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Zinc in PDB 5bwo: Crystal Structure of Human SIRT3 in Complex with A Palmitoyl H3K9 Peptide

Protein crystallography data

The structure of Crystal Structure of Human SIRT3 in Complex with A Palmitoyl H3K9 Peptide, PDB code: 5bwo was solved by W.Gai, H.Jiang, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.15 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.445, 54.636, 113.203, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SIRT3 in Complex with A Palmitoyl H3K9 Peptide (pdb code 5bwo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human SIRT3 in Complex with A Palmitoyl H3K9 Peptide, PDB code: 5bwo:

Zinc binding site 1 out of 1 in 5bwo

Go back to Zinc Binding Sites List in 5bwo
Zinc binding site 1 out of 1 in the Crystal Structure of Human SIRT3 in Complex with A Palmitoyl H3K9 Peptide


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 Palmitoyl H3K9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.1
occ:1.00
SG A:CYS259 2.3 23.5 1.0
SG A:CYS280 2.3 17.5 1.0
SG A:CYS256 2.4 18.9 1.0
SG A:CYS283 2.4 25.9 1.0
HB3 A:CYS280 3.0 29.0 1.0
H A:CYS283 3.0 28.4 1.0
CB A:CYS280 3.1 24.1 1.0
HB2 A:CYS280 3.1 29.0 1.0
HB3 A:CYS256 3.1 29.0 1.0
H A:CYS259 3.2 30.1 1.0
CB A:CYS256 3.2 24.2 1.0
HB2 A:CYS256 3.2 29.0 1.0
HB3 A:CYS259 3.4 29.2 1.0
CB A:CYS259 3.5 24.3 1.0
HB3 A:CYS283 3.6 25.9 1.0
CB A:CYS283 3.6 21.6 1.0
HB A:VAL282 3.6 30.6 1.0
N A:CYS283 3.7 23.6 1.0
H A:GLY285 3.8 28.4 1.0
N A:CYS259 3.9 25.1 1.0
HB A:VAL258 4.0 28.5 1.0
HB3 A:ARG261 4.0 32.9 1.0
HH21 A:ARG261 4.1 38.8 1.0
CA A:CYS283 4.2 24.1 1.0
H A:ARG261 4.2 31.0 1.0
CA A:CYS259 4.2 27.5 1.0
HB2 A:CYS259 4.3 29.2 1.0
H A:VAL282 4.3 29.5 1.0
HA3 A:GLY285 4.4 30.8 1.0
HB2 A:CYS283 4.4 25.9 1.0
HE2 A:PHE263 4.5 33.1 1.0
H A:VAL258 4.5 28.6 1.0
CB A:VAL282 4.5 25.5 1.0
H A:THR284 4.5 28.7 1.0
N A:GLY285 4.5 23.6 1.0
CA A:CYS280 4.5 24.6 1.0
CA A:CYS256 4.7 23.1 1.0
C A:CYS283 4.7 23.4 1.0
H A:GLN260 4.7 33.8 1.0
N A:THR284 4.8 23.9 1.0
HH22 A:ARG261 4.8 38.8 1.0
HB2 A:ARG261 4.8 32.9 1.0
HG12 A:VAL282 4.8 32.1 1.0
C A:VAL282 4.8 25.4 1.0
NH2 A:ARG261 4.8 32.4 1.0
C A:CYS259 4.8 27.2 1.0
CB A:ARG261 4.8 27.4 1.0
HZ A:PHE263 4.9 32.1 1.0
CB A:VAL258 4.9 23.7 1.0
HA A:CYS280 4.9 29.5 1.0
CA A:GLY285 4.9 25.7 1.0
HA A:CYS256 5.0 27.7 1.0
N A:VAL282 5.0 24.6 1.0
N A:GLN260 5.0 28.1 1.0

Reference:

W.Gai, H.Li, H.Jiang, Y.Long, D.Liu. Crystal Structures of SIRT3 Reveal That the Alpha 2-Alpha 3 Loop and Alpha 3-Helix Affect the Interaction with Long-Chain Acyl Lysine. Febs Lett. V. 590 3019 2016.
ISSN: ISSN 0014-5793
PubMed: 27501476
DOI: 10.1002/1873-3468.12345
Page generated: Wed Dec 16 06:05:25 2020

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