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Potassium in PDB 6v7a: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657, PDB code: 6v7a was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.20 / 2.09
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.461, 64.871, 142.393, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.9

Other elements in 6v7a:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 (pdb code 6v7a). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657, PDB code: 6v7a:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6v7a

Go back to Potassium Binding Sites List in 6v7a
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657


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 Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:22.6
occ:1.00
OD1 A:ASP610 2.6 21.0 1.0
O A:ASP612 2.7 21.8 1.0
O A:LEU634 2.7 22.9 1.0
O A:HIS614 2.7 22.6 1.0
O A:ASP610 2.8 22.4 1.0
OG A:SER633 2.9 22.0 1.0
CG A:ASP610 3.2 20.1 1.0
C A:ASP610 3.5 21.0 1.0
C A:ASP612 3.6 20.2 1.0
C A:HIS614 3.7 21.4 1.0
C A:LEU634 3.7 28.6 1.0
CB A:ASP610 3.8 22.1 1.0
N A:ASP612 3.9 20.1 1.0
OD2 A:ASP610 4.0 23.2 1.0
N A:LEU634 4.0 24.7 1.0
CB A:SER633 4.1 19.6 1.0
CB A:HIS635 4.1 19.9 1.0
CA A:ASP612 4.1 20.1 1.0
N A:TRP611 4.1 20.2 1.0
CB A:ASP612 4.2 20.0 1.0
C A:TRP611 4.2 23.5 1.0
CA A:ASP610 4.2 20.7 1.0
CA A:TRP611 4.3 22.3 1.0
CA A:HIS615 4.3 22.4 1.0
N A:HIS615 4.4 21.8 1.0
CA A:SER633 4.4 19.7 1.0
ND1 A:HIS635 4.4 22.4 1.0
N A:HIS614 4.4 20.2 1.0
N A:GLY616 4.5 21.2 1.0
CA A:HIS635 4.5 24.5 1.0
CA A:LEU634 4.5 24.1 1.0
C A:SER633 4.5 21.6 1.0
N A:HIS635 4.5 22.9 1.0
O A:HOH912 4.6 21.6 1.0
C A:VAL613 4.7 19.9 1.0
CA A:HIS614 4.7 20.3 1.0
CG A:HIS635 4.7 24.7 1.0
N A:VAL613 4.7 20.8 1.0
C A:HIS615 4.7 24.1 1.0
OH A:TYR631 4.8 25.0 1.0
CE1 A:HIS573 4.8 23.2 1.0
ND1 A:HIS573 4.9 23.5 1.0
O A:TRP611 5.0 22.2 1.0

Potassium binding site 2 out of 2 in 6v7a

Go back to Potassium Binding Sites List in 6v7a
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657


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 Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2657 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:34.4
occ:1.00
O A:VAL629 2.6 24.7 1.0
O A:PHE623 2.7 24.8 1.0
O A:HOH924 2.8 28.5 1.0
O A:TYR662 2.9 24.9 1.0
O A:ASP626 2.9 32.1 1.0
O A:HOH953 3.2 21.1 1.0
CB A:TYR662 3.6 22.8 1.0
C A:TYR662 3.6 25.1 1.0
C A:PHE623 3.7 26.2 1.0
CB A:PHE623 3.7 25.1 1.0
C A:VAL629 3.9 24.6 1.0
C A:ASP626 4.1 34.2 1.0
CA A:TYR662 4.2 24.2 1.0
CA A:PHE623 4.3 28.5 1.0
N A:TYR631 4.3 22.0 1.0
N A:ASN663 4.4 22.8 1.0
CA A:LEU630 4.5 23.4 1.0
N A:ASP626 4.6 33.4 1.0
N A:GLU624 4.6 25.5 1.0
N A:LEU630 4.7 20.2 1.0
CB A:ASP626 4.7 27.9 1.0
CA A:ASP626 4.7 29.5 1.0
CA A:GLU624 4.7 25.3 1.0
CB A:TYR631 4.8 24.4 1.0
CA A:ASN663 4.8 22.2 1.0
C A:GLU624 4.8 28.7 1.0
CB A:ASN663 4.8 21.1 1.0
O A:GLU624 4.9 26.7 1.0
CG A:TYR662 4.9 25.2 1.0
C A:LEU630 4.9 21.6 1.0
O A:GLY659 4.9 27.3 1.0
CA A:VAL629 4.9 22.6 1.0
CG A:PHE623 4.9 27.2 1.0
CB A:VAL629 5.0 25.3 1.0

Reference:

A.P.Saraswati, N.Relitti, M.Brindisi, J.D.Osko, G.Chemi, S.Federico, A.Grillo, S.Brogi, N.H.Mccabe, R.C.Turkington, O.Ibrahim, J.O'sullivan, S.Lamponi, M.Ghanim, V.P.Kelly, D.Zisterer, R.Amet, P.Hannon Barroeta, F.Vanni, C.Ulivieri, D.Herp, F.Sarno, A.Di Costanzo, F.Saccoccia, G.Ruberti, M.Jung, L.Altucci, S.Gemma, S.Butini, D.W.Christianson, G.Campiani. Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation. Acs Med.Chem.Lett. V. 11 2268 2020.
ISSN: ISSN 1948-5875
PubMed: 33214839
DOI: 10.1021/ACSMEDCHEMLETT.0C00395
Page generated: Mon Dec 14 02:02:37 2020

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