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Zinc in PDB 7ne3: Human TET2 in Complex with Favourable Dna Substrate.

Protein crystallography data

The structure of Human TET2 in Complex with Favourable Dna Substrate., PDB code: 7ne3 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) 43.86 / 2.26
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.994, 87.711, 260.531, 90, 90, 90
R / Rfree (%) 17.5 / 22.6

Other elements in 7ne3:

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

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human TET2 in Complex with Favourable Dna Substrate. (pdb code 7ne3). 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 Favourable Dna Substrate., PDB code: 7ne3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ne3

Go back to Zinc Binding Sites List in 7ne3
Zinc binding site 1 out of 3 in the Human TET2 in Complex with Favourable 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 Favourable Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:49.4
occ:1.00
NE2 A:HIS1380 2.0 67.2 1.0
SG A:CYS1273 2.2 53.9 1.0
SG A:CYS1271 2.3 48.0 1.0
SG A:CYS1193 2.4 52.9 1.0
CE1 A:HIS1380 2.9 58.6 1.0
CD2 A:HIS1380 3.1 61.9 1.0
CB A:CYS1271 3.2 46.6 1.0
CB A:CYS1273 3.3 53.8 1.0
CB A:CYS1193 3.3 50.2 1.0
CB A:ASN1266 4.1 52.7 1.0
ND1 A:HIS1380 4.1 60.7 1.0
N A:ASN1266 4.2 48.9 1.0
CG A:HIS1380 4.2 58.2 1.0
O A:HOH2336 4.2 52.2 1.0
CA A:CYS1193 4.3 43.0 1.0
N A:CYS1273 4.3 53.1 1.0
CA A:CYS1273 4.4 51.4 1.0
O A:HOH2181 4.4 52.9 1.0
CG A:ASN1266 4.6 51.5 1.0
CA A:CYS1271 4.6 53.0 1.0
CA A:ASN1266 4.6 54.1 1.0
CD A:PRO1194 4.8 43.4 1.0
ND2 A:ASN1266 4.8 47.9 1.0
N A:ALA1272 4.9 55.9 1.0
C A:CYS1271 4.9 56.6 1.0
SG A:CYS1378 4.9 49.8 1.0
C A:LEU1265 5.0 53.1 1.0

Zinc binding site 2 out of 3 in 7ne3

Go back to Zinc Binding Sites List in 7ne3
Zinc binding site 2 out of 3 in the Human TET2 in Complex with Favourable 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 Favourable Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:69.5
occ:1.00
ND1 A:HIS1219 2.0 79.0 1.0
SG A:CYS1221 2.2 62.2 1.0
SG A:CYS1135 2.5 80.7 1.0
SG A:CYS1133 2.5 74.9 1.0
CG A:HIS1219 3.0 70.2 1.0
CB A:CYS1133 3.1 75.5 1.0
CE1 A:HIS1219 3.1 71.6 1.0
CB A:CYS1221 3.2 64.7 1.0
CB A:HIS1219 3.2 61.9 1.0
CB A:CYS1135 3.2 87.3 1.0
CA A:HIS1219 3.8 64.2 1.0
N A:CYS1221 3.9 62.3 1.0
CD2 A:HIS1219 4.1 72.1 1.0
NE2 A:HIS1219 4.1 71.8 1.0
CA A:CYS1221 4.2 64.8 1.0
NH1 A:ARG1216 4.3 59.2 1.0
N A:THR1220 4.3 68.0 1.0
N A:CYS1135 4.4 89.6 1.0
CA A:CYS1135 4.4 92.4 1.0
C A:HIS1219 4.5 66.2 1.0
CA A:CYS1133 4.5 85.1 1.0
O A:HOH2294 4.6 81.3 1.0
NH2 A:ARG1216 4.9 66.4 1.0
CZ A:ARG1216 4.9 59.9 1.0
C A:CYS1133 5.0 82.8 1.0

Zinc binding site 3 out of 3 in 7ne3

Go back to Zinc Binding Sites List in 7ne3
Zinc binding site 3 out of 3 in the Human TET2 in Complex with Favourable 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 Favourable Dna Substrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:51.0
occ:1.00
ND1 A:HIS1912 2.1 65.8 1.0
SG A:CYS1298 2.2 55.1 1.0
SG A:CYS1358 2.4 50.1 1.0
SG A:CYS1289 2.4 54.6 1.0
CE1 A:HIS1912 3.0 57.3 1.0
CB A:CYS1289 3.1 44.9 1.0
CG A:HIS1912 3.2 64.6 1.0
CB A:CYS1298 3.3 52.6 1.0
CB A:CYS1358 3.5 52.1 1.0
CB A:HIS1912 3.6 61.5 1.0
CA A:CYS1358 3.7 50.4 1.0
CA A:HIS1912 3.9 58.1 1.0
O A:GLU1357 3.9 54.5 1.0
CD2 A:PHE1300 4.1 52.4 1.0
NE2 A:HIS1912 4.2 63.4 1.0
CD2 A:HIS1912 4.3 62.1 1.0
N A:CYS1358 4.3 53.6 1.0
CA A:CYS1289 4.4 49.7 1.0
CB A:PHE1300 4.4 54.2 1.0
CE A:MET1907 4.4 47.6 1.0
C A:GLU1357 4.4 55.6 1.0
CA A:CYS1298 4.7 51.0 1.0
N A:HIS1912 4.7 57.7 1.0
CG A:PHE1300 4.7 52.2 1.0
O A:HOH2120 4.9 54.1 1.0
C A:CYS1358 5.0 48.0 1.0

Reference:

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
Page generated: Sat Apr 8 00:57:25 2023

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