Zinc in PDB 4nm6: Crystal Structure of TET2-Dna Complex

The structure of Crystal Structure of TET2-Dna Complex, PDB code: 4nm6 was solved by L.Hu, Z.Li, J.Cheng, Q.Rao, W.Gong, M.Liu, P.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.80 / 2.03
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.296, 88.186, 262.962, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.3

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

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Crystal Structure of TET2-Dna Complex (pdb code 4nm6). 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-Dna Complex, PDB code: 4nm6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of TET2-Dna 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-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:51.9 occ:1.00 NE2 A:HIS1380 2.3 43.4 1.0 SG A:CYS1193 2.4 50.0 1.0 SG A:CYS1273 2.5 56.5 1.0 SG A:CYS1271 2.5 48.1 1.0 CB A:CYS1271 3.1 62.6 1.0 CD2 A:HIS1380 3.2 47.7 1.0 CB A:CYS1193 3.2 44.9 1.0 CB A:CYS1273 3.3 47.4 1.0 CE1 A:HIS1380 3.3 42.7 1.0 CB A:ASN1266 4.1 55.7 1.0 CA A:CYS1193 4.2 50.6 1.0 N A:CYS1273 4.3 49.2 1.0 N A:ASN1266 4.3 48.3 1.0 CG A:HIS1380 4.4 41.8 1.0 O A:HOH2133 4.4 62.5 1.0 CA A:CYS1273 4.4 55.2 1.0 ND1 A:HIS1380 4.4 54.5 1.0 CG A:ASN1266 4.5 54.1 1.0 CA A:CYS1271 4.5 57.5 1.0 ND2 A:ASN1266 4.6 52.9 1.0 CA A:ASN1266 4.7 54.2 1.0 CD A:PRO1194 4.8 49.5 1.0 N A:ALA1272 4.8 54.8 1.0 C A:CYS1271 4.9 59.8 1.0 N A:CYS1193 5.0 54.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of TET2-Dna 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-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:77.8 occ:1.00 SG A:CYS1135 2.2 81.5 1.0 ND1 A:HIS1219 2.2 70.7 1.0 SG A:CYS1221 2.2 69.0 1.0 SG A:CYS1133 2.4 76.6 1.0 CB A:CYS1221 3.1 67.7 1.0 CG A:HIS1219 3.2 68.1 1.0 CE1 A:HIS1219 3.2 75.8 1.0 CB A:CYS1135 3.3 79.8 1.0 CB A:HIS1219 3.4 71.0 1.0 CB A:CYS1133 3.9 98.0 1.0 N A:CYS1221 3.9 65.4 1.0 CA A:HIS1219 4.1 73.8 1.0 CA A:CYS1221 4.2 66.4 1.0 N A:THR1220 4.2 67.1 1.0 N A:CYS1135 4.3 85.4 1.0 CD2 A:HIS1219 4.3 71.4 1.0 NE2 A:HIS1219 4.3 74.2 1.0 CA A:CYS1135 4.4 80.2 1.0 NH1 A:ARG1216 4.5 56.6 1.0 CA A:CYS1133 4.6 99.3 1.0 C A:HIS1219 4.6 69.1 1.0 N A:ARG1134 4.7 96.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of TET2-Dna 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-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:52.9 occ:1.00 ND1 A:HIS1912 2.3 47.3 1.0 SG A:CYS1298 2.5 55.8 1.0 SG A:CYS1358 2.5 49.0 1.0 SG A:CYS1289 2.5 48.9 1.0 CE1 A:HIS1912 3.2 51.4 1.0 CB A:CYS1298 3.3 48.2 1.0 CG A:HIS1912 3.3 55.4 1.0 CB A:CYS1289 3.3 45.7 1.0 CB A:CYS1358 3.6 55.6 1.0 CB A:HIS1912 3.7 58.0 1.0 CA A:CYS1358 3.8 46.0 1.0 CA A:HIS1912 3.9 58.4 1.0 O A:GLU1357 4.1 52.9 1.0 CD2 A:PHE1300 4.2 57.1 1.0 NE2 A:HIS1912 4.3 53.5 1.0 N A:CYS1358 4.4 44.8 1.0 CE A:MET1907 4.4 46.3 1.0 CD2 A:HIS1912 4.4 52.2 1.0 C A:GLU1357 4.5 56.2 1.0 CA A:CYS1289 4.5 47.5 1.0 CB A:PHE1300 4.5 53.5 1.0 CA A:CYS1298 4.7 46.4 1.0 N A:HIS1912 4.7 57.1 1.0 CG A:PHE1300 4.9 56.0 1.0 O A:HOH2127 5.0 47.5 1.0

L.Hu, Z.Li, J.Cheng, Q.Rao, W.Gong, M.Liu, Y.G.Shi, J.Zhu, P.Wang, Y.Xu. Crystal Structure of TET2-Dna Complex: Insight Into Tet-Mediated 5MC Oxidation. Cell(Cambridge,Mass.) V. 155 1545 2013.
ISSN: ISSN 0092-8674
PubMed: 24315485
DOI: 10.1016/J.CELL.2013.11.020