Iodine in PDB 5wgk: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb, PDB code: 5wgk 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)	34.88 / 1.82
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.670, 83.970, 94.570, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.3

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

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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb (pdb code 5wgk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb, PDB code: 5wgk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I801 b:21.2 occ:0.31 NE1 A:TRP459 3.6 15.8 1.0 CA A:ARG520 4.1 12.1 1.0 N A:ARG520 4.2 12.1 1.0 C A:PRO519 4.3 13.9 1.0 O A:PRO519 4.3 11.0 1.0 CD1 A:TRP459 4.4 10.4 1.0 CB A:ASN523 4.5 11.8 1.0 CB A:PRO519 4.6 16.8 1.0 CE2 A:TRP459 4.6 14.9 1.0 CB A:ARG520 4.7 21.0 1.0 CG A:ASN523 4.8 17.7 1.0 OD1 A:ASN523 4.9 25.9 1.0 CZ2 A:TRP459 5.0 14.2 1.0

Iodine binding site 2 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I802 b:28.2 occ:0.88 O A:HOH1075 3.2 30.0 1.0 NE2 A:HIS463 3.6 17.2 1.0 CA A:SER531 3.9 10.1 1.0 C A:SER531 3.9 10.5 1.0 CD2 A:HIS463 4.0 12.1 1.0 N A:ILE532 4.0 5.6 1.0 CE1 A:PHE583 4.2 8.7 1.0 CB A:SER531 4.4 11.3 1.0 O A:SER531 4.4 8.1 1.0 C09 A:AGJ816 4.4 37.6 0.3 C A:ILE532 4.5 14.7 1.0 O A:ILE532 4.5 9.2 1.0 O A:HOH1002 4.7 30.0 1.0 CA A:ILE532 4.7 10.0 1.0 CE1 A:HIS463 4.8 13.6 1.0 CD1 A:PHE583 4.8 9.5 1.0 N A:PHE533 4.8 6.1 1.0 CD2 A:PHE533 4.8 12.7 1.0 O A:HOH1108 4.9 30.0 1.0 O A:HOH1109 5.0 25.1 1.0

Iodine binding site 3 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I803 b:29.2 occ:0.38 O A:HOH1024 3.5 21.2 1.0 O A:HOH947 3.5 31.8 1.0 N A:ALA733 3.6 6.8 1.0 CD2 A:LEU732 3.8 8.9 1.0 CA A:LEU732 3.9 9.8 1.0 O A:HOH1187 4.0 25.1 1.0 CA A:ALA694 4.0 10.7 1.0 CD A:PRO695 4.1 6.9 1.0 O A:HOH1089 4.3 15.7 1.0 CB A:LEU732 4.3 6.4 1.0 C A:LEU732 4.3 7.2 1.0 C A:ALA694 4.5 13.9 1.0 N A:PRO695 4.5 9.9 1.0 O A:PRO695 4.6 6.6 1.0 CA A:ALA733 4.6 7.9 1.0 O A:SER731 4.7 11.8 1.0 CB A:ALA694 4.7 13.4 1.0 CG A:LEU732 4.7 8.8 1.0 CG A:PRO695 4.8 9.2 1.0 CA A:ARG691 4.8 8.6 1.0 O A:ARG691 4.9 11.1 1.0 O A:ALA690 4.9 8.9 1.0 N A:ALA694 5.0 9.1 1.0

Iodine binding site 4 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I804 b:58.6 occ:0.64 CD A:PRO519 3.6 19.4 1.0 N A:ARG520 3.7 12.1 1.0 CB A:LYS518 3.9 19.8 1.0 N A:PRO519 3.9 15.2 1.0 CB A:PRO519 4.0 16.8 1.0 CG A:PRO519 4.1 19.7 1.0 CB A:ARG520 4.1 21.0 1.0 CA A:PRO519 4.4 16.5 1.0 C A:LYS518 4.5 11.0 1.0 C A:PRO519 4.6 13.9 1.0 CA A:ARG520 4.6 12.1 1.0 CD A:LYS518 4.7 31.5 1.0 CA A:LYS518 4.7 16.7 1.0 CG A:LYS518 4.7 23.7 1.0 O A:HOH1182 4.8 30.1 1.0

