Zinc in PDB 7r76: Cryo-Em Structure of DNMT5 in Apo State

The binding sites of Zinc atom in the Cryo-Em Structure of DNMT5 in Apo State (pdb code 7r76). 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 in Apo State, PDB code: 7r76:
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 in Apo State


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 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:94.4 occ:1.00 SG A:CYS840 2.3 36.5 1.0 SG A:CYS817 2.4 27.9 1.0 CB A:CYS843 2.8 39.3 1.0 SG A:CYS843 3.2 39.3 1.0 CB A:CYS819 3.5 30.0 1.0 CB A:CYS840 3.8 36.5 1.0 O A:CYS843 3.8 39.3 1.0 CB A:CYS817 3.8 27.9 1.0 CA A:CYS843 3.9 39.3 1.0 N A:CYS843 4.0 39.3 1.0 C A:CYS843 4.3 39.3 1.0 N A:CYS840 4.4 36.5 1.0 N A:CYS819 4.5 29.7 1.0 SG A:CYS819 4.5 30.0 1.0 CA A:CYS840 4.6 36.5 1.0 CA A:CYS819 4.6 29.7 1.0 O A:ASP625 4.9 31.5 1.0 O A:CYS840 5.0 36.5 1.0 CA A:CYS817 5.0 27.9 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of DNMT5 in Apo State


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 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:76.5 occ:1.00 ND1 A:HIS1348 2.1 40.5 1.0 SG A:CYS1271 2.3 56.0 1.0 SG A:CYS1200 2.3 49.8 1.0 SG A:CYS1274 2.3 44.5 1.0 CB A:CYS1271 2.6 56.0 1.0 CG A:HIS1348 3.0 40.5 1.0 CE1 A:HIS1348 3.1 40.5 1.0 CB A:CYS1200 3.1 49.8 1.0 CB A:HIS1348 3.3 40.5 1.0 CB A:CYS1274 3.4 44.5 1.0 CA A:CYS1271 4.0 56.0 1.0 N A:CYS1274 4.1 44.5 1.0 CD2 A:HIS1348 4.1 40.5 1.0 NE2 A:HIS1348 4.1 40.5 1.0 CA A:CYS1274 4.4 44.5 1.0 CA A:CYS1200 4.5 49.8 1.0 O A:VAL1344 4.6 38.6 1.0 CA A:SER1345 4.7 36.7 1.0 N A:CYS1271 4.8 56.0 1.0 OG A:SER1345 4.8 36.7 1.0 CA A:HIS1348 4.8 40.5 1.0 C A:CYS1271 4.9 56.0 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of DNMT5 in Apo State


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 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2403 b:39.2 occ:1.00 CD2 A:HIS849 2.2 28.2 1.0 SG A:CYS835 2.3 29.7 1.0 SG A:CYS832 2.3 30.7 1.0 SG A:CYS1065 2.3 33.0 1.0 CG A:HIS849 3.1 28.2 1.0 NE2 A:HIS849 3.2 28.2 1.0 O A:GLN833 3.4 32.2 1.0 CB A:CYS1065 3.5 33.0 1.0 CB A:CYS832 3.6 30.7 1.0 CB A:HIS849 3.6 28.2 1.0 CB A:CYS835 3.6 29.7 1.0 O A:CYS835 4.2 29.7 1.0 ND1 A:HIS849 4.3 28.2 1.0 CA A:CYS1065 4.3 33.0 1.0 CE1 A:HIS849 4.3 28.2 1.0 N A:CYS835 4.3 29.7 1.0 N A:VAL850 4.4 31.2 1.0 CA A:CYS835 4.4 29.7 1.0 C A:GLN833 4.5 32.2 1.0 N A:GLN833 4.6 32.2 1.0 CG2 A:VAL850 4.6 31.2 1.0 CA A:HIS849 4.7 28.2 1.0 C A:CYS835 4.7 29.7 1.0 C A:HIS849 4.7 28.2 1.0 N A:CYS1065 4.8 33.0 1.0 CA A:CYS832 4.9 30.7 1.0 C A:GLU834 4.9 32.6 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of DNMT5 in Apo State


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 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2404 b:157.4 occ:1.00 CB A:HIS2083 2.9 122.3 1.0 CG A:HIS2083 3.5 122.3 1.0 SG A:CYS2104 3.7 118.5 1.0 CD2 A:HIS2083 3.8 122.3 1.0 O A:CYS2081 3.8 124.5 1.0 SG A:CYS2081 3.9 124.5 1.0 CA A:HIS2083 4.1 122.3 1.0 N A:HIS2083 4.1 122.3 1.0 CE A:LYS2106 4.5 122.2 1.0 C A:GLY2082 4.7 121.6 1.0 C A:CYS2081 4.7 124.5 1.0 ND1 A:HIS2083 4.7 122.3 1.0 CB A:CYS2081 4.8 124.5 1.0 CB A:CYS2104 4.9 118.5 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of DNMT5 in Apo State


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 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2405 b:140.6 occ:1.00 CG A:HIS2101 1.8 117.8 1.0 CB A:HIS2101 2.0 117.8 1.0 ND1 A:HIS2101 2.3 117.8 1.0 SG A:CYS2099 2.3 109.2 1.0 CD2 A:HIS2101 2.5 117.8 1.0 N A:HIS2101 3.0 117.8 1.0 CA A:HIS2101 3.0 117.8 1.0 CE1 A:HIS2101 3.1 117.8 1.0 CD2 A:LEU2096 3.1 105.5 1.0 NE2 A:HIS2101 3.2 117.8 1.0 O A:CYS2099 3.3 109.2 1.0 C A:CYS2099 3.3 109.2 1.0 CB A:CYS2099 3.4 109.2 1.0 CB A:LEU2096 3.5 105.5 1.0 C A:GLY2100 3.5 113.9 1.0 CA A:CYS2099 3.7 109.2 1.0 N A:GLY2100 3.8 113.9 1.0 N A:CYS2099 3.9 109.2 1.0 CG A:LEU2096 3.9 105.5 1.0 O A:GLY2100 4.1 113.9 1.0 CA A:GLY2100 4.1 113.9 1.0 C A:HIS2101 4.2 117.8 1.0 CB A:CYS2123 4.5 114.6 1.0 O A:HIS2101 4.5 117.8 1.0 CA A:LEU2096 4.8 105.5 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