Chlorine 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
Bromine (Br) 6 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Human SIRT6 3-318 in Complex with Adp-Ribose and the Activator Mdl-801, PDB code: 6xvg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6xvg

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Chlorine binding site 1 out of 12 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 Chlorine with other atoms in the Cl 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:Cl404

b:76.2
occ:1.00
 CL1 A:8L9404 0.0 76.2 1.0
C09 A:8L9404 1.8 0.1 1.0
C01 A:8L9404 2.7 0.6 1.0
C07 A:8L9404 2.8 0.2 1.0
C40 A:8L9404 3.2 87.8 1.0
C42 A:8L9404 3.9 89.0 1.0
C43 A:8L9404 3.9 85.7 1.0
C03 A:8L9404 4.0 1.0 1.0
CG2 A:ILE185 4.0 52.3 1.0
C39 A:8L9404 4.1 82.2 1.0
C06 A:8L9404 4.1 0.3 1.0
CG2 A:VAL115 4.1 39.9 1.0
F1 A:8L9404 4.2 80.6 1.0
SD A:MET157 4.5 75.0 1.0
CE A:MET157 4.5 78.1 1.0
C04 A:8L9404 4.5 0.2 1.0
CG1 A:VAL115 4.9 37.4 1.0

Chlorine binding site 2 out of 12 in 6xvg

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Chlorine binding site 2 out of 12 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 Chlorine with other atoms in the Cl 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
A:Cl404

b:0.7
occ:1.00
 CL2 A:8L9404 0.0 0.7 1.0
C03 A:8L9404 1.8 1.0 1.0
C01 A:8L9404 2.7 0.6 1.0
C04 A:8L9404 2.8 0.2 1.0
O A:HOH529 3.3 50.6 1.0
O1D A:AR6401 3.6 55.5 1.0
O2D A:AR6401 3.8 47.5 1.0
C09 A:8L9404 4.0 0.1 1.0
C06 A:8L9404 4.1 0.3 1.0
CE3 A:TRP188 4.2 1.0 1.0
CZ3 A:TRP188 4.3 0.3 1.0
C2D A:AR6401 4.4 47.9 1.0
C1D A:AR6401 4.5 50.2 1.0
C07 A:8L9404 4.5 0.2 1.0
CD2 A:TRP188 4.6 1.0 1.0
CH2 A:TRP188 4.8 0.6 1.0
CZ2 A:TRP71 4.9 64.3 1.0
O A:LEU186 4.9 56.7 1.0
N A:TRP188 4.9 86.6 1.0

Chlorine binding site 3 out of 12 in 6xvg

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Chlorine binding site 3 out of 12 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 Chlorine with other atoms in the Cl 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
B:Cl404

b:0.3
occ:1.00
 CL1 B:8L9404 0.0 0.3 1.0
C09 B:8L9404 1.8 0.8 1.0
C01 B:8L9404 2.7 0.4 1.0
C07 B:8L9404 2.8 0.7 1.0
C40 B:8L9404 3.3 96.1 1.0
F1 B:8L9404 3.9 0.5 1.0
C39 B:8L9404 3.9 0.7 1.0
CG2 B:ILE185 3.9 48.9 1.0
C03 B:8L9404 4.0 0.4 1.0
C06 B:8L9404 4.1 0.8 1.0
C42 B:8L9404 4.2 98.0 1.0
CG2 B:VAL115 4.2 43.4 1.0
C43 B:8L9404 4.4 97.8 1.0
C04 B:8L9404 4.5 0.8 1.0
CG1 B:VAL115 4.7 44.7 1.0
CZ B:PHE64 4.8 46.1 1.0
SD B:MET157 4.9 77.5 1.0

Chlorine binding site 4 out of 12 in 6xvg

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Chlorine binding site 4 out of 12 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 Chlorine with other atoms in the Cl 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
B:Cl404

b:0.8
occ:1.00
 CL2 B:8L9404 0.0 0.8 1.0
C03 B:8L9404 1.8 0.4 1.0
C04 B:8L9404 2.7 0.8 1.0
C01 B:8L9404 2.7 0.4 1.0
O1D B:AR6401 3.7 60.9 1.0
CE2 B:TRP188 3.9 0.4 1.0
CD2 B:TRP188 3.9 0.3 1.0
C06 B:8L9404 4.0 0.8 1.0
C09 B:8L9404 4.0 0.8 1.0
O2D B:AR6401 4.1 50.4 1.0
NE1 B:TRP188 4.2 0.3 1.0
CE3 B:TRP188 4.2 0.8 1.0
CZ2 B:TRP188 4.2 0.8 1.0
CG B:TRP188 4.2 0.8 1.0
CD1 B:TRP188 4.4 0.8 1.0
N B:TRP188 4.4 76.4 1.0
CH2 B:TRP188 4.5 0.2 1.0
CZ3 B:TRP188 4.5 0.5 1.0
CA B:TRP188 4.5 84.8 1.0
C07 B:8L9404 4.5 0.7 1.0
C1D B:AR6401 4.7 49.8 1.0
C2D B:AR6401 4.7 50.1 1.0
C B:ASP187 4.9 66.2 1.0
O B:LEU186 4.9 55.4 1.0
CB B:TRP188 5.0 99.6 1.0

