Zinc in PDB 5ikf: Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1

The structure of Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1, PDB code: 5ikf was solved by C.Brugger, T.Schalch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.22 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.680, 52.850, 81.970, 90.00, 115.63, 90.00
R / Rfree (%)	19.9 / 24.7

The structure of Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1 (pdb code 5ikf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1, PDB code: 5ikf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1


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 the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:64.4 occ:1.00 NE2 A:HIS1318 2.1 54.5 1.0 SG A:CYS1323 2.3 50.6 1.0 SG A:CYS1314 2.3 49.5 1.0 SG A:CYS1311 2.3 49.8 1.0 HB2 A:CYS1323 2.9 52.7 1.0 CD2 A:HIS1318 2.9 54.1 1.0 HB3 A:CYS1311 3.0 74.5 1.0 CE1 A:HIS1318 3.0 56.5 1.0 CB A:CYS1323 3.1 43.9 1.0 HA A:CYS1323 3.1 57.5 1.0 HD2 A:PRO1324 3.1 57.0 1.0 HD2 A:HIS1318 3.1 64.9 1.0 CB A:CYS1311 3.1 62.0 1.0 HD3 A:PRO1324 3.3 57.0 1.0 HE1 A:HIS1318 3.3 67.8 1.0 HB2 A:CYS1311 3.3 74.5 1.0 H A:CYS1314 3.3 57.6 1.0 HB3 A:CYS1314 3.3 49.2 1.0 HB2 B:SER421 3.4 86.9 1.0 HG B:SER421 3.5 93.6 1.0 CB A:CYS1314 3.5 41.0 1.0 OG B:SER421 3.5 78.0 1.0 CA A:CYS1323 3.6 47.9 1.0 CD A:PRO1324 3.6 47.5 1.0 HB2 A:CYS1313 3.9 66.8 1.0 CB B:SER421 3.9 72.4 1.0 HB3 A:CYS1323 3.9 52.7 1.0 N A:CYS1314 4.0 48.0 1.0 CG A:HIS1318 4.1 54.6 1.0 ND1 A:HIS1318 4.1 53.2 1.0 HB2 A:CYS1314 4.2 49.2 1.0 HB3 B:SER421 4.3 86.9 1.0 CA A:CYS1314 4.4 51.4 1.0 N A:PRO1324 4.4 54.2 1.0 C A:CYS1323 4.4 51.5 1.0 H A:LEU1325 4.5 64.3 1.0 H A:ILE1316 4.6 65.9 1.0 HD12 A:LEU1325 4.6 57.1 1.0 H A:CYS1313 4.6 77.5 1.0 CA A:CYS1311 4.6 53.8 1.0 HB A:ILE1316 4.6 67.2 1.0 CB A:CYS1313 4.7 55.7 1.0 N A:CYS1323 4.8 50.0 1.0 HD1 A:HIS1318 4.8 63.9 1.0 O A:ILE1316 4.9 64.0 1.0 CG A:PRO1324 4.9 41.0 1.0 H A:GLY1315 4.9 69.9 1.0 HB3 A:CYS1313 4.9 66.8 1.0 HG2 A:PRO1324 4.9 49.2 1.0 O A:CYS1311 4.9 60.8 1.0 C A:CYS1311 5.0 55.6 1.0 HB2 A:LEU1325 5.0 68.0 1.0 HA A:CYS1311 5.0 64.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1


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 the C-Terminal Domain of the MIT1 Nucleosome Remodeler in Complex with CLR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:48.3 occ:1.00 NE2 A:HIS1340 2.0 46.7 1.0 SG A:CYS1347 2.3 52.9 1.0 SG A:CYS1336 2.4 46.1 1.0 SG A:CYS1333 2.4 44.8 1.0 HB3 A:CYS1333 2.6 49.2 1.0 CB A:CYS1333 2.9 41.0 1.0 CD2 A:HIS1340 2.9 54.0 1.0 HB2 A:CYS1347 3.0 53.6 1.0 HD2 A:HIS1340 3.0 64.8 1.0 HA A:CYS1347 3.1 55.7 1.0 CE1 A:HIS1340 3.1 55.4 1.0 CB A:CYS1347 3.1 44.6 1.0 HB2 A:CYS1333 3.2 49.2 1.0 HB2 A:LEU1335 3.4 59.6 1.0 HE1 A:HIS1340 3.4 66.5 1.0 H A:CYS1336 3.4 59.1 1.0 HD2 A:PRO1348 3.4 81.4 1.0 HB3 A:CYS1336 3.4 63.3 1.0 CB A:CYS1336 3.6 52.8 1.0 CA A:CYS1347 3.6 46.4 1.0 N A:CYS1336 3.9 49.2 1.0 HB3 A:CYS1347 4.0 53.6 1.0 HG1 A:THR1338 4.1 53.0 1.0 CG A:HIS1340 4.1 44.9 1.0 HD12 A:LEU1335 4.1 49.2 1.0 CD A:PRO1348 4.2 67.9 1.0 ND1 A:HIS1340 4.2 41.0 1.0 HD3 A:PRO1348 4.2 81.4 1.0 H A:LEU1335 4.3 67.8 1.0 HB3 B:SER371 4.3 53.5 1.0 HB2 A:CYS1336 4.3 63.3 1.0 H A:MET1349 4.3 91.6 1.0 CA A:CYS1333 4.3 41.0 1.0 CB A:LEU1335 4.3 49.7 1.0 CA A:CYS1336 4.4 47.2 1.0 C A:CYS1347 4.5 55.1 1.0 N A:PRO1348 4.6 54.6 1.0 O A:CYS1333 4.6 60.3 1.0 HG B:SER371 4.6 69.9 1.0 C A:CYS1333 4.7 44.5 1.0 HB3 A:MET1349 4.7 76.1 1.0 H A:THR1338 4.7 49.2 1.0 N A:CYS1347 4.7 45.2 1.0 H A:CYS1333 4.7 60.4 1.0 C A:LEU1335 4.7 48.4 1.0 HG A:LEU1335 4.8 49.2 1.0 O A:THR1338 4.8 51.4 1.0 OG1 A:THR1338 4.8 44.2 1.0 HB3 A:LEU1335 4.8 59.6 1.0 N A:LEU1335 4.8 56.5 1.0 HB2 A:MET1349 4.9 76.1 1.0 HA A:CYS1333 4.9 49.2 1.0 CA A:LEU1335 4.9 47.3 1.0 CD1 A:LEU1335 5.0 41.0 1.0 CG A:LEU1335 5.0 41.0 1.0 HD1 A:HIS1340 5.0 49.2 1.0

G.Job, C.Brugger, T.Xu, B.R.Lowe, Y.Pfister, C.Qu, S.Shanker, J.I.Banos Sanz, J.F.Partridge, T.Schalch. Shrec Silences Heterochromatin Via Distinct Remodeling and Deacetylation Modules. Mol.Cell V. 62 207 2016.
ISSN: ISSN 1097-2765
PubMed: 27105116
DOI: 10.1016/J.MOLCEL.2016.03.016