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Zinc in PDB 5d7n: Crystal Structure of Human SIRT3 at An Improved Resolution

Protein crystallography data

The structure of Crystal Structure of Human SIRT3 at An Improved Resolution, PDB code: 5d7n was solved by T.Rumpf, S.Gerhardt, O.Einsle, M.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.66 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.990, 143.850, 89.460, 90.00, 116.33, 90.00
R / Rfree (%) 17.5 / 20.3

Other elements in 5d7n:

The structure of Crystal Structure of Human SIRT3 at An Improved Resolution also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SIRT3 at An Improved Resolution (pdb code 5d7n). 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 at An Improved Resolution, PDB code: 5d7n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 1 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.9
occ:1.00
SG A:CYS280 2.3 22.8 1.0
SG A:CYS259 2.3 24.9 1.0
SG A:CYS256 2.3 20.1 1.0
SG A:CYS283 2.3 22.6 1.0
CB A:CYS280 3.0 22.0 1.0
CB A:CYS256 3.2 19.6 1.0
CB A:CYS259 3.3 25.6 1.0
CB A:CYS283 3.4 23.7 1.0
N A:CYS259 3.7 24.3 1.0
N A:CYS283 3.8 25.0 1.0
CA A:CYS259 4.0 25.6 1.0
CA A:CYS283 4.2 23.7 1.0
CA A:CYS280 4.5 22.1 1.0
N A:GLY285 4.6 20.5 1.0
CA A:CYS256 4.6 18.8 1.0
C A:CYS283 4.7 22.4 1.0
CB A:VAL282 4.7 27.4 1.0
CB A:VAL258 4.7 21.1 1.0
C A:CYS259 4.7 26.0 1.0
N A:THR284 4.8 22.9 1.0
C A:VAL258 4.8 23.4 1.0
C A:VAL282 4.9 26.6 1.0
N A:GLN260 4.9 26.2 1.0
NH1 A:ARG261 5.0 32.9 1.0

Zinc binding site 2 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 2 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:13.5
occ:1.00
SG B:CYS283 2.3 14.3 1.0
SG B:CYS259 2.3 14.0 1.0
SG B:CYS280 2.3 13.3 1.0
SG B:CYS256 2.4 12.7 1.0
CB B:CYS280 3.1 13.7 1.0
CB B:CYS256 3.2 12.7 1.0
CB B:CYS259 3.3 14.5 1.0
CB B:CYS283 3.5 14.3 1.0
N B:CYS259 3.7 14.4 1.0
N B:CYS283 3.9 14.6 1.0
CA B:CYS259 4.1 14.7 1.0
CA B:CYS283 4.2 14.5 1.0
CA B:CYS280 4.5 13.9 1.0
CA B:CYS256 4.6 12.4 1.0
N B:GLY285 4.6 13.1 1.0
CB B:VAL258 4.7 14.0 1.0
N B:THR284 4.7 13.9 1.0
C B:CYS283 4.7 14.2 1.0
NH1 B:ARG261 4.8 16.6 1.0
CB B:VAL282 4.8 15.2 1.0
C B:CYS259 4.8 15.2 1.0
C B:VAL258 4.8 14.5 1.0
N B:GLN260 5.0 15.6 1.0
C B:VAL282 5.0 15.3 1.0

Zinc binding site 3 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 3 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:22.7
occ:1.00
SG C:CYS280 2.3 25.8 1.0
SG C:CYS256 2.3 20.2 1.0
SG C:CYS283 2.3 25.3 1.0
SG C:CYS259 2.3 24.1 1.0
CB C:CYS280 3.0 24.4 1.0
CB C:CYS256 3.1 19.1 1.0
CB C:CYS259 3.3 23.7 1.0
CB C:CYS283 3.5 26.3 1.0
N C:CYS259 3.7 21.9 1.0
N C:CYS283 3.9 27.9 1.0
CA C:CYS259 4.1 23.2 1.0
CA C:CYS283 4.2 27.0 1.0
CA C:CYS280 4.5 24.8 1.0
CA C:CYS256 4.6 18.1 1.0
N C:GLY285 4.7 21.7 1.0
CB C:VAL258 4.7 20.1 1.0
NH1 C:ARG261 4.7 32.9 1.0
C C:CYS283 4.8 25.9 1.0
N C:THR284 4.8 25.8 1.0
C C:CYS259 4.8 23.5 1.0
CB C:VAL282 4.8 31.6 1.0
C C:VAL258 4.9 21.2 1.0
N C:GLN260 5.0 23.9 1.0
C C:VAL282 5.0 29.5 1.0

