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Bromine 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:

Fluorine (F) 6 atoms
Zinc (Zn) 6 atoms
Chlorine (Cl) 12 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 6 binding sites of Bromine where determined in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801, PDB code: 6xvg:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br404

b:82.6
occ:1.00
 BR1 A:8L9404 0.0 82.6 1.0
C38 A:8L9404 1.9 74.2 1.0
C36 A:8L9404 2.8 82.1 1.0
C39 A:8L9404 2.9 82.2 1.0
O A:PRO62 3.0 37.3 1.0
F1 A:8L9404 3.1 80.6 1.0
CG2 A:ILE61 3.8 35.4 1.0
CZ A:PHE64 4.0 47.0 1.0
C A:PRO62 4.0 37.6 1.0
CG A:PRO62 4.0 41.5 1.0
C35 A:8L9404 4.2 84.2 1.0
CE2 A:PHE64 4.2 44.7 1.0
C40 A:8L9404 4.2 87.8 1.0
CG2 A:VAL70 4.3 45.9 1.0
CD A:PRO62 4.3 40.0 1.0
CE1 A:PHE64 4.6 47.6 1.0
O32 A:8L9404 4.6 87.0 1.0
N A:PRO62 4.6 38.1 1.0
CZ A:PHE82 4.7 49.8 1.0
C42 A:8L9404 4.7 89.0 1.0
O A:ASP63 4.7 42.4 1.0
CA A:PRO62 4.8 41.0 1.0
CB A:PRO62 4.9 42.4 1.0
CD2 A:PHE64 4.9 46.6 1.0
N A:ASP63 5.0 35.3 1.0

Bromine binding site 2 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br404

b:0.1
occ:1.00
 BR1 B:8L9404 0.0 0.1 1.0
C38 B:8L9404 1.9 98.7 1.0
C36 B:8L9404 2.8 0.3 1.0
C39 B:8L9404 2.9 0.7 1.0
F1 B:8L9404 3.0 0.5 1.0
O B:PRO62 3.4 47.8 1.0
CZ B:PHE64 3.9 46.1 1.0
CG2 B:ILE61 4.0 44.4 1.0
C35 B:8L9404 4.2 0.8 1.0
CE2 B:PHE64 4.2 46.9 1.0
C40 B:8L9404 4.2 96.1 1.0
CG B:PRO62 4.3 45.0 1.0
C B:PRO62 4.4 41.9 1.0
CE1 B:PHE64 4.5 47.3 1.0
CD B:PRO62 4.5 42.0 1.0
CZ B:PHE82 4.6 53.6 1.0
CG2 B:VAL70 4.6 54.5 1.0
C42 B:8L9404 4.7 98.0 1.0
O32 B:8L9404 4.8 0.8 1.0
O B:HOH516 4.8 36.2 1.0
N B:PRO62 4.9 45.2 1.0
O B:HOH530 4.9 46.6 1.0
CD2 B:PHE64 5.0 44.7 1.0

Bromine binding site 3 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br1006

b:82.5
occ:1.00
 BR1 C:8L91006 0.0 82.5 1.0
C38 C:8L91006 1.9 80.5 1.0
C36 C:8L91006 2.8 78.8 1.0
C39 C:8L91006 2.9 84.9 1.0
F1 C:8L91006 3.0 95.8 1.0
O C:PRO62 3.0 41.5 1.0
CG2 C:ILE61 3.7 41.5 1.0
CZ C:PHE64 3.9 56.0 1.0
C C:PRO62 4.1 41.5 1.0
C35 C:8L91006 4.1 94.1 1.0
C40 C:8L91006 4.2 94.8 1.0
CG C:PRO62 4.2 48.7 1.0
CE2 C:PHE64 4.2 54.1 1.0
CG2 C:VAL70 4.3 59.3 1.0
CD C:PRO62 4.4 49.5 1.0
CE1 C:PHE64 4.4 56.9 1.0
N C:PRO62 4.6 48.4 1.0
CZ C:PHE82 4.7 54.5 1.0
C42 C:8L91006 4.7 96.4 1.0
CA C:PRO62 4.9 44.9 1.0
O C:ASP63 4.9 45.0 1.0
O32 C:8L91006 4.9 0.4 1.0
CZ C:PHE86 4.9 53.6 1.0
CD2 C:PHE64 5.0 53.9 1.0

