Chlorine in PDB 6mr5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.010, 46.460, 96.400, 90.00, 119.19, 90.00
R / Rfree (%) 19 / 22.6

Other elements in 6mr5:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor (pdb code 6mr5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6mr5

Go back to Chlorine Binding Sites List in 6mr5
Chlorine binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:47.4
occ:1.00
CL2 A:W45804 0.0 47.4 1.0
C16 A:W45804 1.7 29.3 1.0
O A:HOH982 2.6 26.0 1.0
C15 A:W45804 2.7 27.8 1.0
C18 A:W45804 2.7 34.6 1.0
CL1 A:W45804 3.1 47.1 1.0
CD A:PRO464 3.5 29.5 1.0
O B:HOH1044 3.7 25.1 1.0
CG A:PRO464 3.9 25.0 1.0
C14 A:W45804 3.9 28.7 1.0
C20 A:W45804 4.0 32.3 1.0
CD1 B:PHE642 4.2 22.7 1.0
O B:ALA641 4.2 24.1 1.0
C21 A:W45804 4.4 26.4 1.0
CE1 B:PHE642 4.5 21.9 1.0
CA B:PHE642 4.8 22.7 1.0
N A:PRO464 4.8 26.9 1.0
C B:ALA641 4.9 26.2 1.0
CB A:PRO464 4.9 25.9 1.0

Chlorine binding site 2 out of 4 in 6mr5

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Chlorine binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:47.1
occ:1.00
CL1 A:W45804 0.0 47.1 1.0
C18 A:W45804 1.7 34.6 1.0
O A:HOH982 2.4 26.0 1.0
C20 A:W45804 2.7 32.3 1.0
C16 A:W45804 2.7 29.3 1.0
CL2 A:W45804 3.1 47.4 1.0
CD2 A:HIS463 3.7 30.5 1.0
NE2 A:HIS463 3.9 30.4 1.0
C21 A:W45804 3.9 26.4 1.0
O A:HOH1001 4.0 28.0 1.0
C15 A:W45804 4.0 27.8 1.0
CE1 B:PHE642 4.2 21.9 1.0
O B:HOH1051 4.2 34.2 1.0
O B:HOH1073 4.2 35.5 1.0
CD A:PRO464 4.3 29.5 1.0
C14 A:W45804 4.5 28.7 1.0
CG A:HIS463 4.6 27.9 1.0
CD1 B:PHE642 4.6 22.7 1.0
NH2 B:ARG636 4.6 26.2 1.0
NH1 B:ARG636 4.7 21.5 1.0
OD2 A:ASP460 4.7 34.2 1.0
CE1 A:HIS463 4.8 31.1 1.0
CZ B:ARG636 4.8 23.4 1.0
CG A:PRO464 5.0 25.0 1.0

Chlorine binding site 3 out of 4 in 6mr5

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Chlorine binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:57.6
occ:1.00
CL2 B:W45804 0.0 57.6 1.0
C16 B:W45804 1.7 46.2 1.0
C15 B:W45804 2.7 41.4 1.0
C18 B:W45804 2.7 44.4 1.0
CL1 B:W45804 3.1 60.8 1.0
OG A:SER461 3.9 43.9 1.0
C14 B:W45804 3.9 44.8 1.0
O A:TRP459 4.0 39.4 1.0
CG B:PRO464 4.0 24.4 1.0
C20 B:W45804 4.0 41.3 1.0
CD B:PRO464 4.0 22.1 1.0
N A:SER461 4.1 36.3 1.0
O A:HOH933 4.3 37.1 1.0
CD1 B:LEU712 4.3 31.2 1.0
CD2 A:HIS462 4.4 43.4 1.0
C21 B:W45804 4.5 44.7 1.0
CA A:ASP460 4.6 36.8 1.0
CB A:SER461 4.7 40.0 1.0
OD1 A:ASP460 4.7 32.9 1.0
C A:ASP460 4.8 40.7 1.0
CA A:SER461 4.9 38.2 1.0
C A:TRP459 5.0 39.1 1.0
NE2 A:HIS462 5.0 43.1 1.0

Chlorine binding site 4 out of 4 in 6mr5

Go back to Chlorine Binding Sites List in 6mr5
Chlorine binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:60.8
occ:1.00
CL1 B:W45804 0.0 60.8 1.0
C18 B:W45804 1.7 44.4 1.0
C20 B:W45804 2.7 41.3 1.0
C16 B:W45804 2.7 46.2 1.0
O A:HOH1007 2.9 44.0 1.0
CL2 B:W45804 3.1 57.6 1.0
NE2 B:HIS463 3.7 28.4 1.0
CD2 B:HIS463 3.8 30.7 1.0
NE2 A:HIS462 3.9 43.1 1.0
C21 B:W45804 3.9 44.7 1.0
C15 B:W45804 4.0 41.4 1.0
CD B:PRO464 4.1 22.1 1.0
CD2 A:HIS462 4.1 43.4 1.0
CG B:PRO464 4.4 24.4 1.0
CE1 B:HIS463 4.4 24.0 1.0
C14 B:W45804 4.5 44.8 1.0
CZ B:PHE583 4.6 27.8 1.0
CG B:HIS463 4.6 24.3 1.0
CE1 A:HIS462 4.7 43.4 1.0
CE1 B:PHE583 4.9 24.1 1.0
ND1 B:HIS463 4.9 23.4 1.0

Reference:

N.J.Porter, S.Shen, C.Barinka, A.P.Kozikowski, D.W.Christianson. Molecular Basis For the Selective Inhibition of Histone Deacetylase 6 By A Mercaptoacetamide Inhibitor. Acs Med Chem Lett V. 9 1301 2018.
ISSN: ISSN 1948-5875
PubMed: 30613344
DOI: 10.1021/ACSMEDCHEMLETT.8B00487
Page generated: Sat Dec 12 13:22:02 2020

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