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Potassium in PDB 5g0j: Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A, PDB code: 5g0j 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) 50.00 / 2.88
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.224, 187.224, 102.718, 90.00, 90.00, 120.00
R / Rfree (%) 17.56 / 21.41

Other elements in 5g0j:

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

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A (pdb code 5g0j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) in Complex with Nexturastat A, PDB code: 5g0j:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 5g0j

Go back to Potassium Binding Sites List in 5g0j
Potassium binding site 1 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) 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 Intact) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1812

b:88.8
occ:1.00
 O A:HOH2060 2.6 48.5 1.0
OD2 A:ASP230 2.6 71.0 1.0
OD1 A:ASP230 2.7 65.1 1.0
OD2 A:ASP323 2.8 79.6 1.0
CG A:ASP230 3.0 67.3 1.0
OH A:TYR363 3.0 76.0 1.0
ND1 A:HIS232 3.0 82.8 1.0
NE2 A:HIS192 3.6 72.1 1.0
CA A:GLY361 3.7 68.2 1.0
CG A:HIS232 3.8 80.2 1.0
CG A:ASP323 3.9 77.2 1.0
CE1 A:HIS232 3.9 82.5 1.0
CZ A:TYR363 3.9 73.7 1.0
CB A:HIS232 3.9 75.7 1.0
N A:GLY361 4.0 68.2 1.0
CE2 A:TYR363 4.0 64.8 1.0
CE1 A:HIS192 4.1 71.3 1.0
OD1 A:ASP323 4.2 79.2 1.0
NE2 A:HIS193 4.4 82.0 1.0
CB A:ASP230 4.5 59.2 1.0
N A:HIS232 4.6 72.6 1.0
C A:GLY361 4.8 72.8 1.0
CD2 A:HIS192 4.8 72.5 1.0
CD2 A:HIS232 4.9 82.8 1.0
NE2 A:HIS232 4.9 82.8 1.0
CA A:HIS232 4.9 74.2 1.0
C A:GLU360 5.0 72.4 1.0

Potassium binding site 2 out of 5 in 5g0j

Go back to Potassium Binding Sites List in 5g0j
Potassium binding site 2 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) 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 Intact) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1813

b:0.4
occ:1.00
 O A:TYR662 2.4 96.2 1.0
O A:ASP626 2.5 0.5 1.0
O A:PHE623 2.8 0.8 1.0
O A:VAL629 2.9 85.8 1.0
CB A:TYR662 3.1 94.4 1.0
C A:TYR662 3.2 95.4 1.0
CA A:TYR662 3.7 92.4 1.0
C A:ASP626 3.7 0.3 1.0
C A:PHE623 3.9 0.5 1.0
C A:VAL629 4.1 84.5 1.0
O A:GLY659 4.1 0.2 1.0
N A:ASN663 4.2 89.6 1.0
CB A:PHE623 4.4 93.8 1.0
CG A:TYR662 4.4 98.4 1.0
CB A:ASN663 4.5 86.1 1.0
CA A:ASP626 4.6 0.8 1.0
N A:ASP626 4.6 0.1 1.0
CA A:LEU630 4.6 82.5 1.0
CA A:ASN663 4.6 88.8 1.0
N A:ASP627 4.7 96.2 1.0
N A:TYR662 4.7 92.9 1.0
CA A:GLY659 4.7 97.9 1.0
O A:GLU624 4.8 0.3 1.0
N A:TYR631 4.8 91.0 1.0
CA A:PHE623 4.8 93.2 1.0
C A:GLU624 4.8 0.5 1.0
CA A:ASP627 4.8 94.2 1.0
N A:GLU624 4.8 0.1 1.0
N A:LEU630 4.8 81.9 1.0
CA A:GLU624 4.9 0.1 1.0
C A:GLY659 4.9 0.3 1.0
CB A:ASP626 5.0 0.1 1.0

Potassium binding site 3 out of 5 in 5g0j

Go back to Potassium Binding Sites List in 5g0j
Potassium binding site 3 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) 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 Intact) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1814

b:0.1
occ:1.00
 OD1 A:ASP228 2.4 78.7 1.0
O A:ASP230 2.6 69.7 1.0
O A:HIS232 2.6 79.3 1.0
O A:VAL252 2.8 80.5 1.0
OG A:SER251 2.8 82.8 1.0
O A:ASP228 2.9 69.4 1.0
CG A:ASP228 3.3 76.3 1.0
CB A:HIS253 3.6 82.0 1.0
C A:ASP230 3.6 68.2 1.0
C A:HIS232 3.6 80.0 1.0
C A:VAL252 3.6 81.4 1.0
C A:ASP228 3.7 69.8 1.0
CB A:ASP228 3.8 68.0 1.0
ND1 A:HIS253 4.0 88.7 1.0
N A:ASP230 4.0 59.1 1.0
CB A:SER251 4.0 79.0 1.0
N A:VAL252 4.0 75.7 1.0
C A:SER251 4.1 79.5 1.0
OD2 A:ASP228 4.2 78.9 1.0
CA A:SER251 4.2 77.2 1.0
CA A:HIS253 4.2 80.2 1.0
CA A:HIS233 4.2 77.9 1.0
CA A:ASP230 4.2 59.0 1.0
CG A:HIS253 4.2 86.4 1.0
N A:HIS253 4.2 78.9 1.0
N A:HIS233 4.2 77.6 1.0
CB A:ASP230 4.3 59.2 1.0
N A:HIS232 4.3 72.6 1.0
C A:TRP229 4.4 63.9 1.0
CA A:ASP228 4.4 67.3 1.0
C A:VAL231 4.5 74.4 1.0
N A:TRP229 4.5 66.2 1.0
N A:VAL231 4.6 66.9 1.0
CA A:VAL252 4.6 75.7 1.0
CA A:HIS232 4.6 74.2 1.0
O A:HOH2064 4.6 62.1 1.0
N A:GLY234 4.7 77.9 1.0
CA A:TRP229 4.7 65.1 1.0
O A:SER251 4.7 79.5 1.0
CA A:VAL231 4.8 67.1 1.0
C A:HIS233 4.9 80.3 1.0
O A:TRP229 4.9 60.9 1.0
O A:VAL231 4.9 75.6 1.0

