Sodium in PDB 6thv: X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A

Protein crystallography data

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv was solved by C.Barinka, L.Motlova, M.Svoboda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.90 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.278, 93.713, 51.574, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 16.9

Other elements in 6thv:

The structure of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A also contains other interesting chemical elements:

Potassium (K) 3 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A (pdb code 6thv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A, PDB code: 6thv:

Sodium binding site 1 out of 1 in 6thv

Go back to Sodium Binding Sites List in 6thv
Sodium binding site 1 out of 1 in the X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Danio Rerio Histone Deacetylase 6 (HDAC6; Catalytic Domain 2) in Complex with Tubastatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na810

b:42.6
occ:0.50
O A:HOH972 2.3 32.2 1.0
O A:HOH1230 2.4 45.5 1.0
O A:HOH1220 2.6 41.0 1.0
O A:HOH1183 2.8 49.4 1.0
O A:HOH1042 3.3 13.0 1.0
NE A:ARG492 3.7 9.9 1.0
OE1 A:GLN554 3.8 12.3 1.0
OD1 A:ASN551 3.9 9.8 1.0
NH2 A:ARG492 4.2 10.2 1.0
CZ A:ARG492 4.2 9.3 1.0
NE2 A:GLN554 4.3 12.2 1.0
CD A:ARG492 4.3 9.9 1.0
CD A:GLN554 4.5 11.3 1.0
O A:HOH1258 4.5 27.3 1.0
O A:HOH949 4.6 13.3 1.0
O A:HOH1006 4.7 22.0 1.0
OH A:TYR595 4.9 10.8 1.0

Reference:

C.Barinka, L.Motlova, M.Svoboda. X-Ray Structure of Danio Rerio Histone Deacetylase 6 (HDAC6) CD2 in Complex with A Inhibitor Tubastatin A To Be Published.
Page generated: Tue Dec 15 14:20:29 2020

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