Zinc in PDB 5zgc: Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide

The structure of Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide, PDB code: 5zgc was solved by H.Li, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.16 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.512, 138.512, 242.876, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 28

The binding sites of Zinc atom in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide (pdb code 5zgc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide, PDB code: 5zgc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of SIRT3 in Complex with H4K16BHB 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 SIRT3 in Complex with H4K16BHB Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:68.2 occ:1.00 SG A:CYS283 2.2 62.4 1.0 SG A:CYS280 2.3 61.5 1.0 SG A:CYS259 2.3 60.9 1.0 SG A:CYS256 2.5 63.5 1.0 CB A:CYS259 3.0 53.5 1.0 CB A:CYS280 3.0 58.2 1.0 CB A:CYS256 3.2 51.7 1.0 CB A:CYS283 3.4 64.8 1.0 N A:CYS259 3.8 59.8 1.0 N A:CYS283 3.9 55.9 1.0 CA A:CYS259 4.0 58.9 1.0 CG2 A:VAL258 4.1 62.4 1.0 CA A:CYS283 4.2 59.7 1.0 CA A:CYS280 4.5 63.9 1.0 CB A:VAL282 4.6 64.1 1.0 C A:CYS259 4.6 58.7 1.0 N A:GLY285 4.6 54.6 1.0 CA A:CYS256 4.7 52.5 1.0 C A:CYS283 4.8 57.9 1.0 N A:GLN260 4.8 61.5 1.0 CG1 A:VAL282 4.9 58.1 1.0 CB A:ARG261 4.9 53.8 1.0 C A:VAL282 4.9 58.5 1.0 N A:THR284 4.9 60.7 1.0 CA A:GLY285 5.0 57.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide


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 SIRT3 in Complex with H4K16BHB Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:92.9 occ:1.00 SG B:CYS259 2.1 87.7 1.0 SG B:CYS280 2.2 97.8 1.0 SG B:CYS283 2.4 98.8 1.0 SG B:CYS256 2.6 93.3 1.0 CB B:CYS280 2.8 96.5 1.0 CB B:CYS256 3.3 86.1 1.0 CB B:CYS259 3.4 86.2 1.0 CB B:CYS283 3.4 0.3 1.0 N B:CYS283 3.5 96.7 1.0 CA B:CYS283 3.9 0.1 1.0 CA B:CYS280 4.3 0.1 1.0 C B:CYS283 4.3 0.0 1.0 N B:CYS259 4.3 88.4 1.0 CA B:CYS259 4.4 88.3 1.0 CB B:VAL282 4.5 98.6 1.0 N B:THR284 4.5 99.9 1.0 N B:GLY285 4.5 0.7 1.0 CD B:ARG261 4.5 0.2 1.0 C B:VAL282 4.6 95.7 1.0 CG1 B:VAL282 4.6 91.2 1.0 CG1 B:VAL258 4.7 0.7 1.0 CA B:CYS256 4.7 81.6 1.0 CG B:ARG261 4.8 98.0 1.0 CA B:VAL282 4.9 95.8 1.0 N B:VAL282 4.9 0.1 1.0 CA B:GLY285 5.0 98.8 1.0 O B:GLY285 5.0 90.5 1.0 O B:CYS283 5.0 99.9 1.0 C B:CYS280 5.0 98.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide


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 SIRT3 in Complex with H4K16BHB Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:52.6 occ:1.00 SG C:CYS259 2.1 46.0 1.0 SG C:CYS280 2.2 39.1 1.0 SG C:CYS283 2.3 62.8 1.0 SG C:CYS256 2.6 55.0 1.0 CB C:CYS280 2.9 45.2 1.0 CB C:CYS259 3.1 46.4 1.0 CB C:CYS283 3.2 48.1 1.0 CB C:CYS256 3.5 53.4 1.0 N C:CYS283 3.8 37.8 1.0 N C:CYS259 3.8 56.0 1.0 CA C:CYS283 4.0 44.4 1.0 CA C:CYS259 4.0 46.5 1.0 CA C:CYS280 4.4 45.5 1.0 C C:CYS283 4.5 53.8 1.0 N C:THR284 4.5 58.2 1.0 N C:GLY285 4.6 52.0 1.0 C C:CYS259 4.7 55.7 1.0 CB C:VAL282 4.9 50.4 1.0 CA C:CYS256 4.9 55.8 1.0 C C:VAL258 4.9 58.6 1.0 C C:CYS280 5.0 49.1 1.0 C C:VAL282 5.0 46.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide


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 SIRT3 in Complex with H4K16BHB Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:57.2 occ:1.00 SG D:CYS259 2.2 41.0 1.0 SG D:CYS256 2.4 74.0 1.0 SG D:CYS280 2.4 48.5 1.0 SG D:CYS283 2.6 49.7 1.0 CB D:CYS259 3.0 59.1 1.0 CB D:CYS280 3.1 52.5 1.0 CB D:CYS256 3.1 61.7 1.0 CB D:CYS283 3.5 48.8 1.0 N D:CYS259 3.7 61.2 1.0 CA D:CYS259 3.9 61.6 1.0 N D:CYS283 4.1 55.8 1.0 CA D:CYS283 4.3 48.4 1.0 C D:CYS259 4.5 60.8 1.0 CA D:CYS280 4.6 56.2 1.0 CA D:CYS256 4.6 68.6 1.0 N D:GLN260 4.7 66.4 1.0 CB D:VAL282 4.7 45.8 1.0 N D:THR284 4.9 54.8 1.0 C D:CYS283 4.9 50.6 1.0 N D:GLY285 4.9 56.2 1.0 C D:VAL258 4.9 59.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide


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 SIRT3 in Complex with H4K16BHB Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:0.1 occ:1.00 SG E:CYS259 2.1 0.3 1.0 SG E:CYS283 2.3 0.9 1.0 SG E:CYS256 2.4 0.5 1.0 SG E:CYS280 2.4 0.4 1.0 CB E:CYS259 3.0 0.1 1.0 CB E:CYS283 3.5 0.6 1.0 CB E:CYS256 3.5 0.2 1.0 CB E:CYS280 3.5 0.5 1.0 N E:CYS259 3.9 0.2 1.0 CA E:CYS259 4.0 0.7 1.0 CG1 E:VAL282 4.0 0.4 1.0 CG1 E:VAL258 4.0 0.8 1.0 N E:CYS283 4.2 0.9 1.0 CA E:CYS283 4.4 0.1 1.0 C E:CYS259 4.6 0.6 1.0 C E:VAL282 4.7 0.6 1.0 N E:GLN260 4.7 0.4 1.0 N E:GLY285 4.9 0.7 1.0 CA E:CYS256 4.9 0.3 1.0 CA E:CYS280 5.0 0.6 1.0

H.Li, X.Zhang. Crystal Structure of SIRT3 in Complex with H4K16BHB Peptide To Be Published.