR662 4.9 53.7 1.0
CA B:ASN663 4.9 51.3 1.0
CB B:TYR631 4.9 49.2 1.0
CA B:VAL629 5.0 42.7 1.0

Potassium binding site 8 out of 8 in 5g0i

Go back to Potassium Binding Sites List in 5g0i
Potassium binding site 8 out of 8 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Cleaved) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1807

b:70.4
occ:1.00
 O B:TYR280 2.3 93.0 1.0
O B:HOH2068 2.4 41.5 1.0
C B:TYR280 2.9 95.7 1.0
O B:VAL247 3.1 92.7 1.0
O B:PHE241 3.2 98.3 1.0
O B:HOH2066 3.3 52.8 1.0
CB B:TYR280 3.4 0.5 1.0
O B:ASP244 3.5 0.9 1.0
N B:ASN281 3.7 90.3 1.0
CA B:TYR280 3.7 98.3 1.0
C B:PHE241 4.0 96.7 1.0
CA B:ASN281 4.1 86.3 1.0
CB B:ASN281 4.1 87.1 1.0
N B:TYR249 4.2 78.0 1.0
CB B:PHE241 4.3 85.1 1.0
C B:VAL247 4.3 91.3 1.0
O B:GLY277 4.4 0.4 1.0
C B:ASP244 4.5 0.2 1.0
CA B:LEU248 4.6 84.5 1.0
OD1 B:ASN281 4.6 79.5 1.0
CB B:TYR249 4.7 74.9 1.0
N B:TYR280 4.7 0.7 1.0
N B:GLU242 4.8 95.6 1.0
O B:GLU242 4.8 0.6 1.0
CG B:TYR280 4.8 0.4 1.0
CA B:PHE241 4.8 87.9 1.0
C B:LEU248 4.9 82.7 1.0
CG B:ASN281 4.9 93.1 1.0
C B:GLU242 4.9 0.7 1.0
CA B:GLU242 4.9 99.5 1.0
N B:ASP244 5.0 0.3 1.0

Reference:

Y.Miyake, J.J.Keusch, L.Wang, M.Saito, D.Hess, X.Wang, B.J.Melancon, P.Helquist, H.Gut, P.Matthias. Structural Insights Into HDAC6 Tubulin Deacetylation and Its Selective Inhibition Nat.Chem.Biol. V. 12 748 2016.
ISSN: ISSN 1552-4450
PubMed: 27454931
DOI: 10.1038/NCHEMBIO.2140
Page generated: Mon Aug 12 13:40:27 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy