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

Go back to Zinc Binding Sites List in 8bbk
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

Go back to Zinc Binding Sites List in 8bbk
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

Go back to Zinc Binding Sites List in 8bbk
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

Go back to Zinc Binding Sites List in 8bbk
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

Go back to Zinc Binding Sites List in 8bbk
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

Go back to Zinc Binding Sites List in 8bbk
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy