Zinc in PDB 6a59: Structure of Histone Demethylase REF6 at 1.8A

The structure of Structure of Histone Demethylase REF6 at 1.8A, PDB code: 6a59 was solved by Z.Tian, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.82
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	63.445, 63.445, 43.533, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 23

The binding sites of Zinc atom in the Structure of Histone Demethylase REF6 at 1.8A (pdb code 6a59). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Histone Demethylase REF6 at 1.8A, PDB code: 6a59:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Histone Demethylase REF6 at 1.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Histone Demethylase REF6 at 1.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:40.4 occ:1.00 SG A:CYS1250 2.2 30.9 1.0 SG A:CYS1245 2.3 31.9 1.0 NE2 A:HIS1263 2.4 30.6 1.0 NE2 A:HIS1280 2.6 45.8 1.0 CD2 A:HIS1263 3.0 29.9 1.0 CB A:CYS1250 3.1 31.6 1.0 CB A:CYS1245 3.1 33.1 1.0 CD2 A:HIS1280 3.1 44.6 1.0 CE1 A:HIS1263 3.5 31.3 1.0 CE1 A:HIS1280 3.6 45.1 1.0 CB A:MET1247 4.1 43.2 1.0 CG A:HIS1263 4.3 29.8 1.0 CG A:HIS1280 4.3 42.2 1.0 CG A:MET1247 4.3 45.5 1.0 ND1 A:HIS1263 4.5 29.8 1.0 ND1 A:HIS1280 4.5 45.1 1.0 CA A:CYS1250 4.5 32.7 1.0 CA A:CYS1245 4.5 34.0 1.0 CB A:MET1252 4.8 30.2 1.0 N A:MET1247 5.0 39.2 1.0

Zinc binding site 2 out of 4 in the Structure of Histone Demethylase REF6 at 1.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Histone Demethylase REF6 at 1.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:41.8 occ:1.00 SG A:CYS1268 2.2 31.8 1.0 SG A:CYS1273 2.3 35.9 1.0 NE2 A:HIS1290 2.6 52.8 1.0 NE2 A:HIS1286 2.8 44.9 1.0 CD2 A:HIS1286 2.9 43.8 1.0 CB A:CYS1268 3.1 29.8 1.0 CB A:CYS1273 3.1 35.9 1.0 CE1 A:HIS1290 3.3 51.2 1.0 CD2 A:HIS1290 3.3 53.1 1.0 CE1 A:HIS1286 4.0 46.9 1.0 ND1 A:HIS1290 4.2 49.3 1.0 CG A:HIS1290 4.2 50.2 1.0 CG A:HIS1286 4.3 44.7 1.0 O A:HOH1550 4.4 51.8 1.0 CA A:CYS1268 4.5 28.5 1.0 CB A:ILE1270 4.6 31.6 1.0 CA A:CYS1273 4.6 36.1 1.0 CG1 A:ILE1270 4.7 32.5 1.0 ND1 A:HIS1286 4.8 46.0 1.0 CB A:LYS1275 4.8 34.7 1.0

Zinc binding site 3 out of 4 in the Structure of Histone Demethylase REF6 at 1.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Histone Demethylase REF6 at 1.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:41.2 occ:1.00 SG A:CYS1298 2.2 28.2 1.0 SG A:CYS1303 2.3 32.3 1.0 NE2 A:HIS1320 2.5 33.8 1.0 NE2 A:HIS1316 2.6 34.3 1.0 CD2 A:HIS1316 2.9 33.2 1.0 CD2 A:HIS1320 3.0 32.8 1.0 CB A:CYS1303 3.0 33.4 1.0 CB A:CYS1298 3.1 28.1 1.0 CE1 A:HIS1320 3.7 34.7 1.0 CE1 A:HIS1316 3.9 35.4 1.0 CB A:TRP1300 4.2 30.4 1.0 CG A:HIS1316 4.2 33.0 1.0 CG A:HIS1320 4.3 31.6 1.0 CA A:CYS1303 4.5 34.4 1.0 CA A:CYS1298 4.5 28.1 1.0 ND1 A:HIS1320 4.6 33.5 1.0 CB A:MET1305 4.6 38.6 1.0 ND1 A:HIS1316 4.7 35.1 1.0 C A:CYS1303 5.0 34.6 1.0

Zinc binding site 4 out of 4 in the Structure of Histone Demethylase REF6 at 1.8A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Histone Demethylase REF6 at 1.8A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1404 b:62.3 occ:1.00 SG A:CYS1328 2.2 47.5 1.0 SG A:CYS1333 2.4 49.9 1.0 ND1 A:HIS1352 2.8 85.4 1.0 NE2 A:HIS1346 2.8 58.3 1.0 CD2 A:HIS1346 3.0 57.6 1.0 CB A:CYS1328 3.1 43.5 1.0 CB A:CYS1333 3.4 50.1 1.0 CG A:HIS1352 3.4 83.8 1.0 CE1 A:HIS1352 3.5 86.2 1.0 CB A:HIS1352 3.7 82.6 1.0 CE1 A:HIS1346 4.1 59.5 1.0 CD2 A:HIS1352 4.3 85.0 1.0 NE2 A:HIS1352 4.3 86.0 1.0 CG A:HIS1346 4.4 57.5 1.0 CA A:CYS1328 4.6 44.0 1.0 CB A:GLU1330 4.7 55.6 1.0 CB A:GLN1335 4.7 39.5 1.0 OG1 A:THR1350 4.8 74.3 1.0 CA A:CYS1333 4.8 50.7 1.0 ND1 A:HIS1346 4.9 59.2 1.0

Z.Tian, Z.Chen. Structure of Histone Demethylase REF6 Complexed with Dna To Be Published.