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Zinc in PDB 4bn5: Structure of Human SIRT3 in Complex with SRT1720 Inhibitor

Protein crystallography data

The structure of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor, PDB code: 4bn5 was solved by G.T.T.Nguyen, S.Schaefer, M.Gertz, M.Weyand, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 3.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 227.820, 246.060, 127.340, 90.00, 123.88, 90.00
R / Rfree (%) 20.791 / 26.534

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor (pdb code 4bn5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor, PDB code: 4bn5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4bn5

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Zinc binding site 1 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1397

b:86.2
occ:1.00
 SG A:CYS259 1.9 0.2 1.0
SG A:CYS280 2.3 0.2 1.0
CB A:CYS256 2.3 92.3 1.0
SG A:CYS256 2.4 96.7 1.0
CB A:CYS280 2.4 0.1 1.0
SG A:CYS283 2.5 0.6 1.0
CB A:CYS259 3.6 0.4 1.0
C A:CYS259 3.7 99.4 1.0
O A:CYS259 3.7 0.3 1.0
CA A:CYS256 3.8 87.6 1.0
CA A:CYS280 3.9 1.0 1.0
N A:GLN260 4.0 94.8 1.0
CA A:CYS259 4.0 0.5 1.0
CB A:CYS283 4.1 0.9 1.0
N A:ARG261 4.1 92.3 1.0
N A:CYS259 4.3 99.4 1.0
CE1 A:PHE263 4.3 93.4 1.0
N A:CYS256 4.3 85.0 1.0
CB A:ARG261 4.4 96.5 1.0
NE A:ARG261 4.4 0.5 1.0
CZ A:PHE263 4.5 97.3 1.0
N A:CYS283 4.5 0.5 1.0
C A:CYS256 4.7 86.4 1.0
N A:CYS280 4.7 0.2 1.0
CD A:ARG261 4.8 0.8 1.0
CB A:VAL282 4.9 0.7 1.0
C A:CYS280 4.9 0.5 1.0
CA A:ARG261 4.9 92.5 1.0
O A:CYS256 4.9 86.0 1.0
CA A:GLN260 4.9 91.8 1.0
CA A:CYS283 5.0 0.5 1.0

Zinc binding site 2 out of 12 in 4bn5

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Zinc binding site 2 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1397

b:86.2
occ:1.00
 CB B:CYS283 2.0 0.9 1.0
CB B:CYS259 2.0 0.5 1.0
SG B:CYS283 2.1 99.1 1.0
SG B:CYS259 2.2 98.1 1.0
SG B:CYS280 2.5 1.0 1.0
SG B:CYS256 2.5 94.3 1.0
CA B:CYS283 2.8 0.6 1.0
N B:CYS259 2.8 98.7 1.0
CA B:CYS259 2.8 0.2 1.0
N B:CYS283 3.0 0.1 1.0
C B:VAL282 3.8 0.9 1.0
C B:VAL258 4.1 97.3 1.0
CB B:CYS280 4.1 99.4 1.0
CB B:CYS256 4.1 89.9 1.0
C B:CYS283 4.2 0.2 1.0
C B:CYS259 4.2 97.0 1.0
O B:VAL282 4.2 0.2 1.0
CG2 B:VAL258 4.3 98.1 1.0
CB B:VAL258 4.6 99.1 1.0
CA B:VAL258 4.7 95.4 1.0
N B:GLN260 4.8 92.7 1.0
CA B:VAL282 4.8 0.7 1.0
N B:THR284 4.8 0.2 1.0
O B:CYS283 4.9 0.9 1.0
N B:VAL258 4.9 91.2 1.0
N B:GLY285 5.0 0.1 1.0
O B:CYS259 5.0 98.7 1.0

