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Chlorine in PDB 8ak8: Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide

Enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide

All present enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide:
2.3.1.286;

Protein crystallography data

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide, PDB code: 8ak8 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) 45.54 / 1.73
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 91.074, 91.074, 143.197, 90, 90, 120
R / Rfree (%) 16.2 / 19.3

Other elements in 8ak8:

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide 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 4-Hydroxybenzamide (pdb code 8ak8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide, PDB code: 8ak8:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8ak8

Go back to Chlorine Binding Sites List in 8ak8
Chlorine binding site 1 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide


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 4-Hydroxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:58.0
occ:1.00
 N A:PHE86 2.9 29.9 1.0
OE1 A:GLU87 3.2 39.0 1.0
CB A:THR85 3.3 31.9 1.0
C3 A:PEG403 3.4 61.3 1.0
CA A:THR85 3.5 30.6 1.0
CD2 A:PHE86 3.6 34.3 1.0
C A:THR85 3.7 29.9 1.0
C2 A:PEG403 3.8 59.4 1.0
CB A:PHE86 3.9 28.6 1.0
CA A:PHE86 3.9 28.9 1.0
O2 A:PEG403 4.0 62.8 1.0
CG2 A:THR85 4.1 35.2 1.0
CG A:PHE86 4.1 31.1 1.0
CD A:GLU87 4.3 34.6 1.0
N A:GLU87 4.4 24.1 1.0
OG1 A:THR85 4.4 31.0 1.0
C1 A:PEG403 4.6 58.1 1.0
CE2 A:PHE86 4.6 34.6 1.0
C A:PHE86 4.7 26.5 1.0
OE2 A:GLU87 4.7 37.7 1.0
C4 A:PEG403 4.7 61.0 1.0
CG1 A:VAL153 4.8 36.0 1.0
O A:HOH527 4.9 43.4 1.0
O A:THR85 4.9 31.4 1.0
N A:THR85 5.0 29.8 1.0

Chlorine binding site 2 out of 4 in 8ak8

Go back to Chlorine Binding Sites List in 8ak8
Chlorine binding site 2 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide


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 4-Hydroxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:87.0
occ:1.00
 O1' A:HBD410 3.0 72.9 1.0
O16 A:P6G404 3.2 61.8 1.0
C17 A:P6G404 3.3 59.2 1.0
C18 A:P6G404 3.5 63.1 1.0
C1' A:HBD410 3.6 67.4 1.0
O19 A:P6G404 3.7 65.1 1.0
CH2 A:TRP71 3.9 39.3 1.0
N1' A:HBD410 4.2 64.6 1.0
C1 A:HBD410 4.5 61.6 1.0
C15 A:P6G404 4.5 59.0 1.0
CZ3 A:TRP71 4.5 38.9 1.0
CZ2 A:TRP71 4.7 41.9 1.0
CE A:MET157 4.7 71.0 1.0
CE1 A:PHE64 4.8 28.6 1.0
C2 A:HBD410 4.9 53.6 1.0
CG1 A:VAL70 5.0 31.8 1.0

Chlorine binding site 3 out of 4 in 8ak8

Go back to Chlorine Binding Sites List in 8ak8
Chlorine binding site 3 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide


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 4-Hydroxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl411

b:55.5
occ:1.00
 N B:PHE86 2.9 31.1 1.0
O2 A:PEG405 3.3 63.0 1.0
CD2 B:PHE86 3.4 35.0 1.0
C2 A:PEG405 3.4 67.0 1.0
CB B:THR85 3.5 32.8 1.0
OE1 B:GLU87 3.5 37.3 1.0
CA B:THR85 3.5 30.6 1.0
C3 A:PEG405 3.6 62.9 1.0
C B:THR85 3.7 31.2 1.0
CB B:PHE86 3.8 29.1 1.0
CA B:PHE86 3.9 30.2 1.0
CG B:PHE86 4.0 30.2 1.0
CG2 B:THR85 4.2 41.9 1.0
C1 A:PEG405 4.3 63.7 1.0
CE2 B:PHE86 4.3 35.1 1.0
OG1 B:THR85 4.6 30.0 1.0
CD B:GLU87 4.6 36.1 1.0
N B:GLU87 4.6 29.4 1.0
C B:PHE86 4.8 28.5 1.0
CG1 B:VAL153 4.9 39.4 1.0
O B:THR85 4.9 29.0 1.0
N B:THR85 4.9 32.3 1.0

Chlorine binding site 4 out of 4 in 8ak8

Go back to Chlorine Binding Sites List in 8ak8
Chlorine binding site 4 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 4-Hydroxybenzamide


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 4-Hydroxybenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl412

b:89.5
occ:1.00
 O1' B:HBD410 3.3 56.8 1.0
C17 B:P6G403 3.3 71.4 1.0
C18 B:P6G403 3.4 74.0 1.0
O16 B:P6G403 3.4 77.7 1.0
O19 B:P6G403 3.5 69.7 1.0
C1' B:HBD410 3.7 65.2 1.0
N1' B:HBD410 4.1 65.3 1.0
CH2 B:TRP71 4.3 57.2 1.0
CE B:MET157 4.3 74.8 1.0
C1 B:HBD410 4.5 56.6 1.0
C15 B:P6G403 4.7 69.6 1.0
CE1 B:PHE64 4.8 37.0 1.0
CZ3 B:TRP71 4.9 58.5 1.0
CZ2 B:TRP71 5.0 51.5 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: Thu Dec 28 03:00:16 2023

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