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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

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