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

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 6xvg

Go back to Zinc Binding Sites List in 6xvg
Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:66.0
occ:1.00
 SG A:CYS144 2.2 67.3 1.0
SG A:CYS166 2.3 58.6 1.0
SG A:CYS141 2.3 62.4 1.0
SG A:CYS177 2.4 68.5 1.0
CB A:CYS166 3.0 60.0 1.0
CB A:CYS141 3.2 71.1 1.0
CB A:CYS177 3.4 70.7 1.0
CB A:CYS144 3.4 72.0 1.0
N A:CYS144 3.8 78.7 1.0
CA A:CYS144 4.1 74.7 1.0
CA A:CYS166 4.5 57.6 1.0
N A:GLY179 4.5 69.9 1.0
CA A:GLY179 4.6 71.1 1.0
CA A:CYS141 4.6 66.8 1.0
CB A:LYS143 4.6 85.6 1.0
CB A:VAL168 4.8 70.5 1.0
CA A:CYS177 4.8 71.2 1.0
CG2 A:VAL168 4.8 75.7 1.0
C A:CYS144 4.8 75.4 1.0
OG1 A:THR146 4.8 61.8 1.0
C A:LYS143 4.9 76.4 1.0
CB A:THR146 4.9 60.5 1.0
N A:LYS145 5.0 79.3 1.0

Zinc binding site 2 out of 6 in 6xvg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:60.7
occ:1.00
 SG B:CYS144 2.2 55.0 1.0
SG B:CYS141 2.2 57.3 1.0
SG B:CYS166 2.3 59.9 1.0
SG B:CYS177 2.5 73.8 1.0
CB B:CYS166 3.0 61.5 1.0
CB B:CYS141 3.1 56.5 1.0
CB B:CYS144 3.3 59.0 1.0
CB B:CYS177 3.4 73.4 1.0
N B:CYS144 3.7 66.9 1.0
CA B:CYS144 4.0 61.3 1.0
CA B:CYS166 4.5 62.1 1.0
N B:GLY179 4.5 66.7 1.0
CA B:CYS141 4.5 55.1 1.0
CA B:GLY179 4.6 63.1 1.0
CB B:LYS143 4.7 70.3 1.0
C B:CYS144 4.7 62.9 1.0
CG2 B:VAL168 4.7 70.7 1.0
CE B:LYS170 4.7 89.5 1.0
C B:LYS143 4.8 67.2 1.0
CA B:CYS177 4.8 69.7 1.0
CB B:VAL168 4.8 66.3 1.0
OG1 B:THR146 4.9 50.3 1.0
CB B:THR146 4.9 48.0 1.0
N B:LYS145 4.9 61.5 1.0

Zinc binding site 3 out of 6 in 6xvg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1003

b:63.4
occ:1.00
 SG C:CYS144 2.1 63.9 1.0
SG C:CYS177 2.4 76.6 1.0
SG C:CYS141 2.4 64.8 1.0
SG C:CYS166 2.5 56.8 1.0
CB C:CYS144 3.1 69.7 1.0
CB C:CYS141 3.2 60.7 1.0
CB C:CYS166 3.2 53.6 1.0
CB C:CYS177 3.3 76.7 1.0
N C:CYS144 3.6 72.1 1.0
CA C:CYS144 3.9 64.0 1.0
N C:GLY179 4.6 74.3 1.0
C C:CYS144 4.6 63.6 1.0
CA C:CYS141 4.7 59.5 1.0
CA C:CYS166 4.7 52.9 1.0
CA C:GLY179 4.7 65.9 1.0
CA C:CYS177 4.7 71.8 1.0
C C:LYS143 4.7 66.0 1.0
OG1 C:THR146 4.7 56.8 1.0
CB C:LYS143 4.7 62.8 1.0
N C:LYS145 4.8 67.4 1.0
CB C:THR146 4.8 58.0 1.0
CB C:VAL168 4.9 84.5 1.0
CG1 C:VAL168 4.9 88.6 1.0

