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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Go back to Chlorine Binding Sites List in 6xvg
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy