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Zinc in PDB 4bvh: Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose

Protein crystallography data

The structure of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose, PDB code: 4bvh was solved by 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) 34.44 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.710, 66.530, 201.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.159 / 22.581

Other elements in 4bvh:

The structure of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose (pdb code 4bvh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose, PDB code: 4bvh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4bvh

Go back to Zinc Binding Sites List in 4bvh
Zinc binding site 1 out of 3 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


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 the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1395

b:42.7
occ:1.00
SG A:CYS280 2.2 43.4 1.0
SG A:CYS259 2.3 39.1 1.0
SG A:CYS283 2.5 44.2 1.0
SG A:CYS256 2.5 36.5 1.0
CB A:CYS280 2.8 40.7 1.0
CB A:CYS256 3.2 43.1 1.0
CB A:CYS259 3.5 43.5 1.0
CB A:CYS283 3.5 51.1 1.0
N A:CYS283 3.7 52.1 1.0
N A:CYS259 3.9 46.9 1.0
CA A:CYS283 4.1 50.4 1.0
CA A:CYS259 4.2 45.7 1.0
CA A:CYS280 4.3 42.2 1.0
N A:GLY285 4.6 38.5 1.0
CA A:CYS256 4.7 39.3 1.0
C A:CYS283 4.7 50.9 1.0
CB A:VAL282 4.8 54.2 1.0
C A:VAL282 4.8 59.7 1.0
N A:THR284 4.9 54.3 1.0
CB A:VAL258 4.9 49.9 1.0
C A:CYS259 5.0 52.4 1.0

Zinc binding site 2 out of 3 in 4bvh

Go back to Zinc Binding Sites List in 4bvh
Zinc binding site 2 out of 3 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


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 the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1396

b:87.2
occ:1.00
SG B:CYS256 2.3 59.6 1.0
SG B:CYS280 2.3 34.0 1.0
SG B:CYS283 2.4 74.2 1.0
N B:CYS259 2.7 46.7 1.0
SG B:CYS259 2.9 59.7 1.0
CB B:CYS280 3.1 56.0 1.0
CB B:VAL258 3.2 50.8 1.0
CB B:CYS259 3.3 53.2 1.0
CB B:CYS256 3.4 58.8 1.0
CA B:CYS259 3.6 52.6 1.0
C B:VAL258 3.7 47.0 1.0
CG2 B:VAL258 3.7 58.8 1.0
CA B:VAL258 3.7 48.8 1.0
CB B:CYS283 3.8 56.7 1.0
N B:VAL258 4.0 42.6 1.0
N B:GLN260 4.3 57.1 1.0
CG1 B:VAL258 4.3 48.8 1.0
N B:GLY285 4.3 51.5 1.0
C B:CYS259 4.5 62.1 1.0
CA B:CYS280 4.6 59.3 1.0
CA B:GLY285 4.7 50.6 1.0
CA B:CYS283 4.7 60.7 1.0
N B:CYS283 4.7 61.4 1.0
CA B:CYS256 4.7 47.0 1.0
O B:VAL258 4.8 51.0 1.0
C B:CYS283 4.8 64.3 1.0
C B:CYS256 5.0 41.1 1.0

Zinc binding site 3 out of 3 in 4bvh

Go back to Zinc Binding Sites List in 4bvh
Zinc binding site 3 out of 3 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


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 the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1400

b:27.5
occ:1.00
SG C:CYS280 2.2 25.7 1.0
SG C:CYS259 2.2 28.9 1.0
SG C:CYS283 2.4 31.9 1.0
SG C:CYS256 2.4 25.3 1.0
CB C:CYS280 3.0 27.1 1.0
CB C:CYS256 3.1 23.5 1.0
CB C:CYS259 3.3 29.5 1.0
CB C:CYS283 3.5 28.2 1.0
N C:CYS259 3.7 30.4 1.0
N C:CYS283 3.8 29.5 1.0
CA C:CYS259 4.1 31.2 1.0
CA C:CYS283 4.2 30.9 1.0
CA C:CYS280 4.5 28.5 1.0
N C:GLY285 4.5 29.6 1.0
CA C:CYS256 4.6 21.1 1.0
C C:CYS283 4.7 31.2 1.0
C C:CYS259 4.8 33.6 1.0
N C:THR284 4.8 30.6 1.0
CB C:VAL282 4.8 33.8 1.0
CB C:VAL258 4.8 31.9 1.0
CA C:GLY285 4.9 29.3 1.0
C C:VAL282 4.9 35.5 1.0
C C:VAL258 4.9 35.2 1.0
CB C:ARG261 4.9 24.7 1.0
N C:GLN260 4.9 31.3 1.0
NH1 C:ARG261 5.0 23.8 0.5

Reference:

M.Gertz, F.Fischer, G.T.T.Nguyen, M.Lakshminarasimhan, M.Schutkowski, M.Weyand, C.Steegborn. Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Proc.Natl.Acad.Sci.Usa V. 110 E2772 2013.
ISSN: ISSN 0027-8424
PubMed: 23840057
DOI: 10.1073/PNAS.1303628110
Page generated: Wed Dec 16 05:06:24 2020

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