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Fluorine in PDB 6xvg: Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801

Enzymatic activity of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801

All present enzymatic activity of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801:
2.3.1.286;

Protein crystallography data

The structure of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801, PDB code: 6xvg 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) 46.39 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.510, 136.534, 89.873, 90.00, 117.71, 90.00
R / Rfree (%) 20.4 / 23

Other elements in 6xvg:

The structure of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Bromine (Br) 6 atoms
Chlorine (Cl) 12 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 (pdb code 6xvg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801, PDB code: 6xvg:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6xvg

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Fluorine binding site 1 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:80.6
occ:1.00
 F1 A:8L9404 0.0 80.6 1.0
C39 A:8L9404 1.4 82.2 1.0
C38 A:8L9404 2.4 74.2 1.0
C40 A:8L9404 2.4 87.8 1.0
BR1 A:8L9404 3.1 82.6 1.0
CG2 A:VAL115 3.3 39.9 1.0
CZ A:PHE64 3.4 47.0 1.0
C36 A:8L9404 3.6 82.1 1.0
C42 A:8L9404 3.6 89.0 1.0
CE2 A:PHE64 3.9 44.7 1.0
C35 A:8L9404 4.1 84.2 1.0
CL1 A:8L9404 4.2 76.2 1.0
CE1 A:PHE64 4.5 47.6 1.0
CB A:VAL115 4.7 37.8 1.0
CZ A:PHE86 4.8 46.5 1.0
C43 A:8L9404 4.9 85.7 1.0

Fluorine binding site 2 out of 6 in 6xvg

Go back to Fluorine Binding Sites List in 6xvg
Fluorine binding site 2 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:0.5
occ:1.00
 F1 B:8L9404 0.0 0.5 1.0
C39 B:8L9404 1.4 0.7 1.0
C38 B:8L9404 2.3 98.7 1.0
C40 B:8L9404 2.4 96.1 1.0
BR1 B:8L9404 3.0 0.1 1.0
CG2 B:VAL115 3.0 43.4 1.0
C36 B:8L9404 3.6 0.3 1.0
CZ B:PHE64 3.6 46.1 1.0
C42 B:8L9404 3.7 98.0 1.0
CL1 B:8L9404 3.9 0.3 1.0
O B:HOH530 4.0 46.6 1.0
C35 B:8L9404 4.1 0.8 1.0
CE2 B:PHE64 4.2 46.9 1.0
CB B:VAL115 4.5 40.9 1.0
CE1 B:PHE64 4.6 47.3 1.0
CZ B:PHE86 4.8 49.5 1.0
C43 B:8L9404 5.0 97.8 1.0
CG1 B:VAL115 5.0 44.7 1.0

Fluorine binding site 3 out of 6 in 6xvg

Go back to Fluorine Binding Sites List in 6xvg
Fluorine binding site 3 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1006

b:95.8
occ:1.00
 F1 C:8L91006 0.0 95.8 1.0
C39 C:8L91006 1.4 84.9 1.0
C38 C:8L91006 2.3 80.5 1.0
C40 C:8L91006 2.4 94.8 1.0
BR1 C:8L91006 3.0 82.5 1.0
CZ C:PHE64 3.0 56.0 1.0
CG2 C:VAL115 3.2 42.1 1.0
CE2 C:PHE64 3.6 54.1 1.0
C36 C:8L91006 3.6 78.8 1.0
C42 C:8L91006 3.7 96.4 1.0
CE1 C:PHE64 4.1 56.9 1.0
C35 C:8L91006 4.1 94.1 1.0
CB C:VAL115 4.6 43.0 1.0
N C:VAL115 4.8 35.1 1.0
C43 C:8L91006 4.9 92.8 1.0
CD2 C:PHE64 4.9 53.9 1.0

