Zinc in PDB 6a58: Structure of Histone Demethylase REF6

The structure of Structure of Histone Demethylase REF6, PDB code: 6a58 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 / 1.57
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	62.494, 62.494, 43.157, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.4

The binding sites of Zinc atom in the Structure of Histone Demethylase REF6 (pdb code 6a58). 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, PDB code: 6a58:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:32.6 occ:0.90 NE2 A:HIS1263 2.1 24.9 1.0 NE2 A:HIS1280 2.2 40.6 1.0 SG A:CYS1250 2.3 27.4 1.0 SG A:CYS1245 2.3 28.2 1.0 CE1 A:HIS1280 2.7 41.8 1.0 CD2 A:HIS1263 3.0 24.9 1.0 CB A:CYS1250 3.1 28.5 1.0 CB A:CYS1245 3.1 27.6 1.0 CE1 A:HIS1263 3.1 25.5 1.0 CD2 A:HIS1280 3.5 41.6 1.0 ND1 A:HIS1280 3.9 41.9 1.0 CG A:HIS1263 4.2 24.5 1.0 ND1 A:HIS1263 4.2 24.3 1.0 CB A:MET1247 4.2 35.4 1.0 CG A:HIS1280 4.3 39.0 1.0 CG A:MET1247 4.4 36.4 1.0 CA A:CYS1250 4.5 28.5 1.0 CA A:CYS1245 4.6 27.7 1.0 CB A:MET1252 4.8 26.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:38.4 occ:1.00 NE2 A:HIS1290 2.2 37.9 1.0 SG A:CYS1268 2.2 28.5 1.0 SG A:CYS1273 2.2 33.3 1.0 NE2 A:HIS1286 2.2 37.8 1.0 CD2 A:HIS1286 2.9 37.1 1.0 CD2 A:HIS1290 3.0 39.6 1.0 CB A:CYS1273 3.1 33.1 1.0 CB A:CYS1268 3.2 27.3 1.0 CE1 A:HIS1290 3.2 39.6 1.0 CE1 A:HIS1286 3.4 37.8 1.0 CG A:HIS1286 4.1 38.5 1.0 CG A:HIS1290 4.2 38.9 1.0 ND1 A:HIS1290 4.2 39.3 1.0 O A:HOH1560 4.3 49.7 1.0 ND1 A:HIS1286 4.3 37.6 1.0 CA A:CYS1273 4.6 33.9 1.0 CA A:CYS1268 4.6 26.5 1.0 CB A:ILE1270 4.6 28.6 1.0 CB A:LYS1275 4.8 33.1 1.0 CD A:LYS1275 4.8 35.8 1.0 CG1 A:ILE1270 4.8 29.3 1.0 CG A:LYS1275 5.0 34.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:31.1 occ:0.80 NE2 A:HIS1320 2.1 26.0 1.0 NE2 A:HIS1316 2.1 28.4 1.0 SG A:CYS1303 2.3 29.0 1.0 SG A:CYS1298 2.3 27.6 1.0 CD2 A:HIS1316 2.9 27.9 1.0 CD2 A:HIS1320 3.0 25.5 1.0 CB A:CYS1303 3.1 29.6 1.0 CE1 A:HIS1320 3.1 27.5 1.0 CB A:CYS1298 3.2 27.1 1.0 CE1 A:HIS1316 3.2 28.4 1.0 CG A:HIS1316 4.1 27.7 1.0 CG A:HIS1320 4.2 25.5 1.0 ND1 A:HIS1320 4.2 26.6 1.0 ND1 A:HIS1316 4.2 28.2 1.0 CB A:TRP1300 4.3 27.2 1.0 CA A:CYS1303 4.5 30.7 1.0 CA A:CYS1298 4.6 27.2 1.0 CB A:MET1305 4.6 36.2 1.0 CG A:MET1305 4.9 39.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1404 b:56.5 occ:1.00 SG A:CYS1328 2.1 46.1 1.0 NE2 A:HIS1346 2.2 44.9 1.0 ND1 A:HIS1352 2.2 65.0 1.0 SG A:CYS1333 2.3 48.2 1.0 CD2 A:HIS1346 3.0 45.2 1.0 CB A:CYS1328 3.1 43.5 1.0 CE1 A:HIS1352 3.2 64.9 1.0 CG A:HIS1352 3.2 65.6 1.0 CE1 A:HIS1346 3.2 44.4 1.0 CB A:CYS1333 3.3 48.4 1.0 CB A:HIS1352 3.5 66.2 1.0 CG A:HIS1346 4.2 46.1 1.0 NE2 A:HIS1352 4.3 65.2 1.0 ND1 A:HIS1346 4.3 45.9 1.0 CD2 A:HIS1352 4.3 65.3 1.0 CB A:GLU1330 4.5 56.0 1.0 CA A:CYS1328 4.5 43.1 1.0 CB A:GLN1335 4.6 38.2 1.0 OG1 A:THR1350 4.7 64.3 1.0 CA A:CYS1333 4.7 48.3 1.0 OE1 A:GLN1335 5.0 43.4 1.0 CA A:HIS1352 5.0 66.7 1.0

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