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Zinc in PDB 5d9y: Crystal Structure of TET2-5FC Complex

Protein crystallography data

The structure of Crystal Structure of TET2-5FC Complex, PDB code: 5d9y 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) 36.77 / 1.97
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.154, 87.958, 268.020, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.8

Other elements in 5d9y:

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

Iron (Fe) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TET2-5FC Complex (pdb code 5d9y). 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 TET2-5FC Complex, PDB code: 5d9y:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5d9y

Go back to Zinc Binding Sites List in 5d9y
Zinc binding site 1 out of 3 in the Crystal Structure of TET2-5FC 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 TET2-5FC Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:45.7
occ:1.00
ND1 A:HIS1219 2.1 38.1 1.0
SG A:CYS1221 2.1 38.8 1.0
SG A:CYS1133 2.2 43.7 1.0
SG A:CYS1135 2.6 53.6 1.0
CG A:HIS1219 3.1 41.7 1.0
CE1 A:HIS1219 3.1 41.8 1.0
CB A:CYS1135 3.2 50.5 1.0
CB A:CYS1221 3.2 40.4 1.0
CB A:HIS1219 3.3 40.7 1.0
CB A:CYS1133 3.7 53.6 1.0
N A:CYS1221 3.9 42.4 1.0
CA A:HIS1219 4.0 46.7 1.0
N A:CYS1135 4.1 54.1 1.0
N A:THR1220 4.1 44.9 1.0
NH1 A:ARG1216 4.2 30.9 1.0
NE2 A:HIS1219 4.2 46.6 1.0
CD2 A:HIS1219 4.2 48.4 1.0
CA A:CYS1221 4.2 44.0 1.0
CA A:CYS1135 4.3 57.1 1.0
C A:HIS1219 4.5 45.5 1.0
CA A:CYS1133 4.6 49.8 1.0
N A:ARG1134 4.7 53.8 1.0
CZ A:ARG1216 4.8 31.3 1.0
NH2 A:ARG1216 4.9 39.2 1.0
C A:THR1220 5.0 41.6 1.0

Zinc binding site 2 out of 3 in 5d9y

Go back to Zinc Binding Sites List in 5d9y
Zinc binding site 2 out of 3 in the Crystal Structure of TET2-5FC 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 TET2-5FC Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:19.8
occ:1.00
NE2 A:HIS1380 2.1 27.4 1.0
SG A:CYS1273 2.2 25.2 1.0
SG A:CYS1271 2.2 20.1 1.0
SG A:CYS1193 2.4 20.4 1.0
CB A:CYS1271 3.0 28.2 1.0
CE1 A:HIS1380 3.0 19.0 1.0
CD2 A:HIS1380 3.1 23.4 1.0
CB A:CYS1273 3.3 26.8 1.0
CB A:CYS1193 3.4 19.1 1.0
ND1 A:HIS1380 4.2 20.3 1.0
CB A:ASN1266 4.2 19.8 1.0
N A:ASN1266 4.2 21.3 1.0
O A:HOH2263 4.2 24.9 1.0
CG A:HIS1380 4.3 21.6 1.0
N A:CYS1273 4.3 19.7 1.0
CA A:CYS1193 4.4 22.6 1.0
O A:HOH2339 4.4 28.1 1.0
CA A:CYS1273 4.4 27.0 1.0
CA A:CYS1271 4.4 24.9 1.0
CG A:ASN1266 4.5 21.9 1.0
ND2 A:ASN1266 4.6 26.4 1.0
CA A:ASN1266 4.7 23.1 1.0
N A:ALA1272 4.8 22.2 1.0
C A:CYS1271 4.8 26.5 1.0
O A:HOH2338 4.8 35.2 1.0
CD A:PRO1194 4.9 22.1 1.0
C A:LEU1265 4.9 24.2 1.0
SG A:CYS1378 5.0 22.2 1.0

Zinc binding site 3 out of 3 in 5d9y

Go back to Zinc Binding Sites List in 5d9y
Zinc binding site 3 out of 3 in the Crystal Structure of TET2-5FC 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 TET2-5FC Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:23.1
occ:1.00
ND1 A:HIS1912 2.2 29.4 1.0
SG A:CYS1298 2.2 24.4 1.0
SG A:CYS1289 2.3 21.6 1.0
SG A:CYS1358 2.4 19.2 1.0
CE1 A:HIS1912 3.0 24.4 1.0
CB A:CYS1289 3.1 21.5 1.0
CG A:HIS1912 3.2 26.5 1.0
CB A:CYS1298 3.3 24.1 1.0
CB A:CYS1358 3.5 17.5 1.0
CB A:HIS1912 3.6 26.1 1.0
CA A:CYS1358 3.8 21.1 1.0
CA A:HIS1912 3.9 24.4 1.0
O A:GLU1357 4.1 25.1 1.0
NE2 A:HIS1912 4.2 29.7 1.0
CD2 A:HIS1912 4.3 28.8 1.0
N A:CYS1358 4.4 21.1 1.0
CE A:MET1907 4.4 22.4 1.0
CA A:CYS1289 4.4 16.8 1.0
CD2 A:PHE1300 4.4 26.9 1.0
C A:GLU1357 4.5 27.5 1.0
CB A:PHE1300 4.6 24.6 1.0
CA A:CYS1298 4.7 22.8 1.0
N A:HIS1912 4.7 27.6 1.0
O A:HOH2125 4.9 22.9 1.0

Reference:

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
Page generated: Wed Dec 16 06:08:12 2020

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