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Iodine in PDB 5eek: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5eek was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.01 / 1.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.881, 94.429, 51.698, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 16.3

Other elements in 5eek:

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

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

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A (pdb code 5eek). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 31 binding sites of Iodine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5eek:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 31 in 5eek

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Iodine binding site 1 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2005

b:29.0
occ:0.84
 N A:NH42031 3.2 25.1 1.0
O A:HOH2340 3.4 24.9 1.0
N A:GLY655 3.5 11.6 1.0
CA A:GLY655 3.8 12.0 1.0
CG A:LEU656 3.9 18.8 1.0
C A:GLY655 4.0 13.9 1.0
CB A:LYS653 4.0 10.9 1.0
O A:GLY655 4.1 15.1 1.0
CD2 A:LEU656 4.1 19.3 1.0
N A:VAL654 4.1 9.9 1.0
CA A:LYS653 4.1 10.4 1.0
C A:LYS653 4.1 9.9 1.0
CD1 A:LEU656 4.5 20.7 1.0
O A:HOH2113 4.6 27.8 1.0
N A:LEU656 4.6 13.8 1.0
C A:VAL654 4.7 11.3 1.0
NE2 A:GLN620 4.8 12.2 1.0
CD A:LYS653 4.8 16.1 1.0
O A:LYS653 4.8 10.9 1.0
CG A:LYS653 4.9 12.8 1.0

Iodine binding site 2 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 2 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2006

b:32.0
occ:0.36
 N A:NH42030 2.4 25.5 1.0
N A:ARG520 3.6 15.0 1.0
CD A:PRO519 3.7 18.0 1.0
CB A:LYS518 3.7 22.6 1.0
N A:PRO519 3.8 17.6 1.0
CB A:ARG520 3.9 16.9 0.4
CB A:PRO519 4.0 17.1 1.0
CG A:PRO519 4.2 16.9 1.0
CB A:ARG520 4.3 15.9 0.6
C A:LYS518 4.3 17.7 1.0
CA A:PRO519 4.4 17.1 1.0
CA A:ARG520 4.4 15.4 0.4
C A:PRO519 4.5 15.6 1.0
CD A:LYS518 4.5 28.8 1.0
CG A:ARG520 4.6 15.8 0.6
CA A:ARG520 4.6 15.0 0.6
CA A:LYS518 4.6 19.8 1.0
O A:HOH2184 4.6 30.9 1.0
CG A:LYS518 4.6 26.1 1.0

Iodine binding site 3 out of 31 in 5eek

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Iodine binding site 3 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2007

b:19.0
occ:0.28
 NE1 A:TRP459 3.6 12.7 1.0
CA A:ARG520 4.0 15.0 0.6
CA A:ARG520 4.1 15.4 0.4
N A:ARG520 4.1 15.0 1.0
CB A:ARG520 4.3 15.9 0.6
C A:PRO519 4.3 15.6 1.0
CD1 A:TRP459 4.3 12.4 1.0
O A:PRO519 4.3 15.1 1.0
CB A:PRO519 4.5 17.1 1.0
CB A:ASN523 4.6 13.9 1.0
CE2 A:TRP459 4.6 13.0 1.0
CB A:ARG520 4.9 16.9 0.4
ND2 A:ASN523 5.0 19.2 1.0
CG A:ASN523 5.0 16.8 1.0
CZ2 A:TRP459 5.0 13.2 1.0

Iodine binding site 4 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 4 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2008

b:37.4
occ:0.48
 I A:IOD2008 0.0 37.4 0.5
I A:IOD2009 2.7 31.2 0.5
I A:IOD2008 2.8 66.5 0.5
CD1 A:LEU712 3.8 16.4 1.0
O A:HOH2139 3.9 35.1 1.0
C16 A:TSN2004 4.0 26.0 1.0
CB A:PRO464 4.1 13.2 1.0
CG A:PRO464 4.2 13.6 1.0
CG A:PRO711 4.2 16.3 1.0
CD A:PRO464 4.5 12.6 1.0
C3 A:TSN2004 4.5 20.6 1.0
CB A:PRO711 4.6 15.8 1.0
N2 A:TSN2004 4.9 24.6 1.0

Iodine binding site 5 out of 31 in 5eek

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Iodine binding site 5 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2008

b:66.5
occ:0.52
 I A:IOD2008 0.0 66.5 0.5
I A:IOD2008 2.8 37.4 0.5
CG A:PRO711 3.3 16.3 1.0
O A:HOH2428 3.3 22.7 1.0
I A:IOD2014 3.9 32.4 0.3
CB A:PRO464 4.0 13.2 1.0
O A:TYR745 4.0 13.8 1.0
CD A:PRO711 4.2 14.7 1.0
O A:HOH2168 4.3 18.9 1.0
CB A:PRO711 4.4 15.8 1.0
CB A:TYR745 4.4 10.2 1.0
CD1 A:LEU712 4.5 16.4 1.0
CA A:PRO464 4.6 12.3 1.0
C A:TYR745 4.8 11.2 1.0
O A:HOH2203 4.9 20.5 1.0
CG A:PRO464 4.9 13.6 1.0

