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Zinc in PDB 5btr: Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide

Protein crystallography data

The structure of Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide, PDB code: 5btr was solved by D.Cao, M.Wang, X.Qiu, D.Liu, H.Jiang, N.Yang, R.M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.63 / 3.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 133.890, 133.890, 106.707, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide (pdb code 5btr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide, PDB code: 5btr:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5btr

Go back to Zinc Binding Sites List in 5btr
Zinc binding site 1 out of 3 in the Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:64.6
occ:1.00
SG A:CYS395 2.3 58.9 1.0
SG A:CYS374 2.3 60.3 1.0
SG A:CYS398 2.3 73.5 1.0
SG A:CYS371 2.6 70.7 1.0
CB A:CYS398 3.1 70.2 1.0
CB A:CYS395 3.2 64.0 1.0
CB A:CYS374 3.4 65.8 1.0
CB A:CYS371 3.5 66.8 1.0
N A:CYS398 3.7 70.3 1.0
N A:CYS374 3.9 66.9 1.0
CA A:CYS398 3.9 73.0 1.0
CA A:CYS374 4.2 65.9 1.0
CB A:ALA405 4.5 77.8 1.0
CA A:CYS395 4.7 62.9 1.0
CB A:ARG397 4.7 58.9 1.0
CB A:ILE373 4.7 56.3 1.0
C A:ARG397 4.8 70.1 1.0
CA A:CYS371 4.9 69.2 1.0
C A:ILE373 5.0 73.0 1.0
N A:ARG397 5.0 61.1 1.0

Zinc binding site 2 out of 3 in 5btr

Go back to Zinc Binding Sites List in 5btr
Zinc binding site 2 out of 3 in the Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:0.5
occ:1.00
SG B:CYS398 2.3 0.5 1.0
SG B:CYS395 2.5 0.9 1.0
SG B:CYS374 2.5 0.6 1.0
CB B:CYS398 2.9 0.5 1.0
SG B:CYS371 3.0 0.7 1.0
CB B:CYS395 3.3 0.5 1.0
CB B:CYS374 3.4 0.4 1.0
N B:CYS398 3.7 0.9 1.0
CA B:CYS398 3.9 0.1 1.0
N B:CYS374 3.9 0.8 1.0
CB B:CYS371 4.0 0.8 1.0
CA B:CYS374 4.3 0.4 1.0
CB B:ALA405 4.5 0.8 1.0
CB B:ILE373 4.6 0.7 1.0
CA B:CYS395 4.8 0.4 1.0
C B:ARG397 4.9 0.5 1.0
C B:ILE373 5.0 1.0 1.0

Zinc binding site 3 out of 3 in 5btr

Go back to Zinc Binding Sites List in 5btr
Zinc binding site 3 out of 3 in the Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SIRT1 in Complex with Resveratrol and An Amc- Containing Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:0.1
occ:1.00
SG C:CYS395 2.8 0.1 1.0
SG C:CYS371 3.1 0.9 1.0
CB C:CYS395 3.5 1.0 1.0
SG C:CYS374 3.6 0.1 1.0
CB C:ILE373 3.6 0.6 1.0
CB C:ALA405 3.7 0.9 1.0
N C:CYS374 3.9 0.1 1.0
CB C:CYS374 4.1 0.8 1.0
CD1 C:ILE373 4.2 0.9 1.0
CB C:CYS371 4.3 1.0 1.0
CG1 C:ILE373 4.3 0.5 1.0
CG2 C:ILE373 4.4 0.6 1.0
CA C:ILE373 4.4 0.6 1.0
N C:ILE373 4.5 0.1 1.0
CA C:ALA405 4.6 0.6 1.0
C C:ILE373 4.6 0.9 1.0
CA C:CYS374 4.6 0.4 1.0
CA C:CYS395 5.0 0.1 1.0

Reference:

D.Cao, M.Wang, X.Qiu, D.Liu, H.Jiang, N.Yang, R.M.Xu. Structural Basis For Allosteric, Substrate-Dependent Stimulation of SIRT1 Activity By Resveratrol Genes Dev. V. 29 1316 2015.
ISSN: ISSN 0890-9369
PubMed: 26109052
DOI: 10.1101/GAD.265462.115
Page generated: Wed Dec 16 06:05:05 2020

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