Chlorine in PDB 8ak7: Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine

Enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine

All present enzymatic activity of Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine:
2.3.1.286;

Protein crystallography data

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine, PDB code: 8ak7 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) 43.40 / 1.81
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 91.072, 91.072, 143.251, 90, 90, 120
R / Rfree (%) 20.1 / 23.3

Other elements in 8ak7:

The structure of Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine 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 6-O-Methylguanine (pdb code 8ak7). 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 6-O-Methylguanine, PDB code: 8ak7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8ak7

Go back to Chlorine Binding Sites List in 8ak7
Chlorine binding site 1 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine


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 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:57.3
occ:1.00
 NE2 B:HIS68 3.1 40.8 1.0
O B:HOH561 3.1 72.8 1.0
N A:ALA79 3.3 45.8 1.0
O A:ALA79 3.6 41.8 1.0
CD2 B:HIS68 3.7 43.1 1.0
CB A:LEU78 3.7 48.3 1.0
NH1 B:ARG76 4.1 84.9 1.0
CA A:LEU78 4.1 42.4 1.0
CA A:ALA79 4.1 41.6 1.0
C A:LEU78 4.2 43.0 1.0
CB A:ALA79 4.2 39.4 1.0
CE1 B:HIS68 4.2 43.5 1.0
C A:ALA79 4.3 40.4 1.0
CE A:MET73 4.4 45.4 1.0
CD2 A:LEU78 4.5 49.6 1.0
CG A:LEU78 4.6 49.5 1.0
O B:PRO67 4.9 47.2 1.0
CG B:HIS68 5.0 42.3 1.0

Chlorine binding site 2 out of 4 in 8ak7

Go back to Chlorine Binding Sites List in 8ak7
Chlorine binding site 2 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine


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 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:77.0
occ:1.00
 N A:PHE86 2.9 31.7 1.0
OE1 A:GLU87 3.0 47.0 1.0
CB A:THR85 3.4 37.7 1.0
CD2 A:PHE86 3.6 36.8 1.0
CA A:THR85 3.6 33.8 1.0
CB A:PHE86 3.7 33.9 1.0
C A:THR85 3.8 32.8 1.0
C2 B:PEG401 3.8 62.8 1.0
CA A:PHE86 3.9 33.3 1.0
C1 B:PEG401 3.9 62.2 1.0
CG A:PHE86 4.0 35.3 1.0
CD A:GLU87 4.1 41.7 1.0
C3 B:PEG401 4.1 69.5 1.0
CG2 A:THR85 4.2 46.4 1.0
N A:GLU87 4.4 35.7 1.0
OG1 A:THR85 4.5 38.1 1.0
O2 B:PEG401 4.5 65.8 1.0
OE2 A:GLU87 4.6 39.9 1.0
CG1 A:VAL153 4.6 42.4 1.0
CE2 A:PHE86 4.6 37.8 1.0
C A:PHE86 4.7 33.2 1.0
O A:HOH532 4.7 43.6 1.0
CG2 A:VAL153 4.9 41.5 1.0
O A:THR85 5.0 30.9 1.0

Chlorine binding site 3 out of 4 in 8ak7

Go back to Chlorine Binding Sites List in 8ak7
Chlorine binding site 3 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine


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 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:63.2
occ:1.00
 NE2 A:HIS68 3.5 39.7 1.0
N B:ALA79 3.5 63.3 1.0
O B:ALA79 4.0 60.3 1.0
CD2 A:HIS68 4.0 40.2 1.0
CB B:ALA79 4.1 59.6 1.0
CA B:ALA79 4.3 60.2 1.0
CB B:LEU78 4.3 78.6 1.0
NH1 A:ARG76 4.4 80.9 1.0
CA B:LEU78 4.4 70.9 1.0
C B:LEU78 4.5 67.3 1.0
C B:ALA79 4.6 59.9 1.0
CE1 A:HIS68 4.7 41.8 1.0
CD2 B:LEU78 4.7 81.8 1.0
O A:PRO67 5.0 36.0 1.0
CB A:PRO67 5.0 36.3 1.0

Chlorine binding site 4 out of 4 in 8ak7

Go back to Chlorine Binding Sites List in 8ak7
Chlorine binding site 4 out of 4 in the Human SIRT6 in Complex with Adp-Ribose and Fragment 6-O-Methylguanine


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 6-O-Methylguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl410

b:70.8
occ:1.00
 O2 A:PEG406 2.8 74.2 1.0
N B:PHE86 2.9 35.7 1.0
OE1 B:GLU87 3.3 44.9 1.0
CB B:THR85 3.4 40.6 1.0
CD2 B:PHE86 3.5 40.1 1.0
CA B:THR85 3.5 37.1 1.0
C3 A:PEG406 3.5 78.0 1.0
C B:THR85 3.7 38.0 1.0
CB B:PHE86 3.7 35.6 1.0
CA B:PHE86 3.9 35.6 1.0
CG B:PHE86 4.0 38.8 1.0
C2 A:PEG406 4.0 74.0 1.0
CG2 B:THR85 4.2 44.1 1.0
C4 A:PEG406 4.3 78.5 1.0
CD B:GLU87 4.4 45.0 1.0
OG1 B:THR85 4.4 39.0 1.0
C1 A:PEG406 4.5 69.2 1.0
CE2 B:PHE86 4.5 37.2 1.0
N B:GLU87 4.5 37.1 1.0
C B:PHE86 4.8 37.2 1.0
OE2 B:GLU87 4.9 45.9 1.0
O B:THR85 4.9 32.1 1.0
CG1 B:VAL153 4.9 49.7 1.0
N B:THR85 5.0 37.4 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 06:37:39 2024

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