Zinc binding site 3 out of 12 in 4bn5

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Zinc binding site 3 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1398

b:86.2
occ:1.00
 CB C:CYS259 2.1 0.3 1.0
CB C:CYS283 2.1 0.2 1.0
SG C:CYS259 2.1 0.8 1.0
SG C:CYS283 2.2 0.7 1.0
SG C:CYS280 2.5 0.3 1.0
SG C:CYS256 2.5 0.8 1.0
N C:CYS259 2.7 0.0 1.0
CA C:CYS259 2.7 0.0 1.0
CA C:CYS283 2.9 0.7 1.0
N C:CYS283 3.0 0.2 1.0
C C:VAL258 3.9 0.7 1.0
C C:VAL282 4.1 0.0 1.0
CB C:CYS280 4.1 0.3 1.0
CB C:CYS256 4.1 98.1 1.0
CB C:VAL258 4.1 0.7 1.0
C C:CYS259 4.2 0.2 1.0
CG1 C:VAL258 4.2 0.9 1.0
C C:CYS283 4.2 0.1 1.0
CB C:VAL282 4.4 0.1 1.0
CA C:VAL258 4.6 0.2 1.0
N C:GLN260 4.7 99.0 1.0
CG1 C:VAL282 4.7 0.7 1.0
CA C:VAL282 4.8 0.4 1.0
N C:THR284 4.8 0.1 1.0
O C:VAL258 4.9 0.2 1.0
O C:VAL282 4.9 0.4 1.0
N C:VAL258 4.9 0.6 1.0

Zinc binding site 4 out of 12 in 4bn5

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Zinc binding site 4 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1397

b:86.2
occ:1.00
 CB D:CYS259 2.0 0.9 1.0
SG D:CYS259 2.1 0.2 1.0
CB D:CYS283 2.1 0.2 1.0
SG D:CYS283 2.2 0.0 1.0
SG D:CYS280 2.5 0.7 1.0
SG D:CYS256 2.5 0.8 1.0
CA D:CYS259 2.6 0.5 1.0
N D:CYS259 2.6 0.4 1.0
CA D:CYS283 3.1 0.3 1.0
N D:CYS283 3.3 0.3 1.0
C D:VAL258 3.9 0.5 1.0
C D:CYS259 4.1 0.8 1.0
CB D:CYS280 4.1 0.4 1.0
CB D:CYS256 4.1 0.8 1.0
C D:VAL282 4.2 0.4 1.0
C D:CYS283 4.4 0.0 1.0
CB D:VAL258 4.5 0.2 1.0
CB D:VAL282 4.6 0.0 1.0
CA D:VAL258 4.6 0.2 1.0
N D:GLN260 4.7 0.2 1.0
O D:VAL258 4.7 0.1 1.0
ND1 E:HIS187 4.8 0.8 1.0
CG1 D:VAL258 4.8 0.8 1.0
N D:VAL258 4.9 0.5 1.0
O D:CYS259 4.9 0.8 1.0
O D:VAL282 4.9 0.4 1.0
CA D:VAL282 5.0 0.3 1.0
N D:THR284 5.0 0.9 1.0

Zinc binding site 5 out of 12 in 4bn5

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Zinc binding site 5 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1397

b:86.2
occ:1.00
 SG E:CYS256 2.3 95.3 1.0
SG E:CYS259 2.3 0.2 1.0
SG E:CYS283 2.4 0.9 1.0
SG E:CYS280 2.4 0.7 1.0
CB E:CYS259 3.4 0.1 1.0
CB E:CYS280 3.4 99.4 1.0
CB E:CYS256 3.4 91.8 1.0
CB E:CYS283 3.6 0.2 1.0
N E:CYS283 3.8 0.3 1.0
N E:CYS259 3.9 98.6 1.0
CA E:CYS259 4.2 0.4 1.0
CA E:CYS283 4.2 0.0 1.0
CB E:VAL282 4.5 0.7 1.0
C E:CYS283 4.6 0.7 1.0
N E:GLY285 4.6 0.3 1.0
N E:GLN260 4.7 94.7 1.0
N E:THR284 4.8 0.7 1.0
CA E:CYS280 4.8 0.5 1.0
CB E:VAL258 4.8 0.4 1.0
C E:VAL282 4.8 0.6 1.0
CA E:CYS256 4.9 88.5 1.0
C E:CYS259 4.9 97.9 1.0
N E:VAL282 4.9 0.1 1.0
CA E:GLY285 5.0 0.4 1.0
O E:GLY285 5.0 96.4 1.0

Zinc binding site 6 out of 12 in 4bn5

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Zinc binding site 6 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1397

b:86.2
occ:1.00
 CB F:CYS259 2.1 0.8 1.0
CB F:CYS283 2.1 0.1 1.0
SG F:CYS283 2.2 0.6 1.0
SG F:CYS259 2.2 0.1 1.0
SG F:CYS280 2.5 0.5 1.0
SG F:CYS256 2.5 0.5 1.0
CA F:CYS283 2.8 0.8 1.0
CA F:CYS259 2.8 0.3 1.0
N F:CYS259 2.9 0.4 1.0
N F:CYS283 3.0 0.4 1.0
C F:VAL282 4.0 0.5 1.0
C F:VAL258 4.1 0.5 1.0
CB F:CYS280 4.1 1.0 1.0
CB F:CYS256 4.2 0.6 1.0
C F:CYS259 4.2 0.7 1.0
C F:CYS283 4.2 0.3 1.0
CB F:VAL282 4.3 0.6 1.0
CG1 F:VAL258 4.5 0.4 1.0
O F:VAL282 4.6 0.5 1.0
CA F:VAL282 4.7 0.9 1.0
N F:GLN260 4.8 0.2 1.0
N F:THR284 4.9 0.7 1.0
CA F:VAL258 4.9 0.4 1.0
CG1 F:VAL282 4.9 0.3 1.0
O F:CYS259 4.9 0.1 1.0
O F:VAL258 4.9 0.2 1.0
O F:CYS283 5.0 0.4 1.0

Zinc binding site 7 out of 12 in 4bn5

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Zinc binding site 7 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1397

b:86.2
occ:1.00
 CB G:CYS283 2.0 0.7 1.0
CB G:CYS259 2.1 0.6 1.0
SG G:CYS283 2.2 0.4 1.0
SG G:CYS259 2.2 99.8 1.0
SG G:CYS280 2.5 0.5 1.0
SG G:CYS256 2.5 98.0 1.0
CA G:CYS259 2.7 0.8 1.0
N G:CYS259 2.7 0.9 1.0
CA G:CYS283 2.8 0.8 1.0
N G:CYS283 2.9 0.2 1.0
C G:VAL258 4.0 0.3 1.0
C G:VAL282 4.1 0.8 1.0
C G:CYS259 4.1 0.8 1.0
CB G:CYS256 4.1 94.2 1.0
CB G:CYS280 4.1 0.7 1.0
C G:CYS283 4.2 1.0 1.0
CB G:VAL282 4.5 0.6 1.0
N G:GLN260 4.6 97.2 1.0
CG2 G:VAL258 4.6 0.1 1.0
N G:THR284 4.7 0.7 1.0
CB G:VAL258 4.7 0.1 1.0
CA G:VAL258 4.8 0.1 1.0
CA G:VAL282 4.8 0.3 1.0
O G:VAL282 4.9 1.0 1.0
O G:VAL258 4.9 1.0 1.0

Zinc binding site 8 out of 12 in 4bn5

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Zinc binding site 8 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1397

b:86.2
occ:1.00
 CB H:CYS283 2.0 0.7 1.0
CB H:CYS259 2.1 0.8 1.0
SG H:CYS283 2.2 0.3 1.0
SG H:CYS259 2.2 0.9 1.0
SG H:CYS280 2.5 0.1 1.0
SG H:CYS256 2.5 0.4 1.0
CA H:CYS283 2.7 0.9 1.0
N H:CYS259 2.8 0.9 1.0
CA H:CYS259 2.9 0.1 1.0
N H:CYS283 3.0 0.1 1.0
C H:VAL282 4.1 0.6 1.0
C H:VAL258 4.1 0.5 1.0
CB H:CYS256 4.1 0.6 1.0
C H:CYS283 4.1 0.3 1.0
CB H:CYS280 4.2 0.2 1.0
C H:CYS259 4.3 0.2 1.0
CG1 H:VAL258 4.4 0.2 1.0
N H:THR284 4.7 0.4 1.0
CB H:VAL282 4.7 0.1 1.0
O H:VAL282 4.7 0.9 1.0
N H:GLN260 4.8 0.1 1.0
CA H:VAL258 4.9 0.6 1.0
CA H:VAL282 4.9 0.8 1.0
N H:VAL258 4.9 0.9 1.0
O H:CYS283 5.0 0.2 1.0
O H:VAL258 5.0 0.2 1.0

Zinc binding site 9 out of 12 in 4bn5

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Zinc binding site 9 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1397

b:86.2
occ:1.00
 CB I:CYS283 2.0 0.8 1.0
SG I:CYS283 2.2 0.4 1.0
CB I:CYS259 2.2 0.3 1.0
SG I:CYS259 2.2 0.6 1.0
SG I:CYS280 2.5 0.0 1.0
SG I:CYS256 2.5 0.3 1.0
CA I:CYS283 2.8 0.2 1.0
N I:CYS259 2.9 0.9 1.0
CA I:CYS259 3.0 0.8 1.0
N I:CYS283 3.0 0.4 1.0
C I:VAL282 3.9 0.9 1.0
CB I:CYS256 4.1 0.5 1.0
CB I:CYS280 4.1 1.0 1.0
C I:VAL258 4.1 0.4 1.0
C I:CYS283 4.2 0.9 1.0
C I:CYS259 4.4 0.6 1.0
CB I:VAL282 4.6 0.2 1.0
O I:VAL282 4.6 0.1 1.0
CA I:VAL282 4.7 0.1 1.0
CB I:VAL258 4.8 0.1 1.0
CA I:VAL258 4.8 0.1 1.0
N I:THR284 4.8 0.3 1.0
N I:VAL258 4.8 0.3 1.0
CG2 I:VAL258 4.9 0.3 1.0
N I:GLN260 4.9 0.6 1.0
O I:CYS283 5.0 0.9 1.0

Zinc binding site 10 out of 12 in 4bn5

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Zinc binding site 10 out of 12 in the Structure of Human SIRT3 in Complex with SRT1720 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human SIRT3 in Complex with SRT1720 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1397

b:86.2
occ:1.00
 SG J:CYS259 2.4 1.0 1.0
SG J:CYS283 2.4 0.8 1.0
SG J:CYS280 2.4 0.9 1.0
SG J:CYS256 2.4 0.4 1.0
CB J:CYS259 3.2 0.5 1.0
CB J:CYS280 3.3 0.1 1.0
CB J:CYS256 3.5 0.6 1.0
CB J:CYS283 3.6 0.0 1.0
N J:CYS283 3.7 0.6 1.0
CB J:VAL282 4.0 0.1 1.0
N J:CYS259 4.1 0.7 1.0
CA J:CYS283 4.1 1.0 1.0
CA J:CYS259 4.2 0.3 1.0
CG1 J:VAL282 4.4 0.8 1.0
CG1 J:VAL258 4.6 0.7 1.0
C J:VAL282 4.7 0.3 1.0
C J:CYS283 4.7 0.8 1.0
CA J:CYS280 4.7 0.1 1.0
CA J:VAL282 4.8 0.8 1.0
N J:GLY285 4.8 0.8 1.0
N J:VAL282 4.9 0.8 1.0
C J:CYS259 4.9 1.0 1.0
CA J:CYS256 4.9 0.4 1.0
CG2 J:VAL282 4.9 0.6 1.0

Reference:

G.T.T.Nguyen, S.Schaefer, M.Gertz, M.Weyand, C.Steegborn. Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and SRT1720: Binding Details and Inhibition Mechanism Acta Crystallogr.,Sect.D V. 69 1423 2013.
ISSN: ISSN 0907-4449
PubMed: 23897466
DOI: 10.1107/S0907444913015448
Page generated: Wed Dec 16 05:05:39 2020

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