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Chlorine in PDB 5eei: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha

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

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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei 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) 36.26 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.790, 83.551, 86.806, 90.00, 98.09, 90.00
R / Rfree (%) 12.5 / 14.8

Other elements in 5eei:

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

Magnesium (Mg) 2 atoms
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 Saha (pdb code 5eei). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5eei

Go back to Chlorine Binding Sites List in 5eei
Chlorine binding site 1 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2008

b:29.5
occ:1.00
 H A:SER484 2.3 23.4 1.0
HA A:ARG481 2.6 22.3 1.0
HB3 A:LEU483 2.8 21.6 1.0
HG A:SER484 2.9 31.3 1.0
HB3 A:SER484 3.0 27.9 1.0
N A:SER484 3.1 19.5 1.0
H A:LEU483 3.1 19.6 1.0
HA A:GLU478 3.4 18.6 1.0
CA A:ARG481 3.4 18.6 1.0
OG A:SER484 3.5 26.1 1.0
N A:LEU483 3.5 16.4 1.0
C A:ARG481 3.6 18.4 1.0
CB A:SER484 3.6 23.2 1.0
CB A:LEU483 3.7 18.0 1.0
CA A:LEU483 3.9 17.6 1.0
O A:ARG481 3.9 20.5 1.0
CA A:SER484 3.9 20.0 1.0
C A:LEU483 3.9 17.9 1.0
N A:LEU482 4.0 16.5 1.0
HD3 A:ARG481 4.0 36.8 1.0
O A:GLU478 4.0 16.9 1.0
HB3 A:ARG481 4.1 25.1 1.0
H A:LEU482 4.2 19.8 1.0
HB2 A:LEU483 4.2 21.6 1.0
H A:ARG481 4.2 19.4 1.0
O A:HIS477 4.3 16.1 1.0
CA A:GLU478 4.3 15.5 1.0
C A:LEU482 4.3 16.4 1.0
N A:ARG481 4.3 16.2 1.0
CB A:ARG481 4.4 20.9 1.0
HD23 A:LEU483 4.4 23.6 1.0
HB2 A:SER484 4.5 27.9 1.0
HA A:SER484 4.5 24.0 1.0
HD2 A:ARG481 4.6 36.8 1.0
C A:GLU478 4.6 15.6 1.0
HG A:LEU483 4.6 22.1 1.0
CD A:ARG481 4.7 30.6 1.0
CG A:LEU483 4.7 18.5 1.0
HG2 A:GLU478 4.7 24.6 1.0
H A:ARG485 4.7 21.3 1.0
CA A:LEU482 4.8 16.5 1.0
HA A:LEU483 4.8 21.1 1.0
HB3 A:GLU478 4.9 21.2 1.0

Chlorine binding site 2 out of 5 in 5eei

Go back to Chlorine Binding Sites List in 5eei
Chlorine binding site 2 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2009

b:36.4
occ:1.00
 HH11 A:ARG788 2.2 27.2 1.0
HD2 A:ARG788 2.5 22.1 1.0
OD1 A:ASN785 2.8 17.6 1.0
O A:HOH2277 2.8 18.9 1.0
NH1 A:ARG788 3.0 22.6 1.0
HA A:ASN785 3.2 16.8 1.0
HH12 A:ARG788 3.4 27.2 1.0
CD A:ARG788 3.4 18.4 1.0
HE1 A:TYR651 3.6 20.6 1.0
HB3 A:ARG788 3.6 19.9 1.0
CG A:ASN785 3.7 16.2 1.0
HD3 A:ARG788 3.8 22.1 1.0
CZ A:ARG788 3.9 21.4 1.0
OH A:TYR651 4.0 19.6 1.0
HB3 A:ASN785 4.0 17.4 1.0
CA A:ASN785 4.0 14.0 1.0
CE1 A:TYR651 4.1 17.2 1.0
NE A:ARG788 4.1 19.1 1.0
CB A:ASN785 4.1 14.5 1.0
CZ A:TYR651 4.3 17.4 1.0
CG A:ARG788 4.3 18.3 1.0
CB A:ARG788 4.3 16.6 1.0
HG2 A:ARG788 4.4 21.9 1.0
O A:ASN785 4.4 13.2 1.0
HH A:TYR651 4.5 23.5 1.0
HB2 A:ARG788 4.6 19.9 1.0
ND2 A:ASN785 4.7 16.6 1.0
C A:ASN785 4.8 13.9 1.0
HD22 A:ASN785 4.8 19.9 1.0
HE A:ARG788 4.9 22.9 1.0
CD1 A:TYR651 5.0 15.3 1.0