Iodine binding site 6 out of 31 in 5eek

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Iodine binding site 6 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2009

b:31.2
occ:0.45
 I A:IOD2008 2.7 37.4 0.5
CD1 A:LEU712 3.9 16.4 1.0
C3 A:TSN2004 4.0 20.6 1.0
CB A:PRO711 4.0 15.8 1.0
O A:HOH2160 4.1 16.7 1.0
C2 A:TSN2004 4.4 20.3 1.0
O A:PRO711 4.5 14.9 1.0
CG A:PRO711 4.5 16.3 1.0
C16 A:TSN2004 4.5 26.0 1.0
C A:PRO711 4.7 13.2 1.0
CG A:LEU712 4.9 13.6 1.0

Iodine binding site 7 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 7 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2010

b:38.3
occ:0.44
 O A:HOH2430 3.3 30.7 1.0
N A:GLY657 3.5 16.7 1.0
CD2 A:LEU656 4.0 19.3 1.0
CA A:LEU656 4.1 14.4 1.0
CD A:ARG660 4.1 17.5 1.0
NH1 A:ARG660 4.1 18.4 1.0
C A:LEU656 4.3 15.7 1.0
CA A:GLY657 4.4 18.6 1.0
CB A:LEU656 4.6 15.8 1.0
O A:GLY655 4.6 15.1 1.0
NE A:ARG660 4.7 17.6 1.0
CZ A:ARG660 4.7 17.8 1.0
CG A:LEU656 5.0 18.8 1.0

Iodine binding site 8 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 8 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2011

b:44.1
occ:0.48
 I A:IOD2011 0.0 44.1 0.5
I A:IOD2011 2.3 77.2 0.5
ND1 A:HIS724 3.3 21.6 1.0
NE2 A:GLN728 3.7 19.5 1.0
CE A:MET679 3.9 18.7 1.0
CG A:GLN728 3.9 12.4 1.0
CD A:GLN728 4.0 16.1 1.0
CE1 A:HIS724 4.2 22.6 1.0
CG A:HIS724 4.3 17.5 1.0
CB A:HIS724 4.3 11.9 1.0
O A:HIS724 4.5 12.4 1.0
O A:HOH2438 4.6 30.8 1.0
OE1 A:GLN728 4.9 16.4 1.0
CA A:HIS724 4.9 10.3 1.0

Iodine binding site 9 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 9 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2011

b:77.2
occ:0.52
 I A:IOD2011 0.0 77.2 0.5
I A:IOD2011 2.3 44.1 0.5
ND1 A:HIS724 3.2 21.6 1.0
CD2 A:HIS727 3.3 18.1 1.0
CB A:HIS727 3.8 13.8 1.0
CG A:HIS727 3.8 16.8 1.0
CE1 A:HIS724 3.8 22.6 1.0
CG A:HIS724 3.9 17.5 1.0
O A:HIS724 4.0 12.4 1.0
CA A:HIS724 4.1 10.3 1.0
CB A:HIS724 4.2 11.9 1.0
NE2 A:HIS727 4.4 20.3 1.0
CG A:GLN728 4.4 12.4 1.0
CG A:PRO766 4.4 22.4 1.0
CB A:PRO766 4.5 21.7 1.0
C A:HIS724 4.5 10.7 1.0
N A:GLN728 4.7 10.5 1.0
NE2 A:HIS724 4.8 21.2 1.0
CD2 A:HIS724 4.8 20.1 1.0
NE2 A:GLN728 4.9 19.5 1.0
C A:HIS727 5.0 10.5 1.0
CA A:HIS727 5.0 11.2 1.0

Iodine binding site 10 out of 31 in 5eek

Go back to Iodine Binding Sites List in 5eek
Iodine binding site 10 out of 31 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2012

b:67.1
occ:0.48
 I A:IOD2012 0.0 67.1 0.5
I A:IOD2012 2.0 35.9 0.5
O A:PRO695 2.9 10.9 1.0
N A:ALA733 2.9 11.2 1.0
CA A:ALA733 3.4 11.5 1.0
CD A:PRO695 3.5 10.1 1.0
N A:PRO695 3.6 10.6 1.0
C A:ALA694 3.6 10.9 1.0
CA A:ALA694 3.7 11.4 1.0
C A:PRO695 3.9 10.8 1.0
CG A:PRO695 3.9 10.8 1.0
C A:LEU732 4.0 10.2 1.0
N A:NH42032 4.0 29.9 1.0
O A:HOH2305 4.1 28.1 1.0
O A:ALA694 4.1 11.3 1.0
CA A:LEU732 4.2 9.9 1.0
CA A:PRO695 4.3 10.4 1.0
O A:HOH2276 4.3 18.4 1.0
CB A:ALA733 4.3 11.1 1.0
CB A:ALA694 4.4 11.9 1.0
CB A:LEU732 4.5 10.5 1.0
O A:HOH2416 4.6 34.1 1.0
C A:ALA733 4.6 12.3 1.0
CB A:PRO695 4.8 10.6 1.0
N A:ALA734 4.8 12.0 1.0
CD2 A:LEU732 4.8 12.7 1.0
N A:ALA694 4.9 11.7 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Sun Aug 11 20:52:08 2024

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