Zinc in PDB 4ig9: Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A)

The structure of Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A), PDB code: 4ig9 was solved by A.M.Davenport, F.M.Huber, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.64
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.781, 115.781, 350.511, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.3

The binding sites of Zinc atom in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A) (pdb code 4ig9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A), PDB code: 4ig9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:71.8 occ:1.00 SG A:CYS398 2.3 76.8 1.0 SG A:CYS395 2.4 63.5 1.0 SG A:CYS374 2.4 64.8 1.0 SG A:CYS371 2.5 69.3 1.0 CB A:CYS371 3.3 55.8 1.0 CB A:CYS398 3.3 63.9 1.0 CB A:CYS374 3.4 59.5 1.0 CB A:CYS395 3.4 63.2 1.0 N A:CYS398 3.7 69.6 1.0 N A:CYS374 3.8 58.0 1.0 CA A:CYS398 4.1 61.9 1.0 CA A:CYS374 4.1 59.0 1.0 CB A:ARG397 4.5 74.2 1.0 CB A:TYR376 4.7 51.7 1.0 C A:CYS374 4.7 66.6 1.0 C A:ARG397 4.8 69.8 1.0 CA A:CYS371 4.8 49.8 1.0 CA A:CYS395 4.8 60.9 1.0 N A:LYS375 4.9 69.0 1.0

Zinc binding site 2 out of 4 in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:0.5 occ:1.00 SG C:CYS398 2.4 97.1 1.0 SG C:CYS374 2.5 78.7 1.0 SG C:CYS371 2.5 0.0 1.0 CB C:CYS374 2.9 55.3 1.0 N C:CYS374 3.0 82.6 1.0 SG C:CYS395 3.0 73.7 1.0 CB C:CYS371 3.2 85.4 1.0 CA C:CYS374 3.4 60.7 1.0 CB C:CYS398 3.5 0.7 1.0 CB C:CYS395 3.7 85.5 1.0 C C:ILE373 4.1 84.2 1.0 CB C:ILE373 4.1 0.0 1.0 C C:CYS374 4.2 94.1 1.0 N C:CYS398 4.2 79.0 1.0 N C:LYS375 4.4 90.1 1.0 CA C:ILE373 4.4 94.0 1.0 N C:ILE373 4.4 0.3 1.0 CA C:CYS398 4.4 0.7 1.0 CG2 C:ILE373 4.6 0.2 1.0 CA C:CYS371 4.7 65.7 1.0

Zinc binding site 3 out of 4 in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:69.6 occ:1.00 SG E:CYS374 2.3 51.9 1.0 SG E:CYS398 2.3 59.7 1.0 SG E:CYS395 2.5 56.0 1.0 SG E:CYS371 2.5 70.2 1.0 CB E:CYS371 3.2 66.5 1.0 CB E:CYS374 3.3 48.1 1.0 CB E:CYS395 3.4 59.1 1.0 CB E:CYS398 3.5 73.2 1.0 N E:CYS374 3.7 54.2 1.0 N E:CYS398 3.9 56.5 1.0 CA E:CYS374 4.0 33.3 1.0 CA E:CYS398 4.2 59.5 1.0 CB E:ARG397 4.6 49.3 1.0 CB E:ILE373 4.6 54.8 1.0 CA E:CYS371 4.7 63.5 1.0 C E:CYS374 4.7 72.5 1.0 C E:ILE373 4.8 65.7 1.0 CB E:TYR376 4.9 36.5 1.0 N E:LYS375 4.9 69.9 1.0 CA E:CYS395 4.9 64.2 1.0 C E:ARG397 4.9 57.1 1.0

Zinc binding site 4 out of 4 in the Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Nad-Dependent Protein Deacetylase Sirtuin-1 (Open State, 2.64 A) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn601 b:0.6 occ:1.00 SG G:CYS371 2.4 0.3 1.0 SG G:CYS374 2.4 87.8 1.0 SG G:CYS395 2.4 87.3 1.0 SG G:CYS398 2.5 0.5 1.0 CB G:CYS395 3.2 80.2 1.0 CB G:CYS371 3.3 92.3 1.0 CB G:CYS398 3.4 0.4 1.0 CB G:CYS374 3.7 77.5 1.0 N G:CYS374 3.9 83.9 1.0 N G:CYS398 4.0 0.3 1.0 CA G:CYS398 4.3 0.7 1.0 CA G:CYS374 4.4 78.5 1.0 CA G:CYS395 4.7 0.4 1.0 CB G:ILE373 4.7 0.4 1.0 CB G:ALA405 4.7 0.2 1.0 CA G:CYS371 4.7 82.7 1.0 CA G:ALA405 4.8 0.8 1.0 CB G:ARG397 4.8 95.1 1.0 N G:ILE373 5.0 0.5 1.0 C G:ILE373 5.0 97.7 1.0 CB G:TYR376 5.0 91.4 1.0

A.M.Davenport, F.M.Huber, A.Hoelz. Structural and Functional Analysis of Human SIRT1. J.Mol.Biol. V. 426 526 2014.
ISSN: ISSN 0022-2836
PubMed: 24120939
DOI: 10.1016/J.JMB.2013.10.009