Chlorine binding site 5 out of 12 in 6xvg

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Chlorine binding site 5 out of 12 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 Chlorine with other atoms in the Cl 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
C:Cl1006

b:0.4
occ:1.00
 CL1 C:8L91006 0.0 0.4 1.0
C09 C:8L91006 1.8 0.6 1.0
C01 C:8L91006 2.8 0.4 1.0
C07 C:8L91006 2.8 0.5 1.0
OE2 C:GLU74 3.4 0.1 1.0
C03 C:8L91006 4.1 0.9 1.0
CD C:LYS15 4.1 0.1 1.0
C06 C:8L91006 4.1 0.4 1.0
CZ3 C:TRP71 4.1 82.8 1.0
CD C:GLU74 4.5 0.8 1.0
CH2 C:TRP71 4.5 78.3 1.0
C04 C:8L91006 4.6 0.2 1.0
CE3 C:TRP71 4.7 76.2 1.0
CG C:LYS15 4.8 0.9 1.0
OE1 C:GLU74 4.8 0.2 1.0
CE C:LYS15 5.0 0.4 1.0

Chlorine binding site 6 out of 12 in 6xvg

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Chlorine binding site 6 out of 12 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 Chlorine with other atoms in the Cl 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
C:Cl1006

b:1.0
occ:1.00
 CL2 C:8L91006 0.0 1.0 1.0
C03 C:8L91006 1.8 0.9 1.0
C04 C:8L91006 2.7 0.2 1.0
C01 C:8L91006 2.8 0.4 1.0
OD2 C:ASP187 3.2 94.8 1.0
CG D:PRO26 3.7 83.8 1.0
C06 C:8L91006 4.0 0.4 1.0
C09 C:8L91006 4.1 0.6 1.0
CG C:ASP187 4.2 89.4 1.0
CD1 C:TRP188 4.2 0.2 1.0
CB C:TRP188 4.2 0.8 1.0
CB D:PRO26 4.4 83.4 1.0
OD1 C:ASP187 4.5 99.4 1.0
C07 C:8L91006 4.6 0.5 1.0
CG C:TRP188 4.6 0.8 1.0
N C:TRP188 4.7 86.7 1.0
CD D:PRO26 4.8 76.3 1.0

Chlorine binding site 7 out of 12 in 6xvg

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Chlorine binding site 7 out of 12 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl404

b:88.6
occ:1.00
 CL1 D:8L9404 0.0 88.6 1.0
C09 D:8L9404 1.8 0.0 1.0
C07 D:8L9404 2.7 0.7 1.0
C01 D:8L9404 2.8 0.5 1.0
CG2 D:ILE185 3.7 44.4 1.0
C40 D:8L9404 3.7 93.6 1.0
C06 D:8L9404 4.0 0.5 1.0
C03 D:8L9404 4.1 0.5 1.0
C43 D:8L9404 4.2 82.0 1.0
C42 D:8L9404 4.2 89.1 1.0
CG2 D:VAL115 4.2 40.0 1.0
SD D:MET157 4.3 73.2 1.0
C39 D:8L9404 4.5 95.1 1.0
C04 D:8L9404 4.5 0.8 1.0
F1 D:8L9404 4.7 89.2 1.0
CG1 D:VAL115 4.8 46.7 1.0

Chlorine binding site 8 out of 12 in 6xvg

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Chlorine binding site 8 out of 12 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl404

b:0.9
occ:1.00
 CL2 D:8L9404 0.0 0.9 1.0
C03 D:8L9404 1.8 0.5 1.0
C04 D:8L9404 2.7 0.8 1.0
O1D D:AR6401 2.8 53.1 1.0
C01 D:8L9404 2.8 0.5 1.0
C1 D:GOL403 2.8 78.8 1.0
O1 D:GOL403 3.2 78.0 1.0
O2D D:AR6401 3.7 50.4 1.0
C1D D:AR6401 3.7 52.8 1.0
CZ2 D:TRP71 4.0 65.9 1.0
C2D D:AR6401 4.0 50.0 1.0
C06 D:8L9404 4.0 0.5 1.0
C09 D:8L9404 4.1 0.0 1.0
C2 D:GOL403 4.2 75.6 1.0
O2 D:GOL403 4.5 72.5 1.0
C07 D:8L9404 4.5 0.7 1.0
CH2 D:TRP71 4.8 70.1 1.0
CE2 D:TRP71 4.9 64.2 1.0
CD1 D:TRP188 4.9 0.8 1.0

Chlorine binding site 9 out of 12 in 6xvg

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Chlorine binding site 9 out of 12 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl705

b:0.4
occ:1.00
 CL1 E:8L9705 0.0 0.4 1.0
C09 E:8L9705 1.8 0.1 1.0
C01 E:8L9705 2.7 0.6 1.0
C07 E:8L9705 2.8 0.4 1.0
NZ B:LYS15 2.9 0.4 1.0
CE B:LYS15 3.7 0.6 1.0
OE2 B:GLU75 3.8 0.2 1.0
C03 E:8L9705 4.0 0.9 1.0
C06 E:8L9705 4.0 0.6 1.0
C04 E:8L9705 4.6 0.5 1.0
CD B:GLU75 4.7 90.6 1.0

Chlorine binding site 10 out of 12 in 6xvg

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Chlorine binding site 10 out of 12 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl705

b:0.7
occ:1.00
 CL2 E:8L9705 0.0 0.7 1.0
C03 E:8L9705 1.8 0.9 1.0
C01 E:8L9705 2.7 0.6 1.0
C04 E:8L9705 2.8 0.5 1.0
C09 E:8L9705 4.0 0.1 1.0
C06 E:8L9705 4.0 0.6 1.0
O E:GLY155 4.4 77.1 1.0
C07 E:8L9705 4.5 0.4 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: Sat Dec 12 14:37:39 2020

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