Zinc in PDB 8yv8: Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence.

The binding sites of Zinc atom in the Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence. (pdb code 8yv8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence., PDB code: 8yv8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence. within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn401 b:207.5 occ:1.00 SG K:CYS297 2.2 187.6 1.0 SG K:CYS300 2.3 183.2 1.0 SG K:CYS273 2.3 158.4 1.0 SG K:CYS270 2.3 174.4 1.0 CB K:CYS273 2.6 161.1 1.0 CB K:CYS270 2.9 171.1 1.0 N K:CYS273 3.1 162.6 1.0 CB K:CYS300 3.2 184.5 1.0 CA K:CYS273 3.4 161.2 1.0 CB K:CYS297 3.7 185.9 1.0 C K:GLN272 4.3 172.6 1.0 CA K:CYS270 4.3 170.5 1.0 N K:CYS297 4.3 185.6 1.0 CB K:GLN272 4.4 172.6 1.0 CA K:CYS300 4.4 185.2 1.0 C K:CYS273 4.4 159.1 1.0 N K:CYS300 4.5 185.1 1.0 CA K:CYS297 4.5 185.3 1.0 N K:GLN272 4.6 173.1 1.0 N K:ARG274 4.6 138.8 1.0 CA K:GLN272 4.6 172.3 1.0 O K:CYS297 4.7 185.7 1.0 C K:CYS270 4.7 170.5 1.0 C K:CYS297 4.9 185.9 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence. within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn402 b:241.5 occ:1.00 SG K:CYS320 2.3 207.5 1.0 SG K:CYS284 2.3 216.1 1.0 SG K:CYS289 2.3 209.4 1.0 SG K:CYS323 2.3 209.7 1.0 NH1 K:ARG293 2.5 200.8 1.0 CZ K:ARG293 2.6 201.0 1.0 CB K:CYS284 3.0 212.7 1.0 NH2 K:ARG293 3.1 200.6 1.0 NE K:ARG293 3.1 200.6 1.0 CB K:CYS289 3.2 209.3 1.0 CD K:ARG293 3.7 200.2 1.0 CB K:CYS320 3.7 205.9 1.0 CA K:GLY294 4.0 202.6 1.0 CB K:CYS323 4.1 206.9 1.0 CA K:CYS289 4.3 209.2 1.0 N K:GLY294 4.3 202.7 1.0 CA K:CYS284 4.5 212.8 1.0 N K:CYS323 4.6 206.4 1.0 N K:CYS320 4.6 206.1 1.0 CG K:ARG293 4.7 200.1 1.0 CA K:CYS320 4.7 206.2 1.0 CA K:CYS323 4.7 206.9 1.0 C K:ARG293 4.8 200.5 1.0 CB K:ASN286 4.9 210.4 1.0 O K:ARG293 4.9 200.8 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of CDCA7 Bound to Nucleosome Including Hemimethylated Cpg Site in WIDOM601 Positioning Sequence. within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn403 b:213.1 occ:1.00 NE2 K:HIS271 2.0 183.0 1.0 SG K:CYS329 2.2 183.5 1.0 SG K:CYS332 2.3 179.2 1.0 SG K:CYS327 2.4 194.7 1.0 CB K:CYS332 2.8 177.6 1.0 CE1 K:HIS271 3.0 181.7 1.0 CD2 K:HIS271 3.0 183.3 1.0 CB K:CYS329 3.1 180.9 1.0 CB K:CYS327 3.7 196.0 1.0 N K:CYS332 3.8 177.9 1.0 CA K:CYS332 3.9 176.9 1.0 ND1 K:HIS271 4.1 182.6 1.0 CA K:CYS329 4.1 180.1 1.0 N K:CYS329 4.1 180.6 1.0 CG K:HIS271 4.2 183.5 1.0 CG K:PRO322 4.3 199.1 1.0 O K:CYS329 4.6 180.6 1.0 C K:CYS329 4.6 179.4 1.0 CD2 K:PHE331 5.0 173.7 1.0 CA K:CYS327 5.0 196.4 1.0 C K:PHE331 5.0 173.5 1.0

I.Wassing, A.Nishiyama, K.Arita, H.Funabiki. CDCA7 Is A Hemimethylated Dna Adaptor For the Nucleosome Remodeler Hells To Be Published.