Zinc binding site 4 out of 6 in 6xvg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:68.2
occ:1.00
 SG D:CYS144 2.1 59.8 1.0
SG D:CYS141 2.3 61.0 1.0
SG D:CYS177 2.4 70.4 1.0
SG D:CYS166 2.5 69.1 1.0
CB D:CYS166 3.1 60.1 1.0
CB D:CYS141 3.1 59.8 1.0
CB D:CYS144 3.3 63.6 1.0
CB D:CYS177 3.4 72.9 1.0
N D:CYS144 3.7 64.9 1.0
CA D:CYS144 4.0 61.8 1.0
CB D:LYS143 4.5 63.6 1.0
CA D:CYS141 4.6 59.3 1.0
CA D:CYS166 4.6 62.0 1.0
N D:GLY179 4.6 69.0 1.0
CA D:GLY179 4.6 60.2 1.0
C D:CYS144 4.7 64.3 1.0
C D:LYS143 4.7 63.5 1.0
OG1 D:THR146 4.8 58.2 1.0
CA D:CYS177 4.8 74.5 1.0
CB D:THR146 4.9 63.6 1.0
N D:LYS145 4.9 64.6 1.0
CG2 D:VAL168 4.9 77.1 1.0
CB D:VAL168 4.9 77.6 1.0

Zinc binding site 5 out of 6 in 6xvg

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Zinc 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 Zinc with other atoms in the Zn 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:Zn703

b:77.7
occ:1.00
 SG E:CYS144 2.0 77.4 1.0
SG E:CYS141 2.3 72.9 1.0
SG E:CYS177 2.4 90.5 1.0
SG E:CYS166 2.6 74.0 1.0
CB E:CYS144 3.1 84.2 1.0
CB E:CYS141 3.1 74.6 1.0
CB E:CYS166 3.2 70.6 1.0
CB E:CYS177 3.4 80.5 1.0
N E:CYS144 3.6 86.4 1.0
OG1 E:THR146 3.8 96.2 1.0
CA E:CYS144 3.9 78.6 1.0
CB E:LYS143 4.5 72.9 1.0
C E:CYS144 4.6 69.8 1.0
CA E:CYS141 4.6 74.0 1.0
N E:GLY179 4.6 75.9 1.0
CA E:GLY179 4.7 77.6 1.0
C E:LYS143 4.7 82.2 1.0
CA E:CYS166 4.7 70.5 1.0
N E:LYS145 4.8 71.2 1.0
CA E:CYS177 4.8 82.4 1.0
CG2 E:VAL168 4.9 87.5 1.0
CB E:VAL168 4.9 86.1 1.0
CG2 E:THR146 4.9 76.4 1.0
CB E:THR146 4.9 75.2 1.0
CA E:LYS143 5.0 74.3 1.0

Zinc binding site 6 out of 6 in 6xvg

Go back to Zinc Binding Sites List in 6xvg
Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:79.9
occ:1.00
 SG F:CYS144 2.2 72.8 1.0
SG F:CYS141 2.3 73.1 1.0
SG F:CYS166 2.3 73.6 1.0
SG F:CYS177 2.4 96.3 1.0
CB F:CYS166 3.0 66.1 1.0
CB F:CYS141 3.1 76.0 1.0
CB F:CYS144 3.4 77.9 1.0
CB F:CYS177 3.4 85.3 1.0
N F:CYS144 3.7 81.1 1.0
CA F:CYS144 4.1 80.2 1.0
CA F:CYS166 4.5 67.0 1.0
N F:GLY179 4.6 82.7 1.0
CA F:CYS141 4.6 75.0 1.0
CA F:GLY179 4.6 85.0 1.0
CB F:LYS143 4.7 74.5 1.0
C F:CYS144 4.7 83.1 1.0
CB F:VAL168 4.8 81.5 1.0
CG2 F:VAL168 4.8 85.4 1.0
CA F:CYS177 4.8 89.3 1.0
OG1 F:THR146 4.8 83.5 1.0
C F:LYS143 4.8 75.6 1.0
CB F:THR146 4.9 75.9 1.0
N F:LYS145 4.9 85.3 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 Oct 29 11:16:01 2024

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