Fluorine binding site 4 out of 6 in 6xvg

Go back to Fluorine Binding Sites List in 6xvg
Fluorine binding site 4 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F404

b:89.2
occ:1.00
 F1 D:8L9404 0.0 89.2 1.0
C39 D:8L9404 1.4 95.1 1.0
C38 D:8L9404 2.4 83.4 1.0
C40 D:8L9404 2.4 93.6 1.0
CG2 D:VAL115 3.1 40.0 1.0
BR1 D:8L9404 3.2 84.9 1.0
C36 D:8L9404 3.7 84.7 1.0
C42 D:8L9404 3.7 89.1 1.0
CZ D:PHE64 3.7 52.3 1.0
C35 D:8L9404 4.2 90.4 1.0
CE2 D:PHE64 4.2 54.9 1.0
CB D:VAL115 4.5 44.4 1.0
CZ D:PHE86 4.5 59.8 1.0
CE1 D:PHE86 4.7 60.6 1.0
CE1 D:PHE64 4.7 52.0 1.0
CL1 D:8L9404 4.7 88.6 1.0
N D:VAL115 4.8 38.0 1.0
C43 D:8L9404 5.0 82.0 1.0
N D:ASP116 5.0 33.0 1.0

Fluorine binding site 5 out of 6 in 6xvg

Go back to Fluorine Binding Sites List in 6xvg
Fluorine binding site 5 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F705

b:90.3
occ:1.00
 F1 E:8L9705 0.0 90.3 1.0
C39 E:8L9705 1.4 92.5 1.0
C38 E:8L9705 2.4 85.8 1.0
C40 E:8L9705 2.4 89.1 1.0
BR1 E:8L9705 3.0 93.9 1.0
CG2 E:VAL115 3.3 50.8 1.0
C42 E:8L9705 3.6 90.0 1.0
C36 E:8L9705 3.6 81.4 1.0
CZ E:PHE86 3.7 56.1 1.0
CE1 E:PHE86 3.8 56.1 1.0
C35 E:8L9705 4.1 95.9 1.0
CZ E:PHE64 4.2 56.5 1.0
O E:HOH821 4.4 53.4 1.0
N E:ASP116 4.6 42.4 1.0
CG2 E:ILE61 4.7 52.2 1.0
CB E:VAL115 4.7 51.4 1.0
CE1 E:PHE64 4.8 55.5 1.0
C43 E:8L9705 4.8 90.8 1.0
C E:VAL115 4.9 45.4 1.0
CA E:ASP116 4.9 43.9 1.0
CB E:ASP116 4.9 42.7 1.0
N E:VAL115 5.0 45.9 1.0
CE2 E:PHE86 5.0 58.7 1.0

Fluorine binding site 6 out of 6 in 6xvg

Go back to Fluorine Binding Sites List in 6xvg
Fluorine binding site 6 out of 6 in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F403

b:99.2
occ:1.00
 F1 F:8L9403 0.0 99.2 1.0
C39 F:8L9403 1.4 0.6 1.0
C38 F:8L9403 2.4 0.5 1.0
C40 F:8L9403 2.4 0.4 1.0
BR1 F:8L9403 3.1 0.8 1.0
CG2 F:VAL115 3.4 51.0 1.0
C36 F:8L9403 3.6 0.1 1.0
C42 F:8L9403 3.7 0.1 1.0
CZ F:PHE64 3.7 70.5 1.0
CE2 F:PHE64 4.0 67.8 1.0
C35 F:8L9403 4.1 0.3 1.0
CE1 F:PHE64 4.7 73.2 1.0
CZ F:PHE86 4.8 59.1 1.0
CB F:VAL115 4.8 55.3 1.0
N F:VAL115 4.9 50.8 1.0
C43 F:8L9403 4.9 0.8 1.0
CE1 F:PHE86 4.9 61.8 1.0

Reference:

W.You, C.Steegborn. Crystal Structures of SIRT6 Complexes with the Allosteric Activator Mdl-801 Reveal Binding Site and Interaction Details To Be Published.
Page generated: Tue Jul 15 17:33:37 2025

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