Zinc binding site 4 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 4 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:23.3
occ:1.00
SG D:CYS280 2.3 25.0 1.0
SG D:CYS259 2.3 24.7 1.0
SG D:CYS256 2.3 20.1 1.0
SG D:CYS283 2.3 23.2 1.0
CB D:CYS280 3.0 24.5 1.0
CB D:CYS256 3.2 19.7 1.0
CB D:CYS259 3.3 24.8 1.0
CB D:CYS283 3.5 24.8 1.0
N D:CYS259 3.7 24.2 1.0
N D:CYS283 3.9 26.4 1.0
CA D:CYS259 4.1 24.7 1.0
CA D:CYS283 4.2 25.1 1.0
CA D:CYS280 4.5 24.6 1.0
CA D:CYS256 4.6 18.7 1.0
N D:GLY285 4.7 20.4 1.0
NH1 D:ARG261 4.7 34.1 1.0
C D:CYS283 4.8 24.0 1.0
CB D:VAL258 4.8 22.9 1.0
C D:CYS259 4.8 25.0 1.0
N D:THR284 4.8 23.2 1.0
CB D:VAL282 4.8 30.6 1.0
C D:VAL258 4.9 23.6 1.0
N D:GLN260 5.0 24.5 1.0
CB D:ARG261 5.0 27.9 1.0
C D:VAL282 5.0 28.6 1.0

Zinc binding site 5 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 5 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:18.1
occ:1.00
SG E:CYS283 2.3 18.6 1.0
SG E:CYS259 2.3 19.3 1.0
SG E:CYS280 2.3 18.7 1.0
SG E:CYS256 2.3 16.6 1.0
CB E:CYS280 3.1 18.2 1.0
CB E:CYS256 3.2 16.5 1.0
CB E:CYS259 3.3 19.4 1.0
CB E:CYS283 3.5 19.1 1.0
N E:CYS259 3.7 18.6 1.0
N E:CYS283 3.8 20.3 1.0
CA E:CYS259 4.1 19.5 1.0
CA E:CYS283 4.2 19.7 1.0
CA E:CYS280 4.5 18.5 1.0
N E:GLY285 4.6 17.4 1.0
CA E:CYS256 4.7 16.1 1.0
CB E:VAL282 4.7 23.7 1.0
N E:THR284 4.8 18.7 1.0
C E:CYS283 4.8 18.9 1.0
C E:CYS259 4.8 20.2 1.0
CB E:VAL258 4.8 17.8 1.0
C E:VAL258 4.8 18.5 1.0
C E:VAL282 4.9 21.9 1.0
NH1 E:ARG261 4.9 28.4 1.0
N E:GLN260 5.0 20.3 1.0

Zinc binding site 6 out of 6 in 5d7n

Go back to Zinc Binding Sites List in 5d7n
Zinc binding site 6 out of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution


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 at An Improved Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:20.8
occ:1.00
SG F:CYS283 2.3 22.5 1.0
SG F:CYS259 2.3 20.4 1.0
SG F:CYS280 2.3 22.5 1.0
SG F:CYS256 2.4 19.2 1.0
CB F:CYS280 3.1 22.0 1.0
CB F:CYS256 3.2 18.7 1.0
CB F:CYS259 3.3 21.3 1.0
CB F:CYS283 3.4 22.6 1.0
N F:CYS259 3.7 21.3 1.0
N F:CYS283 3.8 24.3 1.0
CA F:CYS259 4.1 21.1 1.0
CA F:CYS283 4.2 23.1 1.0
CB F:VAL282 4.5 27.5 1.0
CA F:CYS280 4.5 22.1 1.0
CA F:CYS256 4.6 17.7 1.0
N F:GLY285 4.7 20.3 1.0
C F:CYS259 4.7 21.0 1.0
CB F:VAL258 4.8 20.7 1.0
C F:CYS283 4.8 22.6 1.0
N F:THR284 4.8 22.0 1.0
C F:VAL282 4.9 25.8 1.0
C F:VAL258 4.9 21.3 1.0
CB F:ARG261 4.9 22.9 1.0
N F:GLN260 4.9 20.4 1.0

Reference:

T.Rumpf, S.Gerhardt, O.Einsle, M.Jung. Seeding For Sirtuins: Microseed Matrix Seeding to Obtain Crystals of Human SIRT3 and SIRT2 Suitable For Soaking. Acta Crystallogr.,Sect.F V. 71 1498 2015.
ISSN: ESSN 2053-230X
PubMed: 26625292
DOI: 10.1107/S2053230X15019986
Page generated: Wed Dec 16 06:08:08 2020

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