Atomistry » Iodine » PDB 6njv-6rq8 » 6pzr
Atomistry »
  Iodine »
    PDB 6njv-6rq8 »
      6pzr »

Iodine in PDB 6pzr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat, PDB code: 6pzr 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) 68.94 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.883, 97.364, 97.642, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzr:

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

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

Iodine Binding Sites:

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

Iodine binding site 1 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 1 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I808

b:32.5
occ:1.00
 NE2 A:HIS614 3.7 24.4 1.0
CD2 A:LEU712 3.8 27.7 1.0
C24 A:P7D804 3.9 30.0 1.0
C09 A:P7D804 4.1 29.1 1.0
CZ A:PHE642 4.1 28.4 1.0
CE1 A:PHE642 4.2 25.8 1.0
CB A:PHE643 4.2 23.7 1.0
O12 A:P7D804 4.2 40.2 1.0
CD2 A:HIS614 4.5 25.1 1.0
O A:LEU712 4.5 25.6 1.0
CB A:LEU712 4.6 23.6 1.0
N14 A:P7D804 4.6 31.0 1.0
CG A:LEU712 4.6 28.7 1.0
CE1 A:HIS614 4.7 22.7 1.0
CE2 A:PHE642 4.8 22.9 1.0
S11 A:P7D804 4.8 40.8 1.0
C17 A:P7D804 4.9 25.4 1.0
CD1 A:PHE642 4.9 30.1 1.0
C08 A:P7D804 4.9 28.2 1.0
C10 A:P7D804 4.9 25.7 1.0
CD1 A:LEU712 4.9 21.8 1.0

Iodine binding site 2 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 2 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I809

b:72.4
occ:1.00
 NE2 A:HIS463 3.7 22.1 1.0
N A:ILE532 3.7 19.8 1.0
C A:SER531 3.9 24.1 1.0
CA A:SER531 4.0 20.5 1.0
CD2 A:HIS463 4.1 17.6 1.0
O A:HOH938 4.1 31.6 1.0
C A:ILE532 4.1 18.4 1.0
N A:PHE533 4.3 20.7 1.0
O A:ILE532 4.3 27.5 1.0
CA A:ILE532 4.4 18.6 1.0
CE1 A:PHE583 4.4 22.4 1.0
CB A:SER531 4.5 23.6 1.0
O A:SER531 4.6 24.5 1.0
CD2 A:PHE533 4.6 21.8 1.0
CB A:PHE533 4.8 22.1 1.0
O A:HOH917 4.9 20.8 1.0
CD1 A:PHE583 4.9 24.5 1.0
CE1 A:HIS463 4.9 24.9 1.0

Iodine binding site 3 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 3 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I810

b:79.2
occ:1.00
 O A:HOH957 3.7 26.2 1.0
CD A:ARG472 3.8 15.2 1.0
O A:SER471 4.0 17.2 1.0
CB A:SER475 4.2 21.6 1.0
C A:SER471 4.4 14.2 1.0
CG A:ARG472 4.4 16.3 1.0
OG A:SER475 4.5 24.9 1.0
OG A:SER471 4.5 19.5 1.0
CA A:ARG472 4.5 13.0 1.0
N A:ARG472 4.6 19.4 1.0
CB A:SER471 4.8 15.5 1.0

Iodine binding site 4 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 4 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I811

b:72.8
occ:1.00
 N A:ARG520 3.6 30.9 1.0
CD A:PRO519 3.9 34.0 1.0
CB A:ARG520 3.9 25.7 1.0
CB A:PRO519 4.1 37.7 1.0
N A:PRO519 4.1 31.6 1.0
CB A:LYS518 4.3 30.8 1.0
CG A:PRO519 4.3 28.3 1.0
CA A:ARG520 4.4 26.8 1.0
CA A:PRO519 4.5 29.8 1.0
C A:PRO519 4.5 33.4 1.0
C A:LYS518 4.7 26.0 1.0

Iodine binding site 5 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 5 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I808

b:39.8
occ:1.00
 NE2 B:HIS614 3.7 22.7 1.0
C24 B:P7D804 4.0 36.9 1.0
C09 B:P7D804 4.1 42.4 1.0
O12 B:P7D804 4.2 37.7 1.0
CZ B:PHE642 4.2 31.2 1.0
CB B:PHE643 4.3 24.9 1.0
CE1 B:PHE642 4.3 24.8 1.0
CD2 B:LEU712 4.4 23.9 1.0
CB B:LEU712 4.4 17.1 1.0
CD1 B:LEU712 4.5 15.8 1.0
CE1 B:HIS614 4.6 24.3 1.0
O B:LEU712 4.6 31.5 1.0
CG B:LEU712 4.6 29.2 1.0
CD2 B:HIS614 4.6 26.4 1.0
N14 B:P7D804 4.6 34.4 1.0
C10 B:P7D804 4.8 40.1 1.0
C08 B:P7D804 4.8 37.3 1.0
S11 B:P7D804 4.8 43.3 1.0
CE2 B:PHE642 4.9 24.1 1.0
C17 B:P7D804 4.9 29.2 1.0

Iodine binding site 6 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 6 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I809

b:58.0
occ:1.00
 NE2 B:HIS463 3.7 19.6 1.0
N B:ILE532 3.8 19.5 1.0
C B:SER531 3.9 20.9 1.0
CA B:SER531 4.0 21.8 1.0
CD2 B:HIS463 4.1 16.2 1.0
C B:ILE532 4.2 22.2 1.0
N B:PHE533 4.4 15.5 1.0
O B:ILE532 4.4 21.2 1.0
CA B:ILE532 4.5 16.9 1.0
CB B:SER531 4.5 25.3 1.0
O B:SER531 4.6 20.7 1.0
CE1 B:PHE583 4.6 14.3 1.0
CD2 B:PHE533 4.7 18.9 1.0
O B:HOH916 4.9 22.9 1.0
CE1 B:HIS463 4.9 17.8 1.0
CB B:PHE533 4.9 18.4 1.0
O B:HOH967 4.9 23.2 1.0

Iodine binding site 7 out of 7 in 6pzr

Go back to Iodine Binding Sites List in 6pzr
Iodine binding site 7 out of 7 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat


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 Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I810

b:64.2
occ:1.00
 N B:ALA733 3.5 21.8 1.0
CA B:ALA694 4.0 20.3 1.0
CA B:LEU732 4.0 15.8 1.0
CD B:PRO695 4.1 12.8 1.0
CD2 B:LEU732 4.1 20.1 1.0
C B:LEU732 4.3 20.2 1.0
CA B:ALA733 4.4 21.5 1.0
CB B:LEU732 4.5 12.6 1.0
CB B:ALA694 4.5 21.6 1.0
C B:ALA694 4.5 21.1 1.0
N B:PRO695 4.5 16.3 1.0
O B:PRO695 4.5 20.7 1.0
O B:SER731 4.7 24.6 1.0
O B:ARG691 4.8 29.1 1.0
CG B:PRO695 4.9 11.7 1.0
CA B:ARG691 4.9 23.3 1.0
CG B:LEU732 5.0 18.6 1.0

Reference:

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540
Page generated: Sun Aug 11 23:53:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy