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Zinc in PDB 3gls: Crystal Structure of Human SIRT3

Protein crystallography data

The structure of Crystal Structure of Human SIRT3, PDB code: 3gls was solved by L.Jin, W.Wei, Y.Jiang, H.Peng, J.Cai, C.Mao, H.Dai, J.E.Bemis, M.R.Jirousek, J.C.Milne, C.H.Westphal, R.B.Perni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.371, 143.935, 91.657, 90.00, 117.10, 90.00
R / Rfree (%) 18.2 / 24.4

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 3gls

Go back to Zinc Binding Sites List in 3gls
Zinc binding site 1 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:38.3
occ:1.00
 SG A:CYS259 2.2 32.9 1.0
SG A:CYS283 2.4 36.2 1.0
SG A:CYS256 2.5 33.2 1.0
SG A:CYS280 2.6 28.6 1.0
CB A:CYS259 2.9 33.6 1.0
CB A:CYS280 3.2 27.2 1.0
CB A:CYS283 3.5 31.4 1.0
CB A:CYS256 3.5 29.4 1.0
N A:CYS259 3.7 33.9 1.0
CA A:CYS259 3.8 34.4 1.0
N A:CYS283 3.9 33.1 1.0
CA A:CYS283 4.2 31.4 1.0
CB A:VAL282 4.5 34.0 1.0
CB A:VAL258 4.6 32.1 1.0
C A:CYS259 4.6 35.2 1.0
C A:VAL258 4.7 33.5 1.0
NE A:ARG261 4.7 48.8 1.0
CA A:CYS280 4.7 29.3 1.0
C A:CYS283 4.7 30.3 1.0
N A:THR284 4.8 30.1 1.0
N A:GLY285 4.8 27.5 1.0
N A:GLN260 4.8 35.6 1.0
C A:VAL282 4.9 34.6 1.0
CB A:ARG261 4.9 37.5 1.0
CA A:CYS256 4.9 29.0 1.0

Zinc binding site 2 out of 6 in 3gls

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Zinc binding site 2 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:22.3
occ:1.00
 SG B:CYS280 2.2 22.1 1.0
SG B:CYS259 2.2 25.1 1.0
SG B:CYS256 2.3 23.6 1.0
SG B:CYS283 2.4 21.1 1.0
CB B:CYS280 2.9 22.1 1.0
CB B:CYS256 3.3 21.1 1.0
CB B:CYS259 3.4 24.6 1.0
CB B:CYS283 3.7 18.3 1.0
N B:CYS283 3.8 18.5 1.0
N B:CYS259 3.8 24.4 1.0
CA B:CYS259 4.2 24.6 1.0
CA B:CYS283 4.3 18.1 1.0
CA B:CYS280 4.4 22.0 1.0
CA B:CYS256 4.7 20.9 1.0
CB B:VAL282 4.7 22.2 1.0
N B:GLY285 4.8 15.0 1.0
C B:CYS259 4.8 24.7 1.0
CB B:VAL258 4.8 23.3 1.0
C B:CYS283 4.8 17.2 1.0
N B:GLN260 4.9 23.4 1.0
N B:THR284 4.9 17.2 1.0
C B:VAL282 4.9 20.4 1.0
C B:VAL258 4.9 24.2 1.0
NH2 B:ARG261 5.0 30.2 1.0
CG1 B:VAL258 5.0 21.1 1.0
C B:CYS280 5.0 22.2 1.0

Zinc binding site 3 out of 6 in 3gls

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Zinc binding site 3 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn5

b:16.0
occ:1.00
 SG C:CYS283 2.2 14.2 1.0
SG C:CYS280 2.4 17.9 1.0
SG C:CYS259 2.4 17.2 1.0
SG C:CYS256 2.4 18.5 1.0
CB C:CYS280 3.2 17.9 1.0
CB C:CYS259 3.2 14.9 1.0
CB C:CYS256 3.3 17.3 1.0
CB C:CYS283 3.5 13.6 1.0
N C:CYS259 3.7 16.1 1.0
N C:CYS283 3.9 15.4 1.0
CA C:CYS259 4.0 15.6 1.0
CA C:CYS283 4.2 14.3 1.0
CB C:VAL282 4.5 17.5 1.0
CB C:VAL258 4.6 14.6 1.0
CA C:CYS280 4.6 17.2 1.0
N C:THR284 4.7 14.2 1.0
NH2 C:ARG261 4.7 25.2 1.0
N C:GLY285 4.7 13.9 1.0
C C:VAL258 4.7 15.9 1.0
CA C:CYS256 4.7 16.9 1.0
C C:CYS259 4.8 15.3 1.0
C C:CYS283 4.8 14.3 1.0
C C:VAL282 4.9 16.5 1.0

Zinc binding site 4 out of 6 in 3gls

Go back to Zinc Binding Sites List in 3gls
Zinc binding site 4 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn6

b:36.7
occ:1.00
 SG D:CYS283 2.1 31.8 1.0
SG D:CYS256 2.4 28.0 1.0
SG D:CYS259 2.4 28.1 1.0
SG D:CYS280 2.5 33.7 1.0
CB D:CYS256 3.1 23.9 1.0
CB D:CYS280 3.1 34.1 1.0
CB D:CYS283 3.3 29.2 1.0
CB D:CYS259 3.4 27.8 1.0
N D:CYS259 3.7 26.9 1.0
N D:CYS283 3.8 31.7 1.0
CA D:CYS283 4.1 30.2 1.0
CA D:CYS259 4.1 27.5 1.0
CD D:ARG261 4.5 34.7 1.0
CA D:CYS256 4.6 23.6 1.0
C D:CYS283 4.6 28.7 1.0
N D:THR284 4.6 28.1 1.0
CA D:CYS280 4.6 33.7 1.0
N D:GLY285 4.7 25.1 1.0
C D:VAL258 4.8 26.1 1.0
CB D:VAL282 4.8 34.4 1.0
CB D:VAL258 4.8 24.8 1.0
C D:CYS259 4.9 27.4 1.0
N D:GLN260 4.9 27.4 1.0
C D:VAL282 4.9 33.4 1.0
N D:VAL258 5.0 24.1 1.0

Zinc binding site 5 out of 6 in 3gls

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Zinc binding site 5 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:33.0
occ:1.00
 SG E:CYS256 2.2 24.7 1.0
SG E:CYS283 2.3 30.9 1.0
SG E:CYS259 2.3 31.4 1.0
SG E:CYS280 2.5 25.1 1.0
CB E:CYS259 3.0 28.4 1.0
CB E:CYS256 3.1 24.8 1.0
CB E:CYS280 3.2 22.2 1.0
CB E:CYS283 3.4 26.9 1.0
N E:CYS259 3.5 29.0 1.0
CA E:CYS259 3.8 28.9 1.0
N E:CYS283 3.9 27.6 1.0
CA E:CYS283 4.2 26.9 1.0
C E:CYS259 4.5 29.3 1.0
N E:GLY285 4.5 23.1 1.0
CA E:CYS256 4.6 24.5 1.0
C E:VAL258 4.6 29.5 1.0
CB E:VAL258 4.7 30.1 1.0
N E:THR284 4.7 24.4 1.0
N E:GLN260 4.7 28.4 1.0
CA E:CYS280 4.7 23.3 1.0
C E:CYS283 4.8 25.7 1.0
CB E:VAL282 4.8 28.0 1.0
CA E:GLY285 4.9 21.8 1.0

Zinc binding site 6 out of 6 in 3gls

Go back to Zinc Binding Sites List in 3gls
Zinc binding site 6 out of 6 in the Crystal Structure of Human SIRT3


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn3

b:21.0
occ:1.00
 SG F:CYS283 2.0 21.3 1.0
SG F:CYS259 2.2 18.4 1.0
SG F:CYS256 2.3 20.1 1.0
SG F:CYS280 2.3 18.3 1.0
CB F:CYS259 3.2 17.5 1.0
CB F:CYS280 3.2 21.0 1.0
CB F:CYS256 3.4 17.6 1.0
CB F:CYS283 3.4 20.4 1.0
N F:CYS283 3.7 20.7 1.0
N F:CYS259 3.8 18.5 1.0
CA F:CYS259 4.0 18.6 1.0
CA F:CYS283 4.1 20.1 1.0
CB F:VAL282 4.3 22.3 1.0
N F:THR284 4.6 17.1 1.0
CA F:CYS280 4.6 21.2 1.0
C F:CYS283 4.7 18.9 1.0
CB F:VAL258 4.7 17.6 1.0
C F:VAL282 4.7 21.8 1.0
C F:CYS259 4.7 18.8 1.0
CA F:CYS256 4.8 16.8 1.0
N F:GLN260 4.8 18.9 1.0
CG1 F:VAL282 4.8 21.4 1.0
C F:VAL258 4.8 17.8 1.0
N F:GLY285 4.9 13.1 1.0
CA F:VAL282 4.9 21.4 1.0
N F:VAL282 5.0 21.8 1.0
C F:CYS280 5.0 21.3 1.0

Reference:

L.Jin, W.Wei, Y.Jiang, H.Peng, J.Cai, C.Mao, H.Dai, W.Choy, J.E.Bemis, M.R.Jirousek, J.C.Milne, C.H.Westphal, R.B.Perni. Crystal Structures of Human SIRT3 Displaying Substrate-Induced Conformational Changes. J.Biol.Chem. V. 284 24394 2009.
ISSN: ISSN 0021-9258
PubMed: 19535340
DOI: 10.1074/JBC.M109.014928
Page generated: Thu Oct 24 13:46:50 2024

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