Chlorine binding site 3 out of 5 in 5eei

Go back to Chlorine Binding Sites List in 5eei
Chlorine binding site 3 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2011

b:59.6
occ:1.00
 HH22 A:ARG476 2.3 21.3 1.0
O1 B:EDO809 2.8 24.4 0.5
C1 B:EDO809 3.1 23.2 0.5
NH2 A:ARG476 3.2 17.8 1.0
HH12 A:ARG476 3.4 19.6 1.0
HD21 A:LEU480 3.6 21.8 1.0
HH21 A:ARG476 3.6 21.3 1.0
HG B:SER749 4.0 21.5 0.8
NH1 A:ARG476 4.0 16.4 1.0
CZ A:ARG476 4.1 16.4 1.0
C2 B:EDO809 4.1 22.4 0.5
HG2 B:ARG708 4.1 27.7 1.0
O A:HOH2106 4.2 39.9 1.0
HD23 A:LEU480 4.2 21.8 1.0
O2 B:EDO809 4.2 25.4 0.5
CD2 A:LEU480 4.3 18.2 1.0
O B:HOH914 4.5 22.6 1.0
HD2 B:ARG708 4.7 31.8 1.0
OG B:SER749 4.7 17.9 0.8
HD3 B:ARG708 4.8 31.8 1.0
HD22 A:LEU480 4.8 21.8 1.0
HH11 A:ARG476 4.8 19.6 1.0
O B:ARG708 4.9 17.1 1.0
CG B:ARG708 5.0 23.1 1.0
HB3 B:ARG708 5.0 23.4 1.0

Chlorine binding site 4 out of 5 in 5eei

Go back to Chlorine Binding Sites List in 5eei
Chlorine binding site 4 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl807

b:40.8
occ:1.00
 CL B:CL808 3.5 59.2 1.0
HA B:THR600 4.4 20.7 1.0
O B:THR600 4.6 20.5 1.0
HB B:THR600 4.6 20.8 1.0
C B:THR600 5.0 17.7 1.0

Chlorine binding site 5 out of 5 in 5eei

Go back to Chlorine Binding Sites List in 5eei
Chlorine binding site 5 out of 5 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl808

b:59.2
occ:1.00
 HH21 B:ARG601 2.0 25.8 1.0
NH2 B:ARG601 2.8 21.5 1.0
HG2 B:ARG601 2.8 25.4 1.0
HD3 B:ARG601 2.9 24.2 1.0
HH22 B:ARG601 3.0 25.8 1.0
HB B:THR600 3.5 20.8 1.0
CL B:CL807 3.5 40.8 1.0
CG B:ARG601 3.6 21.2 1.0
CD B:ARG601 3.6 20.2 1.0
CZ B:ARG601 3.9 20.4 1.0
HD12 B:LEU604 3.9 22.0 1.0
HB3 B:ARG601 4.0 26.3 1.0
HD11 B:LEU604 4.2 22.0 1.0
NE B:ARG601 4.2 20.7 1.0
HG3 B:ARG601 4.3 25.4 1.0
CB B:ARG601 4.3 21.9 1.0
OE2 B:GLU696 4.4 21.2 1.0
CB B:THR600 4.4 17.4 1.0
HD2 B:ARG601 4.4 24.2 1.0
CD1 B:LEU604 4.5 18.4 1.0
H B:ARG601 4.5 20.7 1.0
N B:ARG601 4.5 17.2 1.0
C B:THR600 4.6 17.7 1.0
O3 B:GOL805 4.7 40.6 1.0
O B:HOH1167 4.8 31.4 1.0
O B:THR600 4.9 20.5 1.0
HD13 B:LEU604 4.9 22.0 1.0
HA B:THR600 4.9 20.7 1.0
CA B:THR600 5.0 17.3 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: Sat Jul 12 01:40:22 2025

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