Potassium binding site 4 out of 5 in 5g0j

Go back to Potassium Binding Sites List in 5g0j
Potassium binding site 4 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) 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 Intact) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1815

b:0.1
occ:1.00
 O A:PHE241 2.4 98.4 1.0
O A:TYR280 2.4 96.0 1.0
O A:VAL247 2.6 86.0 1.0
O A:ASP244 2.7 97.8 1.0
CB A:TYR280 3.3 98.9 1.0
C A:TYR280 3.4 95.5 1.0
C A:PHE241 3.5 98.8 1.0
CB A:PHE241 3.8 92.0 1.0
C A:ASP244 3.8 98.1 1.0
C A:VAL247 3.9 86.1 1.0
CA A:TYR280 3.9 96.2 1.0
O A:GLU242 4.1 0.9 1.0
O A:GLY277 4.2 1.0 1.0
CA A:PHE241 4.2 89.8 1.0
N A:GLU242 4.5 99.1 1.0
C A:GLU242 4.5 0.8 1.0
N A:ASN281 4.5 87.0 1.0
N A:ASP244 4.5 99.8 1.0
CA A:ASP244 4.6 97.4 1.0
CG A:TYR280 4.6 0.0 1.0
CA A:LEU248 4.7 79.5 1.0
N A:LEU248 4.7 80.9 1.0
CA A:GLU242 4.7 100.0 1.0
CA A:GLY277 4.7 0.8 1.0
OD1 A:ASN281 4.7 93.5 1.0
N A:PRO245 4.8 92.6 1.0
CA A:PRO245 4.9 91.1 1.0
CA A:VAL247 4.9 84.8 1.0
N A:TYR249 4.9 83.0 1.0
CB A:ASP244 4.9 98.3 1.0
N A:TYR280 4.9 96.8 1.0
C A:GLY277 5.0 0.9 1.0
CB A:ASN281 5.0 81.0 1.0

Potassium binding site 5 out of 5 in 5g0j

Go back to Potassium Binding Sites List in 5g0j
Potassium binding site 5 out of 5 in the Crystal Structure of Danio Rerio HDAC6 CD1 and CD2 (Linker Intact) 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 Intact) in Complex with Nexturastat A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1816

b:97.0
occ:1.00
 O A:LEU634 2.6 0.3 1.0
O A:ASP612 2.6 93.0 1.0
OD1 A:ASP610 2.8 94.6 1.0
OG A:SER633 2.8 97.0 1.0
O A:HIS614 3.0 0.9 1.0
O A:ASP610 3.0 93.1 1.0
C A:LEU634 3.4 0.7 1.0
N A:LEU634 3.5 99.3 1.0
CG A:ASP610 3.6 96.1 1.0
C A:ASP610 3.6 93.2 1.0
CB A:ASP610 3.7 88.7 1.0
C A:ASP612 3.7 94.0 1.0
C A:HIS614 3.8 0.9 1.0
N A:ASP612 3.9 90.0 1.0
CB A:SER633 4.0 94.2 1.0
CB A:HIS635 4.0 0.8 1.0
C A:SER633 4.1 0.2 1.0
CA A:LEU634 4.1 0.2 1.0
CA A:SER633 4.2 92.8 1.0
CA A:HIS615 4.2 99.5 1.0
N A:HIS635 4.2 0.0 1.0
ND1 A:HIS635 4.2 0.8 1.0
C A:TRP611 4.3 94.6 1.0
CA A:ASP612 4.3 88.9 1.0
CA A:ASP610 4.3 87.3 1.0
N A:TRP611 4.3 90.8 1.0
N A:HIS615 4.3 99.9 1.0
CA A:HIS635 4.3 0.6 1.0
CB A:ASP612 4.4 89.8 1.0
CA A:TRP611 4.5 91.5 1.0
N A:HIS614 4.5 95.8 1.0
CG A:HIS635 4.6 0.0 1.0
OD2 A:ASP610 4.7 0.1 1.0
N A:GLY616 4.7 0.3 1.0
OH A:TYR631 4.7 0.5 1.0
C A:VAL613 4.8 96.6 1.0
CA A:HIS614 4.8 98.2 1.0
O A:TRP611 4.8 94.0 1.0
N A:VAL613 4.8 91.9 1.0
C A:HIS615 4.9 0.3 1.0
CB A:LEU634 5.0 99.8 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 13:41:21 2024

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