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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

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