Zinc in PDB 8bbk: Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein

Enzymatic activity of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein

All present enzymatic activity of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein:
2.3.1.286;

Protein crystallography data

The structure of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein, PDB code: 8bbk was solved by C.Steegborn, S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.19 / 3.27
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.215, 110.215, 344.362, 90, 90, 120
R / Rfree (%) 20.2 / 26.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein (pdb code 8bbk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein, PDB code: 8bbk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8bbk

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Zinc binding site 1 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


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 Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:73.3
occ:1.00
 SG A:CYS283 2.2 59.9 1.0
SG A:CYS280 2.3 66.9 1.0
SG A:CYS259 2.3 60.9 1.0
SG A:CYS256 2.3 69.8 1.0
CB A:CYS259 2.9 55.4 1.0
CB A:CYS280 3.0 63.9 1.0
CB A:CYS256 3.4 60.3 1.0
CB A:CYS283 3.5 63.7 1.0
N A:CYS259 3.6 69.7 1.0
CA A:CYS259 3.8 62.2 1.0
N A:CYS283 3.8 65.2 1.0
CA A:CYS283 4.1 64.9 1.0
CA A:CYS280 4.5 63.9 1.0
C A:CYS259 4.5 60.6 1.0
N A:GLY285 4.6 69.1 1.0
N A:THR284 4.6 60.5 1.0
C A:CYS283 4.6 62.1 1.0
CA A:CYS256 4.8 62.2 1.0
CB A:VAL282 4.8 64.7 1.0
N A:GLN260 4.8 60.7 1.0
NH2 A:ARG261 4.8 70.5 1.0
C A:VAL282 4.9 62.9 1.0
C A:VAL258 4.9 73.2 1.0
C A:CYS280 5.0 71.8 1.0
N A:VAL282 5.0 63.7 1.0

Zinc binding site 2 out of 6 in 8bbk

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Zinc binding site 2 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


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 Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:81.5
occ:1.00
 SG B:CYS283 2.3 82.2 1.0
SG B:CYS259 2.3 87.5 1.0
SG B:CYS256 2.3 91.0 1.0
SG B:CYS280 2.4 98.9 1.0
CB B:CYS280 3.1 85.9 1.0
CB B:CYS256 3.3 89.1 1.0
CB B:CYS259 3.3 81.3 1.0
N B:CYS259 3.6 83.3 1.0
CB B:CYS283 3.6 87.6 1.0
N B:CYS283 3.9 83.1 1.0
CA B:CYS259 3.9 87.1 1.0
CA B:CYS283 4.3 83.4 1.0
CB B:VAL282 4.6 89.0 1.0
CA B:CYS280 4.6 80.9 1.0
C B:CYS259 4.6 92.1 1.0
N B:GLY285 4.7 87.5 1.0
CA B:CYS256 4.7 86.0 1.0
N B:GLN260 4.7 88.8 1.0
C B:VAL258 4.7 85.6 1.0
N B:THR284 4.7 84.8 1.0
C B:CYS283 4.8 81.7 1.0
CB B:VAL258 4.8 85.5 1.0
C B:VAL282 4.9 90.8 1.0
N B:VAL282 5.0 90.7 1.0

Zinc binding site 3 out of 6 in 8bbk

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Zinc binding site 3 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


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 Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:133.0
occ:1.00
 SG C:CYS259 2.2 61.0 1.0
SG C:CYS283 2.2 78.5 1.0
SG C:CYS256 2.2 95.7 1.0
SG C:CYS280 2.3 86.9 1.0
CB C:CYS280 2.8 91.4 1.0
CB C:CYS259 3.2 76.5 1.0
CB C:CYS256 3.4 90.3 1.0
CB C:CYS283 3.5 97.3 1.0
N C:CYS283 3.7 92.5 1.0
N C:CYS259 3.7 84.3 1.0
CA C:CYS259 4.0 82.2 1.0
CA C:CYS283 4.0 94.8 1.0
CA C:CYS280 4.3 90.7 1.0
N C:GLY285 4.4 89.4 1.0
N C:THR284 4.5 86.1 1.0
C C:CYS283 4.5 85.4 1.0
CB C:VAL282 4.5 86.5 1.0
C C:VAL282 4.7 90.4 1.0
CA C:CYS256 4.7 88.7 1.0
C C:CYS280 4.8 94.5 1.0
C C:CYS259 4.8 82.2 1.0
CA C:GLY285 4.8 89.2 1.0
N C:VAL282 4.8 90.5 1.0
C C:VAL258 4.9 80.4 1.0
CB C:VAL258 4.9 81.1 1.0
CA C:VAL282 4.9 88.5 1.0
N C:GLN260 5.0 84.5 1.0
O C:CYS280 5.0 90.0 1.0
O C:GLY285 5.0 81.7 1.0