Bromine binding site 4 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br404

b:84.9
occ:1.00
 BR1 D:8L9404 0.0 84.9 1.0
C38 D:8L9404 1.9 83.4 1.0
C36 D:8L9404 2.9 84.7 1.0
C39 D:8L9404 2.9 95.1 1.0
O D:PRO62 3.0 41.4 1.0
F1 D:8L9404 3.2 89.2 1.0
CG2 D:ILE61 3.8 49.5 1.0
CZ D:PHE64 4.0 52.3 1.0
C D:PRO62 4.0 36.7 1.0
CG D:PRO62 4.1 49.4 1.0
C35 D:8L9404 4.2 90.4 1.0
CG2 D:VAL70 4.2 55.6 1.0
C40 D:8L9404 4.2 93.6 1.0
CE2 D:PHE64 4.3 54.9 1.0
CD D:PRO62 4.3 51.8 1.0
CE1 D:PHE64 4.5 52.0 1.0
CZ D:PHE82 4.6 60.1 1.0
N D:PRO62 4.6 49.5 1.0
C42 D:8L9404 4.7 89.1 1.0
O D:ASP63 4.7 51.0 1.0
O32 D:8L9404 4.8 97.2 1.0
CA D:PRO62 4.8 45.3 1.0
CD2 D:PHE64 4.9 50.9 1.0
CB D:PRO62 4.9 47.6 1.0
N D:ASP63 5.0 42.1 1.0

Bromine binding site 5 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br705

b:93.9
occ:1.00
 BR1 E:8L9705 0.0 93.9 1.0
C38 E:8L9705 1.9 85.8 1.0
C39 E:8L9705 2.9 92.5 1.0
C36 E:8L9705 2.9 81.4 1.0
O E:PRO62 2.9 41.7 1.0
F1 E:8L9705 3.0 90.3 1.0
CG2 E:ILE61 3.6 52.2 1.0
CZ E:PHE64 3.9 56.5 1.0
C E:PRO62 4.0 44.8 1.0
CG E:PRO62 4.1 47.3 1.0
CE1 E:PHE64 4.1 55.5 1.0
C35 E:8L9705 4.2 95.9 1.0
C40 E:8L9705 4.2 89.1 1.0
CG2 E:VAL70 4.3 67.4 1.0
CD E:PRO62 4.3 49.2 1.0
O E:HOH821 4.4 53.4 1.0
CE2 E:PHE64 4.4 62.1 1.0
N E:PRO62 4.5 45.8 1.0
CZ E:PHE82 4.6 53.6 1.0
C42 E:8L9705 4.7 90.0 1.0
CA E:PRO62 4.7 48.2 1.0
O E:ASP63 4.8 60.4 1.0
CD1 E:PHE64 4.8 56.2 1.0
CB E:PRO62 4.9 48.9 1.0
N E:ASP63 4.9 43.6 1.0

Bromine binding site 6 out of 6 in 6xvg

Go back to Bromine Binding Sites List in 6xvg
Bromine 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 Bromine with other atoms in the Br 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:Br403

b:0.8
occ:1.00
 BR1 F:8L9403 0.0 0.8 1.0
C38 F:8L9403 1.9 0.5 1.0
C36 F:8L9403 2.8 0.1 1.0
C39 F:8L9403 2.9 0.6 1.0
O F:PRO62 3.1 51.1 1.0
F1 F:8L9403 3.1 99.2 1.0
CG2 F:ILE61 3.9 53.8 1.0
CG F:PRO62 4.0 50.4 1.0
CZ F:PHE64 4.1 70.5 1.0
C F:PRO62 4.1 48.5 1.0
C35 F:8L9403 4.1 0.3 1.0
C40 F:8L9403 4.2 0.4 1.0
CD F:PRO62 4.3 52.7 1.0
CG2 F:VAL70 4.3 70.8 1.0
CZ F:PHE82 4.4 60.9 1.0
CE2 F:PHE64 4.4 67.8 1.0
O32 F:8L9403 4.4 0.6 1.0
CE1 F:PHE64 4.5 73.2 1.0
N F:PRO62 4.6 51.1 1.0
C42 F:8L9403 4.7 0.1 1.0
CA F:PRO62 4.8 49.5 1.0
O F:ASP63 4.9 55.3 1.0
CB F:PRO62 4.9 51.5 1.0
CE2 F:PHE82 5.0 61.1 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: Thu Jul 11 03:07:14 2024

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