Zinc in PDB 7r77: Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna

The binding sites of Zinc atom in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna (pdb code 7r77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna, PDB code: 7r77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna


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 DNMT5 Binary Complex with Hemimethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:76.8 occ:1.00 SG A:CYS817 2.2 26.8 1.0 SG A:CYS819 2.3 30.2 1.0 SG A:CYS840 2.4 27.5 1.0 SG A:CYS843 2.7 30.7 1.0 CB A:CYS819 3.2 30.2 1.0 CB A:CYS817 3.4 26.8 1.0 CB A:CYS843 3.6 30.7 1.0 CB A:CYS840 3.7 27.5 1.0 N A:CYS819 4.0 30.2 1.0 CA A:CYS819 4.2 30.2 1.0 N A:CYS840 4.4 27.5 1.0 N A:CYS843 4.5 30.7 1.0 CA A:CYS843 4.7 30.7 1.0 CA A:CYS840 4.7 27.5 1.0 CA A:CYS817 4.7 26.8 1.0 N A:GLN818 4.8 27.3 1.0 C A:CYS817 4.9 26.8 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna


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 DNMT5 Binary Complex with Hemimethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:87.7 occ:1.00 ND1 A:HIS1348 2.0 43.5 1.0 SG A:CYS1271 2.2 70.3 1.0 SG A:CYS1200 2.2 59.8 1.0 SG A:CYS1274 2.4 53.1 1.0 CB A:CYS1271 2.8 70.3 1.0 CG A:HIS1348 2.9 43.5 1.0 CE1 A:HIS1348 3.0 43.5 1.0 CB A:HIS1348 3.1 43.5 1.0 CB A:CYS1274 3.2 53.1 1.0 CB A:CYS1200 3.5 59.8 1.0 CD2 A:HIS1348 4.0 43.5 1.0 NE2 A:HIS1348 4.1 43.5 1.0 O A:VAL1344 4.2 39.4 1.0 N A:CYS1274 4.2 53.1 1.0 CA A:CYS1271 4.3 70.3 1.0 CA A:CYS1274 4.4 53.1 1.0 CA A:SER1345 4.5 37.1 1.0 CA A:HIS1348 4.6 43.5 1.0 CG1 A:VAL1344 4.6 39.4 1.0 C A:VAL1344 4.7 39.4 1.0 CA A:CYS1200 4.7 59.8 1.0 N A:SER1345 4.8 37.1 1.0 OG A:SER1345 5.0 37.1 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna


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 DNMT5 Binary Complex with Hemimethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2403 b:37.9 occ:1.00 SG A:CYS832 2.2 28.8 1.0 SG A:CYS835 2.4 29.4 1.0 ND1 A:HIS849 2.5 27.7 1.0 SG A:CYS1065 2.6 30.3 1.0 O A:GLU834 2.9 31.4 1.0 CB A:CYS832 3.1 28.8 1.0 CG A:HIS849 3.2 27.7 1.0 CB A:HIS849 3.3 27.7 1.0 O A:CYS835 3.3 29.4 1.0 CB A:CYS1065 3.4 30.3 1.0 CE1 A:HIS849 3.5 27.7 1.0 CB A:CYS835 4.0 29.4 1.0 C A:GLU834 4.1 31.4 1.0 C A:CYS835 4.2 29.4 1.0 CA A:CYS1065 4.2 30.3 1.0 CA A:HIS849 4.3 27.7 1.0 CD2 A:HIS849 4.4 27.7 1.0 CA A:CYS832 4.5 28.8 1.0 NE2 A:HIS849 4.5 27.7 1.0 CA A:CYS835 4.5 29.4 1.0 CB A:TYR837 4.7 25.4 1.0 N A:CYS835 4.8 29.4 1.0 N A:VAL850 4.9 25.4 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2404 b:113.7 occ:1.00 SG A:CYS2081 2.3 75.5 1.0 ND1 A:HIS2083 2.3 80.7 1.0 SG A:CYS2107 2.3 56.6 1.0 CG A:HIS2083 2.6 80.7 1.0 CB A:HIS2083 2.9 80.7 1.0 CB A:CYS2107 3.0 56.6 1.0 CE1 A:HIS2083 3.2 80.7 1.0 CB A:CYS2081 3.3 75.5 1.0 CB A:CYS2104 3.3 58.7 1.0 CD2 A:HIS2083 3.6 80.7 1.0 SG A:CYS2104 3.7 58.7 1.0 NE2 A:HIS2083 3.8 80.7 1.0 N A:HIS2083 3.8 80.7 1.0 CA A:HIS2083 4.0 80.7 1.0 CA A:CYS2107 4.4 56.6 1.0 CA A:CYS2081 4.6 75.5 1.0 CA A:CYS2104 4.7 58.7 1.0 N A:CYS2107 4.7 56.6 1.0 C A:GLY2082 4.8 76.7 1.0 O A:HIS2083 4.8 80.7 1.0 C A:CYS2081 4.8 75.5 1.0 C A:HIS2083 4.9 80.7 1.0 N A:GLY2082 4.9 76.7 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of DNMT5 Binary Complex with Hemimethylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2405 b:103.5 occ:1.00 SG A:CYS2123 2.2 54.1 1.0 SG A:CYS2099 2.2 44.1 1.0 CD2 A:HIS2101 2.4 48.1 1.0 CB A:CYS2099 2.5 44.1 1.0 NE2 A:HIS2101 3.0 48.1 1.0 CB A:CYS2123 3.2 54.1 1.0 SG A:CYS2117 3.4 47.8 1.0 CG A:HIS2101 3.6 48.1 1.0 CB A:ALA2125 3.8 39.5 1.0 CB A:CYS2117 3.8 47.8 1.0 CA A:CYS2099 4.0 44.1 1.0 CE1 A:HIS2101 4.3 48.1 1.0 CB A:HIS2101 4.4 48.1 1.0 ND1 A:HIS2101 4.6 48.1 1.0 CA A:CYS2123 4.6 54.1 1.0 N A:CYS2099 4.7 44.1 1.0 N A:GLY2100 4.8 42.6 1.0 CD1 A:LEU2096 4.8 36.2 1.0 NH1 A:ARG2057 4.8 41.8 1.0 C A:CYS2099 4.9 44.1 1.0 N A:HIS2101 4.9 48.1 1.0 C A:CYS2123 5.0 54.1 1.0

J.Wang, S.Catania, C.Wang, M.J.De La Cruz, B.Rao, H.D.Madhani, D.J.Patel. Structural Insights Into DNMT5-Mediated Atp-Dependent High-Fidelity Epigenome Maintenance. Mol.Cell V. 82 1186 2022.
ISSN: ISSN 1097-2765
PubMed: 35202575
DOI: 10.1016/J.MOLCEL.2022.01.028