Zinc binding site 4 out of 6 in 8bbk

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Zinc binding site 4 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:92.2
occ:1.00
 SG D:CYS259 2.2 82.0 1.0
SG D:CYS283 2.3 81.8 1.0
SG D:CYS280 2.3 89.7 1.0
SG D:CYS256 2.3 83.1 1.0
CB D:CYS280 2.9 82.2 1.0
CB D:CYS259 3.3 83.6 1.0
CB D:CYS256 3.4 76.6 1.0
CB D:CYS283 3.7 86.9 1.0
N D:CYS259 3.7 87.7 1.0
N D:CYS283 3.9 85.4 1.0
CA D:CYS259 4.0 85.0 1.0
CA D:CYS283 4.2 83.6 1.0
N D:THR284 4.4 81.1 1.0
N D:GLY285 4.4 80.7 1.0
CA D:CYS280 4.4 76.8 1.0
C D:CYS283 4.5 85.3 1.0
CB D:VAL282 4.7 79.5 1.0
C D:CYS259 4.7 82.8 1.0
CA D:CYS256 4.8 73.7 1.0
CB D:VAL258 4.8 83.9 1.0
C D:VAL258 4.9 90.7 1.0
C D:CYS280 4.9 80.8 1.0
N D:GLN260 4.9 83.2 1.0
CA D:GLY285 5.0 88.2 1.0
C D:VAL282 5.0 89.6 1.0
N D:VAL282 5.0 83.4 1.0

Zinc binding site 5 out of 6 in 8bbk

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Zinc binding site 5 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:87.2
occ:1.00
 SG E:CYS280 2.3 81.7 1.0
SG E:CYS259 2.3 77.1 1.0
SG E:CYS256 2.3 74.5 1.0
SG E:CYS283 2.4 85.8 1.0
CB E:CYS280 3.0 81.8 1.0
CB E:CYS256 3.4 77.1 1.0
CB E:CYS259 3.5 78.2 1.0
CB E:CYS283 3.6 80.3 1.0
N E:CYS283 3.8 88.3 1.0
N E:CYS259 3.8 79.0 1.0
CA E:CYS283 4.2 83.0 1.0
CA E:CYS259 4.2 82.8 1.0
N E:GLY285 4.5 78.7 1.0
CA E:CYS280 4.5 81.2 1.0
N E:THR284 4.6 80.5 1.0
C E:CYS283 4.7 86.2 1.0
CB E:VAL282 4.7 82.8 1.0
CB E:VAL258 4.7 84.2 1.0
CA E:CYS256 4.7 75.9 1.0
NH2 E:ARG261 4.8 93.3 1.0
C E:VAL282 4.9 89.4 1.0
C E:CYS259 4.9 75.3 1.0
CA E:GLY285 4.9 82.0 1.0
CG1 E:VAL258 4.9 82.2 1.0
C E:VAL258 5.0 79.4 1.0
N E:VAL282 5.0 82.2 1.0

Zinc binding site 6 out of 6 in 8bbk

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Zinc binding site 6 out of 6 in the Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human SIRT3 in Complex with A Fragment of the Human Aros Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:101.2
occ:1.00
 SG F:CYS259 2.3 85.1 1.0
SG F:CYS283 2.3 89.9 1.0
SG F:CYS280 2.4 84.3 1.0
SG F:CYS256 2.6 134.1 1.0
CB F:CYS256 2.9 93.2 1.0
CB F:CYS280 3.1 97.0 1.0
CB F:CYS259 3.2 96.3 1.0
N F:CYS259 3.2 98.4 1.0
CA F:CYS259 3.7 99.0 1.0
CB F:CYS283 3.8 82.6 1.0
N F:CYS283 4.3 103.5 1.0
C F:VAL258 4.4 101.3 1.0
CA F:CYS256 4.4 94.3 1.0
C F:CYS259 4.4 96.4 1.0
N F:GLN260 4.4 93.5 1.0
CB F:VAL258 4.5 89.5 1.0
N F:GLY285 4.5 94.5 1.0
CA F:CYS283 4.6 93.1 1.0
CA F:CYS280 4.6 89.2 1.0
N F:VAL258 4.6 102.4 1.0
CA F:VAL258 4.7 98.5 1.0
CA F:GLY285 4.8 98.4 1.0
CG1 F:VAL258 4.9 86.3 1.0
N F:THR284 4.9 87.2 1.0
O F:GLY285 4.9 99.2 1.0
C F:CYS283 5.0 86.8 1.0

Reference:

S.Weiss, R.S.Adolph, K.Schweimer, A.Difonzo, M.Meleshin, M.Schutkowski, C.Steegborn. Molecular Mechanism of Sirtuin 1 Modulation By the Aros Protein. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36361557
DOI: 10.3390/IJMS232112764
Page generated: Wed Oct 30 18:12:51 2024

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