Atomistry » Chlorine » PDB 5ead-5ehw » 5eei
Atomistry »
  Chlorine »
    PDB 5ead-5ehw »
      5eei »

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 Dec 12 11:41:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy