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Zinc in PDB 5mfz: Human SIRT6 in Complex with Small Molecule UBCS40

Protein crystallography data

The structure of Human SIRT6 in Complex with Small Molecule UBCS40, PDB code: 5mfz was solved by C.Steegborn, W.You, C.Kambach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.68 / 2.10
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 91.364, 91.364, 144.212, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT6 in Complex with Small Molecule UBCS40 (pdb code 5mfz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT6 in Complex with Small Molecule UBCS40, PDB code: 5mfz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5mfz

Go back to Zinc Binding Sites List in 5mfz
Zinc binding site 1 out of 2 in the Human SIRT6 in Complex with Small Molecule UBCS40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT6 in Complex with Small Molecule UBCS40 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:49.3
occ:1.00
SG A:CYS166 2.3 42.1 1.0
SG A:CYS141 2.3 50.7 1.0
SG A:CYS144 2.4 47.7 1.0
SG A:CYS177 2.4 63.2 1.0
CB A:CYS166 3.1 43.5 1.0
CB A:CYS141 3.2 50.3 1.0
CB A:CYS177 3.4 63.7 1.0
CB A:CYS144 3.5 49.0 1.0
N A:CYS144 3.7 60.6 1.0
CA A:CYS144 4.1 54.0 1.0
CA A:CYS166 4.5 40.8 1.0
N A:GLY179 4.5 52.0 1.0
CB A:LYS143 4.7 80.2 1.0
CB A:VAL168 4.7 48.2 1.0
CA A:CYS141 4.7 46.6 1.0
CA A:GLY179 4.7 50.7 1.0
CA A:CYS177 4.8 59.7 1.0
C A:LYS143 4.8 64.2 1.0
C A:CYS144 4.9 53.1 1.0
CG2 A:VAL168 4.9 52.7 1.0
OG1 A:THR146 4.9 49.5 1.0

Zinc binding site 2 out of 2 in 5mfz

Go back to Zinc Binding Sites List in 5mfz
Zinc binding site 2 out of 2 in the Human SIRT6 in Complex with Small Molecule UBCS40


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT6 in Complex with Small Molecule UBCS40 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:62.3
occ:1.00
SG B:CYS141 2.3 60.8 1.0
SG B:CYS144 2.3 66.7 1.0
SG B:CYS166 2.3 61.1 1.0
SG B:CYS177 2.4 67.9 1.0
CB B:CYS166 3.1 54.3 1.0
CB B:CYS141 3.2 64.9 1.0
CB B:CYS144 3.4 66.3 1.0
N B:CYS144 3.5 81.9 1.0
CB B:CYS177 3.6 64.3 1.0
CA B:CYS144 4.0 70.5 1.0
CB B:LYS143 4.5 82.3 1.0
C B:LYS143 4.6 76.8 1.0
CA B:CYS166 4.6 55.8 1.0
CA B:CYS141 4.6 66.1 1.0
N B:GLY179 4.7 78.6 1.0
OG1 B:THR146 4.8 49.1 1.0
C B:CYS144 4.8 63.1 1.0
CA B:LYS143 4.9 79.7 1.0
CA B:CYS177 5.0 70.8 1.0

Reference:

W.You, D.Rotili, T.M.Li, C.Kambach, M.Meleshin, M.Schutkowski, K.F.Chua, A.Mai, C.Steegborn. Structural Basis of Sirtuin 6 Activation By Synthetic Small Molecules. Angew. Chem. Int. Ed. Engl. V. 56 1007 2017.
ISSN: ESSN 1521-3773
PubMed: 27990725
DOI: 10.1002/ANIE.201610082
Page generated: Wed Dec 16 06:32:58 2020

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