Zinc in PDB 7ne6: Human TET2 in Complex with Unfavourable Dna Substrate.

The structure of Human TET2 in Complex with Unfavourable Dna Substrate., PDB code: 7ne6 was solved by D.Rafalski, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.97 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	47.858, 87.943, 261.988, 90, 90, 90
R / Rfree (%)	19.5 / 22.7

The structure of Human TET2 in Complex with Unfavourable Dna Substrate. also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the Human TET2 in Complex with Unfavourable Dna Substrate. (pdb code 7ne6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human TET2 in Complex with Unfavourable Dna Substrate., PDB code: 7ne6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human TET2 in Complex with Unfavourable Dna Substrate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human TET2 in Complex with Unfavourable Dna Substrate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:49.0 occ:1.00 NE2 A:HIS1380 2.1 62.2 1.0 SG A:CYS1273 2.3 50.4 1.0 SG A:CYS1193 2.4 51.4 1.0 SG A:CYS1271 2.4 47.2 1.0 CB A:CYS1271 3.0 48.4 1.0 CE1 A:HIS1380 3.1 59.3 1.0 CD2 A:HIS1380 3.1 59.8 1.0 CB A:CYS1273 3.4 48.0 1.0 CB A:CYS1193 3.4 48.8 1.0 CB A:ASN1266 4.2 49.4 1.0 ND1 A:HIS1380 4.2 57.8 1.0 O A:HOH2380 4.3 51.5 1.0 N A:CYS1273 4.3 51.7 1.0 CG A:HIS1380 4.3 55.4 1.0 N A:ASN1266 4.3 47.5 1.0 O A:HOH2274 4.3 47.8 1.0 CA A:CYS1193 4.3 47.7 1.0 O A:HOH2195 4.4 52.0 1.0 CA A:CYS1271 4.4 51.5 1.0 CA A:CYS1273 4.4 49.1 1.0 CG A:ASN1266 4.6 50.1 1.0 N A:ALA1272 4.7 50.0 1.0 CA A:ASN1266 4.8 49.1 1.0 SG A:CYS1378 4.8 40.2 1.0 CD A:PRO1194 4.9 39.9 1.0 C A:CYS1271 4.9 53.0 1.0 ND2 A:ASN1266 4.9 50.0 1.0

Zinc binding site 2 out of 3 in the Human TET2 in Complex with Unfavourable Dna Substrate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human TET2 in Complex with Unfavourable Dna Substrate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:68.1 occ:1.00 ND1 A:HIS1219 2.0 78.2 1.0 SG A:CYS1221 2.4 60.8 1.0 SG A:CYS1135 2.5 75.1 1.0 SG A:CYS1133 2.5 71.8 1.0 CE1 A:HIS1219 2.8 79.2 1.0 CG A:HIS1219 3.1 75.6 1.0 CB A:CYS1135 3.1 76.1 1.0 CB A:CYS1133 3.2 75.6 1.0 CB A:CYS1221 3.3 63.6 1.0 CB A:HIS1219 3.6 67.5 1.0 N A:CYS1221 3.9 65.8 1.0 NE2 A:HIS1219 4.0 77.7 1.0 CA A:HIS1219 4.0 62.4 1.0 CD2 A:HIS1219 4.1 77.5 1.0 CA A:CYS1221 4.2 65.6 1.0 NH1 A:ARG1216 4.3 58.2 1.0 N A:CYS1135 4.3 81.0 1.0 N A:THR1220 4.3 68.5 1.0 CA A:CYS1135 4.3 79.1 1.0 C A:HIS1219 4.6 56.7 1.0 CA A:CYS1133 4.6 81.6 1.0 C A:CYS1133 4.9 82.9 1.0 CZ A:ARG1216 4.9 59.2 1.0

Zinc binding site 3 out of 3 in the Human TET2 in Complex with Unfavourable Dna Substrate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human TET2 in Complex with Unfavourable Dna Substrate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:43.7 occ:1.00 ND1 A:HIS1912 2.1 59.9 1.0 SG A:CYS1298 2.3 43.2 1.0 SG A:CYS1358 2.3 41.8 1.0 SG A:CYS1289 2.6 47.0 1.0 CE1 A:HIS1912 3.0 58.3 1.0 CB A:CYS1289 3.2 41.4 1.0 CG A:HIS1912 3.2 58.5 1.0 CB A:CYS1298 3.2 44.9 1.0 CB A:CYS1358 3.4 40.4 1.0 CB A:HIS1912 3.6 52.7 1.0 CA A:CYS1358 3.7 41.3 1.0 CA A:HIS1912 3.9 46.9 1.0 NE2 A:HIS1912 4.1 59.9 1.0 CD2 A:PHE1300 4.2 45.5 1.0 CD2 A:HIS1912 4.2 61.4 1.0 O A:GLU1357 4.3 40.4 1.0 N A:CYS1358 4.3 42.7 1.0 CE A:MET1907 4.4 41.5 1.0 CA A:CYS1289 4.5 39.1 1.0 CB A:PHE1300 4.5 46.5 1.0 C A:GLU1357 4.5 42.8 1.0 O A:HOH2176 4.6 46.5 1.0 CA A:CYS1298 4.6 44.8 1.0 N A:HIS1912 4.6 44.5 1.0 CG A:PHE1300 4.9 46.0 1.0 C A:CYS1358 4.9 39.1 1.0

M.Ravichandran, D.Rafalski, C.I.Davies, O.Ortega-Recalde, X.Nan, C.R.Glanfield, A.Kotter, K.Misztal, A.H.Wang, M.Wojciechowski, M.Razew, I.M.Mayyas, O.Kardailsky, U.Schwartz, K.Zembrzycki, I.M.Morison, M.Helm, D.Weichenhan, R.Z.Jurkowska, F.Krueger, C.Plass, M.Zacharias, M.Bochtler, T.A.Hore, T.P.Jurkowski. Pronounced Sequence Specificity of the Tet Enzyme Catalytic Domain Guides Its Cellular Function. Sci Adv V. 8 M2427 2022.
ISSN: ESSN 2375-2548
PubMed: 36070377
DOI: 10.1126/SCIADV.ABM2427