Iodine binding site 5 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I805 b:62.9 occ:0.68 CD1 A:LEU712 3.8 26.1 1.0 C08 A:AGJ816 3.8 41.1 0.7 CG A:PRO711 4.0 14.1 1.0 CB A:PRO464 4.0 11.5 1.0 CG A:PRO464 4.2 14.8 1.0 C06 A:AGJ816 4.4 30.1 0.3 CB A:PRO711 4.4 19.2 1.0 C09 A:AGJ816 4.5 37.6 0.7 CD A:PRO464 4.6 11.8 1.0 C07 A:AGJ816 4.8 43.0 0.7 C05 A:AGJ816 5.0 32.8 0.3

Iodine binding site 6 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I806 b:81.4 occ:0.69 O A:HOH993 3.3 15.7 1.0 CA A:ALA680 3.8 9.3 1.0 CB A:HIS683 3.9 7.3 1.0 O A:MET679 3.9 8.9 1.0 N A:ALA680 4.0 7.0 1.0 C A:MET679 4.0 9.3 1.0 CG A:HIS683 4.2 14.2 1.0 CB A:ALA680 4.3 6.4 1.0 CB A:MET679 4.5 7.6 1.0 ND1 A:HIS683 4.5 27.2 1.0 O A:HOH961 4.6 12.8 1.0 CD2 A:LEU772 4.7 49.9 1.0 CD2 A:HIS683 4.8 21.6 1.0 CA A:MET679 4.9 6.8 1.0

Iodine binding site 7 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I807 b:61.9 occ:0.67 O A:HOH1160 3.3 11.6 1.0 ND2 A:ASN746 3.9 7.6 1.0 CD A:PRO711 4.0 15.0 1.0 CG A:PRO711 4.1 14.1 1.0 CA A:ASN746 4.1 6.1 1.0 CG A:ASN746 4.1 8.5 1.0 O A:HOH1309 4.2 35.0 1.0 CB A:ASN746 4.2 4.4 1.0 O A:GLY709 4.4 9.6 1.0 O A:HOH1120 4.4 30.0 1.0 O A:TYR745 4.4 11.8 1.0 CB A:PRO711 4.7 19.2 1.0 O A:HOH1305 4.7 24.6 1.0 N A:ASN746 4.9 6.8 1.0 OD1 A:ASN746 4.9 10.4 1.0 C A:TYR745 5.0 12.4 1.0

Iodine binding site 8 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I808 b:21.7 occ:0.65 O A:HOH966 3.4 26.9 1.0 O A:HOH1227 3.9 27.9 1.0 OG A:SER731 4.1 11.1 1.0 CA A:GLN728 4.3 8.0 1.0 CB A:SER731 4.3 8.7 1.0 CG A:GLN728 4.3 7.7 1.0 O A:HOH1105 4.3 30.0 1.0 O A:GLN728 4.6 9.2 1.0 CB A:GLN728 4.6 7.4 1.0 O A:HOH1015 4.9 18.2 1.0 C A:GLN728 4.9 9.8 1.0

Iodine binding site 9 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I809 b:87.8 occ:0.77 O A:HOH1043 2.9 12.0 1.0 CA A:SER513 3.8 20.4 1.0 CB A:SER513 4.0 14.8 1.0 CD2 A:HIS516 4.3 19.4 1.0 N A:SER513 4.4 10.8 1.0 O A:LYS512 4.7 10.1 1.0 C A:LYS512 4.8 9.5 1.0 NE2 A:HIS516 4.9 29.6 1.0 O A:HOH907 4.9 30.1 1.0 CG A:LYS512 5.0 11.2 1.0 C A:SER513 5.0 16.9 1.0

Iodine binding site 10 out of 12 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpb


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 Hpb within 5.0Å range: probe atom residue distance (Å) B Occ A:I810 b:85.9 occ:0.72 O A:HOH1239 3.3 29.9 1.0 N A:GLY657 3.4 19.3 1.0 CD A:ARG660 3.9 14.8 1.0 NH1 A:ARG660 4.1 14.0 1.0 CA A:LEU656 4.1 12.5 1.0 C A:LEU656 4.3 16.2 1.0 CA A:GLY657 4.3 15.2 1.0 CD2 A:LEU656 4.3 19.8 1.0 NE A:ARG660 4.5 12.7 1.0 CZ A:ARG660 4.6 17.8 1.0 O A:GLY655 4.7 13.3 1.0 CB A:LEU656 4.7 14.5 1.0 CG A:ARG660 5.0 18.9 1.0

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114