Zinc in PDB 6iso: Human SIRT3 Recognizing H3K4CR

The structure of Human SIRT3 Recognizing H3K4CR, PDB code: 6iso was solved by Y.Wang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.25 / 2.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.085, 138.085, 225.342, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.5

The binding sites of Zinc atom in the Human SIRT3 Recognizing H3K4CR (pdb code 6iso). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Human SIRT3 Recognizing H3K4CR, PDB code: 6iso:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Human SIRT3 Recognizing H3K4CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT3 Recognizing H3K4CR within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.7 occ:1.00 O A:HOH531 1.8 32.2 1.0 SG A:CYS259 2.1 38.0 1.0 CB A:CYS283 2.3 50.1 1.0 SG A:CYS256 2.3 39.3 1.0 SG A:CYS280 2.4 40.7 1.0 CB A:CYS280 2.9 35.6 1.0 CB A:CYS259 3.0 33.6 1.0 SG A:CYS283 3.2 67.5 1.0 CB A:CYS256 3.3 33.9 1.0 CA A:CYS283 3.5 48.4 1.0 N A:CYS283 3.6 53.2 1.0 N A:CYS259 3.7 35.6 1.0 CA A:CYS259 3.9 37.1 1.0 C A:CYS283 4.3 49.4 1.0 CA A:CYS280 4.4 38.5 1.0 N A:GLY285 4.6 47.2 1.0 N A:THR284 4.6 45.8 1.0 CA A:CYS256 4.7 33.4 1.0 C A:CYS259 4.7 40.3 1.0 CB A:VAL282 4.8 49.1 1.0 C A:VAL282 4.8 48.0 1.0 CG A:ARG261 4.8 63.9 1.0 C A:VAL258 4.9 35.8 1.0 CB A:ARG261 5.0 52.0 1.0

Zinc binding site 2 out of 5 in the Human SIRT3 Recognizing H3K4CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT3 Recognizing H3K4CR within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:55.9 occ:1.00 SG B:CYS259 2.3 49.0 1.0 SG B:CYS280 2.3 50.9 1.0 SG B:CYS256 2.4 51.2 1.0 SG B:CYS283 2.5 54.5 1.0 CB B:CYS280 2.8 58.7 1.0 CB B:CYS283 3.0 67.9 1.0 CB B:CYS259 3.2 45.8 1.0 CB B:CYS256 3.4 46.5 1.0 N B:CYS283 3.5 62.8 1.0 CA B:CYS283 3.7 60.6 1.0 N B:CYS259 3.9 45.0 1.0 CA B:CYS259 4.1 44.0 1.0 CA B:CYS280 4.3 56.6 1.0 C B:CYS283 4.3 53.6 1.0 N B:THR284 4.5 51.5 1.0 N B:GLY285 4.5 63.6 1.0 CB B:VAL282 4.6 54.3 1.0 C B:VAL282 4.7 59.8 1.0 CA B:CYS256 4.8 43.6 1.0 C B:CYS280 4.9 57.7 1.0 C B:CYS259 4.9 41.7 1.0 CA B:GLY285 5.0 55.6 1.0

Zinc binding site 3 out of 5 in the Human SIRT3 Recognizing H3K4CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SIRT3 Recognizing H3K4CR within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:33.8 occ:1.00 SG E:CYS280 2.2 35.9 1.0 SG E:CYS259 2.3 28.2 1.0 SG E:CYS256 2.3 34.1 1.0 SG E:CYS283 2.5 47.9 1.0 CB E:CYS280 2.8 33.2 1.0 CB E:CYS283 3.0 40.9 1.0 CB E:CYS259 3.2 29.9 1.0 CB E:CYS256 3.3 35.5 1.0 N E:CYS283 3.7 43.4 1.0 CA E:CYS283 3.9 42.5 1.0 N E:CYS259 3.9 34.5 1.0 CG1 E:VAL258 4.0 42.2 1.0 CA E:CYS259 4.1 33.8 1.0 CA E:CYS280 4.3 34.9 1.0 C E:CYS283 4.4 45.9 1.0 N E:THR284 4.6 47.2 1.0 N E:GLY285 4.7 41.4 1.0 CA E:CYS256 4.7 32.5 1.0 CB E:VAL282 4.8 36.2 1.0 C E:VAL282 4.9 42.2 1.0 C E:CYS259 4.9 36.8 1.0 NE E:ARG261 4.9 43.4 1.0 C E:CYS280 5.0 40.6 1.0 C E:VAL258 5.0 34.4 1.0

Zinc binding site 4 out of 5 in the Human SIRT3 Recognizing H3K4CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SIRT3 Recognizing H3K4CR within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:98.4 occ:1.00 O G:HOH508 2.2 53.8 1.0 O G:HOH530 2.3 20.9 1.0 O G:HOH533 2.4 61.2 1.0 O G:HOH532 2.5 57.4 1.0 SG G:CYS256 2.9 90.5 1.0 CB G:CYS256 3.2 0.8 1.0 C G:VAL258 3.2 57.3 1.0 O G:VAL258 3.4 52.1 1.0 N G:ARG261 3.7 82.5 1.0 N G:GLN260 4.0 65.2 1.0 CA G:GLN260 4.0 70.7 1.0 SG G:CYS283 4.0 96.7 1.0 SG G:CYS280 4.0 66.3 1.0 CB G:ARG261 4.2 91.8 1.0 C G:GLN260 4.3 80.5 1.0 CA G:VAL258 4.3 61.2 1.0 N G:VAL258 4.4 72.5 1.0 CB G:CYS283 4.5 89.5 1.0 CA G:ARG261 4.6 81.4 1.0 N G:CYS283 4.6 0.7 1.0 CA G:CYS256 4.7 94.8 1.0 CB G:VAL258 4.7 63.0 1.0 CB G:CYS280 4.9 63.9 1.0

Zinc binding site 5 out of 5 in the Human SIRT3 Recognizing H3K4CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human SIRT3 Recognizing H3K4CR within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:32.2 occ:1.00 SG I:CYS259 2.1 33.6 1.0 SG I:CYS256 2.2 37.2 1.0 SG I:CYS280 2.3 28.3 1.0 SG I:CYS283 2.5 41.5 1.0 CB I:CYS280 2.9 31.6 1.0 CB I:CYS256 3.1 35.7 1.0 CB I:CYS283 3.1 33.1 1.0 CB I:CYS259 3.4 40.8 1.0 N I:CYS259 3.6 42.0 1.0 O I:CYS259 3.9 73.4 1.0 N I:CYS283 3.9 31.9 1.0 CA I:CYS259 4.0 43.1 1.0 CA I:CYS283 4.0 32.7 1.0 CA I:CYS280 4.4 34.6 1.0 C I:CYS259 4.4 53.2 1.0 CA I:CYS256 4.5 38.2 1.0 C I:CYS283 4.7 31.2 1.0 C I:VAL258 4.7 38.2 1.0 N I:GLY285 4.7 33.6 1.0 CB I:VAL258 4.8 35.6 1.0 N I:THR284 4.8 32.1 1.0 CB I:VAL282 4.9 39.3 1.0 N I:VAL258 5.0 34.4 1.0

X.Bao, Y.Wang, X.Li, X.M.Li, Z.Liu, T.Yang, C.F.Wong, J.Zhang, Q.Hao, X.D.Li. Identification of 'Erasers' For Lysine Crotonylated Histone Marks Using A Chemical Proteomics Approach. Elife V. 3 2014.
ISSN: ESSN 2050-084X
PubMed: 25369635
DOI: 10.7554/ELIFE.02999