Zinc in PDB 5deu: Crystal Structure of TET2-5HMC Complex

The structure of Crystal Structure of TET2-5HMC Complex, PDB code: 5deu was solved by L.Hu, J.Cheng, Q.Rao, Z.Li, J.Li, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.26 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.262, 87.522, 260.864, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.2

The structure of Crystal Structure of TET2-5HMC Complex also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of TET2-5HMC Complex (pdb code 5deu). 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 TET2-5HMC Complex, PDB code: 5deu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of TET2-5HMC Complex


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 TET2-5HMC Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:46.1 occ:1.00 ND1 A:HIS1219 2.1 57.5 1.0 SG A:CYS1133 2.3 57.2 1.0 SG A:CYS1135 2.4 58.2 1.0 SG A:CYS1221 2.4 51.2 1.0 CE1 A:HIS1219 3.0 53.4 1.0 CB A:CYS1135 3.0 55.5 1.0 CG A:HIS1219 3.1 51.0 1.0 CB A:CYS1221 3.3 48.5 1.0 CB A:HIS1219 3.5 52.6 1.0 CB A:CYS1133 3.9 75.7 1.0 O A:HOH2221 4.0 52.8 1.0 N A:CYS1221 4.1 54.8 1.0 NE2 A:HIS1219 4.1 54.4 1.0 CA A:HIS1219 4.1 53.9 1.0 N A:CYS1135 4.2 60.0 1.0 CD2 A:HIS1219 4.2 54.5 1.0 CA A:CYS1135 4.2 62.8 1.0 N A:THR1220 4.3 52.3 1.0 CA A:CYS1221 4.4 53.7 1.0 NH1 A:ARG1216 4.4 44.6 1.0 C A:HIS1219 4.7 56.1 1.0 CA A:CYS1133 4.8 72.7 1.0 N A:ARG1134 4.9 59.2 1.0 NH2 A:ARG1216 5.0 45.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of TET2-5HMC Complex


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 TET2-5HMC Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:35.2 occ:1.00 NE2 A:HIS1380 2.1 29.8 1.0 SG A:CYS1273 2.3 43.4 1.0 SG A:CYS1271 2.4 41.8 1.0 SG A:CYS1193 2.4 36.2 1.0 CE1 A:HIS1380 2.9 30.0 1.0 CB A:CYS1271 3.1 45.8 1.0 CD2 A:HIS1380 3.1 29.1 1.0 CB A:CYS1273 3.3 39.9 1.0 CB A:CYS1193 3.3 34.4 1.0 ND1 A:HIS1380 4.1 33.5 1.0 CB A:ASN1266 4.2 42.5 1.0 CG A:HIS1380 4.2 29.8 1.0 CA A:CYS1193 4.3 35.0 1.0 O A:HOH2376 4.3 56.9 1.0 N A:ASN1266 4.3 39.0 1.0 O A:HOH2207 4.4 42.1 1.0 N A:CYS1273 4.4 41.9 1.0 CA A:CYS1273 4.5 37.6 1.0 CA A:CYS1271 4.5 47.3 1.0 CG A:ASN1266 4.6 45.0 1.0 CA A:ASN1266 4.8 40.8 1.0 ND2 A:ASN1266 4.8 47.0 1.0 CD A:PRO1194 4.8 35.4 1.0 SG A:CYS1378 4.9 34.0 1.0 O A:HOH2380 4.9 68.8 1.0 O A:HOH2161 5.0 62.3 1.0 C A:CYS1271 5.0 52.0 1.0 N A:ALA1272 5.0 46.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of TET2-5HMC Complex


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 TET2-5HMC Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2006 b:33.6 occ:1.00 ND1 A:HIS1912 2.2 33.0 1.0 SG A:CYS1298 2.3 37.2 1.0 SG A:CYS1289 2.3 32.5 1.0 SG A:CYS1358 2.4 38.1 1.0 CE1 A:HIS1912 3.1 38.5 1.0 CB A:CYS1289 3.1 30.3 1.0 CG A:HIS1912 3.3 36.1 1.0 CB A:CYS1298 3.3 34.0 1.0 CB A:CYS1358 3.4 32.7 1.0 CB A:HIS1912 3.7 36.3 1.0 CA A:CYS1358 3.7 33.6 1.0 CA A:HIS1912 3.9 40.1 1.0 O A:GLU1357 4.1 38.7 1.0 NE2 A:HIS1912 4.2 36.1 1.0 CD2 A:PHE1300 4.2 35.7 1.0 N A:CYS1358 4.3 32.2 1.0 CE A:MET1907 4.3 33.2 1.0 CD2 A:HIS1912 4.4 36.6 1.0 CA A:CYS1289 4.4 26.6 1.0 C A:GLU1357 4.5 32.8 1.0 CB A:PHE1300 4.7 38.6 1.0 N A:HIS1912 4.7 37.6 1.0 CA A:CYS1298 4.7 31.9 1.0 O A:HOH2158 4.9 34.6 1.0 C A:CYS1358 4.9 34.9 1.0 CG A:PHE1300 5.0 36.6 1.0

L.Hu, J.Lu, J.Cheng, Q.Rao, Z.Li, H.Hou, Z.Lou, L.Zhang, W.Li, W.Gong, M.Liu, C.Sun, X.Yin, J.Li, X.Tan, P.Wang, Y.Wang, D.Fang, Q.Cui, P.Yang, C.He, H.Jiang, C.Luo, Y.Xu. Structural Insight Into Substrate Preference For Tet-Mediated Oxidation. Nature V. 527 118 2015.
ISSN: ESSN 1476-4687
PubMed: 26524525
DOI: 10.1038/NATURE15713