Chlorine in PDB 8aka: Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol

Enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol

All present enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol:
2.3.1.286;

Protein crystallography data

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol, PDB code: 8aka was solved by W.You, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 1.77
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 91.034, 91.034, 143.196, 90, 90, 120
R / Rfree (%) 17.9 / 20.7

Other elements in 8aka:

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol (pdb code 8aka). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol, PDB code: 8aka:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8aka

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Chlorine binding site 1 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:54.9
occ:1.00
 CG A:PRO80 3.9 38.7 1.0
CE1 A:PHE82 4.1 34.9 1.0
CG1 A:VAL70 4.4 27.4 1.0
CG2 A:VAL70 4.6 23.3 1.0
CZ A:PHE82 4.6 33.7 1.0
C6 A:STL403 4.7 28.7 1.0
CD A:PRO80 4.9 37.4 1.0
CB A:PRO80 5.0 39.3 1.0

Chlorine binding site 2 out of 7 in 8aka

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Chlorine binding site 2 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:73.3
occ:1.00
 CB A:MET157 3.3 45.4 1.0
SD A:MET157 4.0 61.6 1.0
OD1 A:ASP187 4.1 52.4 1.0
CG A:ASP187 4.1 50.5 1.0
CG A:MET157 4.2 51.1 1.0
OD2 A:ASP187 4.3 52.7 1.0
C A:MET157 4.4 41.3 1.0
CA A:MET157 4.5 40.8 1.0
CG2 A:ILE185 4.5 36.5 1.0
N A:GLY158 4.5 40.4 1.0
O A:LEU186 4.6 36.6 1.0
CA A:ASP187 4.7 45.1 1.0
CB A:ASP187 4.7 44.8 1.0
O A:MET157 5.0 39.3 1.0
C13 A:STL403 5.0 49.8 1.0
CA A:GLY158 5.0 38.8 1.0

Chlorine binding site 3 out of 7 in 8aka

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Chlorine binding site 3 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:60.3
occ:1.00
 O A:HOH547 2.5 37.9 1.0
NE A:ARG103 3.5 52.6 1.0
CG A:ARG103 3.5 37.0 1.0
CD1 A:LEU286 3.6 30.1 1.0
CD1 A:LEU289 3.7 36.0 1.0
CG A:LEU289 3.7 33.0 1.0
CB A:LEU286 3.9 33.1 1.0
CD A:ARG103 3.9 44.6 1.0
CB A:ARG103 4.0 31.8 1.0
CD2 A:LEU289 4.2 32.4 1.0
O A:PRO287 4.3 27.6 1.0
CG A:LEU286 4.4 31.6 1.0
CZ A:ARG103 4.5 56.3 1.0
NH1 A:ARG103 4.6 66.3 1.0
CA A:ARG103 4.7 31.4 1.0
O A:ARG103 5.0 34.0 1.0

Chlorine binding site 4 out of 7 in 8aka

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Chlorine binding site 4 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:54.3
occ:1.00
 O A:PRO293 3.4 27.8 1.0
CB A:PRO292 3.7 38.2 1.0
O A:LEU269 3.9 31.4 1.0
O A:HIS268 4.2 37.1 1.0
CZ2 A:TRP42 4.2 34.9 1.0
C A:LEU269 4.3 29.6 1.0
CG A:PRO295 4.5 40.8 1.0
CD A:PRO295 4.6 39.6 1.0
C A:PRO293 4.6 34.0 1.0
CG A:PRO292 4.7 38.0 1.0
N A:GLY270 4.7 30.9 1.0
NE1 A:TRP42 4.7 33.5 1.0
CE2 A:TRP42 4.8 30.1 1.0
CA A:LEU269 4.9 32.8 1.0
CA A:PRO292 4.9 34.9 1.0
CA A:GLY270 5.0 30.9 1.0
C A:PRO292 5.0 34.5 1.0

Chlorine binding site 5 out of 7 in 8aka

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Chlorine binding site 5 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl411

b:53.6
occ:1.00
 O B:HOH537 2.6 46.4 1.0
CD B:ARG103 3.1 52.8 1.0
CD1 B:LEU286 3.6 40.0 1.0
CG B:ARG103 3.6 40.4 1.0
CD1 B:LEU289 3.6 38.0 1.0
CG B:LEU289 3.7 38.2 1.0
CB B:LEU286 3.8 34.8 1.0
CD2 B:LEU289 4.0 36.4 1.0
CB B:ARG103 4.1 37.7 1.0
O B:PRO287 4.2 34.5 1.0
NH1 B:ARG103 4.2 64.8 1.0
CG B:LEU286 4.3 36.5 1.0
NE B:ARG103 4.3 55.7 1.0
CZ B:ARG103 4.8 57.4 1.0
CA B:ARG103 4.8 33.0 1.0
O B:ARG103 5.0 36.7 1.0

Chlorine binding site 6 out of 7 in 8aka

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Chlorine binding site 6 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl412

b:65.8
occ:1.00
 OE1 B:GLN100 3.0 41.4 1.0
CZ B:ARG103 3.6 57.4 1.0
NE B:ARG103 3.6 55.7 1.0
CD B:ARG103 3.9 52.8 1.0
NH1 B:ARG103 3.9 64.8 1.0
CD B:GLN100 3.9 32.0 1.0
CD1 B:LEU289 3.9 38.0 1.0
NH2 B:ARG103 4.0 57.2 1.0
NE2 B:GLN100 4.0 40.2 1.0
CB B:PRO274 4.4 35.8 1.0
CG B:PRO274 4.9 33.6 1.0

Chlorine binding site 7 out of 7 in 8aka

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Chlorine binding site 7 out of 7 in the Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Human SIRT6 in Complex with Adp-Ribose and Fragment Cis-Resveratrol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl413

b:60.4
occ:1.00
 O B:PRO293 3.1 28.9 1.0
CB B:PRO292 3.8 41.7 1.0
C B:PRO293 4.3 31.1 1.0
CG B:PRO295 4.3 44.6 1.0
CD B:PRO295 4.4 40.5 1.0
O B:LEU269 4.5 38.4 1.0
O B:HIS268 4.7 37.7 1.0
CZ2 B:TRP42 4.7 38.2 1.0
N B:PRO293 4.8 33.9 1.0
C B:PRO292 4.8 35.2 1.0
CG B:PRO292 4.8 36.1 1.0
CA B:PRO292 4.9 40.9 1.0
N B:PRO295 4.9 43.0 1.0
C B:LEU269 4.9 33.2 1.0
CD B:PRO293 4.9 33.9 1.0

Reference:

W.You, C.Steegborn. Development of Novel Sirtuin 6 Inhibitors and Activators Based on A Protein Crystallography-Based Fragment Screen To Be Published.
Page generated: Tue Jul 30 06:38:16 2024

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