Zinc in PDB 7r78: Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah

The structure of Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah (pdb code 7r78). 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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah, PDB code: 7r78:
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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah


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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:78.0 occ:1.00 SG A:CYS819 2.3 46.0 1.0 SG A:CYS840 2.3 45.7 1.0 SG A:CYS817 2.3 45.0 1.0 CB A:CYS840 2.6 45.7 1.0 CB A:CYS819 2.7 46.0 1.0 CB A:CYS817 3.3 45.0 1.0 SG A:CYS843 3.7 45.4 1.0 CA A:CYS840 3.8 45.7 1.0 CA A:CYS819 3.9 46.0 1.0 N A:CYS840 3.9 45.7 1.0 N A:CYS819 3.9 46.0 1.0 O A:SER842 4.2 45.3 1.0 CA A:CYS817 4.7 45.0 1.0 C A:CYS840 4.9 45.7 1.0 C A:CYS819 4.9 46.0 1.0 C A:CYS817 5.0 45.0 1.0 CB A:ALA826 5.0 43.7 1.0

Zinc binding site 2 out of 5 in the Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah


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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2403 b:64.5 occ:1.00 ND1 A:HIS849 2.0 38.5 1.0 SG A:CYS1065 2.3 39.3 1.0 SG A:CYS832 2.3 43.8 1.0 CB A:CYS835 2.3 42.4 1.0 CG A:HIS849 2.9 38.5 1.0 CE1 A:HIS849 2.9 38.5 1.0 SG A:CYS835 3.0 42.4 1.0 CB A:CYS832 3.1 43.8 1.0 CB A:HIS849 3.2 38.5 1.0 CB A:CYS1065 3.4 39.3 1.0 CA A:CYS835 3.7 42.4 1.0 NE2 A:HIS849 4.0 38.5 1.0 CD2 A:HIS849 4.0 38.5 1.0 N A:CYS835 4.1 42.4 1.0 CA A:CYS1065 4.3 39.3 1.0 CA A:HIS849 4.4 38.5 1.0 C A:CYS835 4.4 42.4 1.0 CA A:CYS832 4.5 43.8 1.0 CB A:TYR837 4.7 35.8 1.0 N A:SER836 4.8 39.0 1.0 N A:VAL850 4.8 42.2 1.0 O A:GLN833 4.9 45.1 1.0 C A:CYS832 5.0 43.8 1.0 C A:GLU834 5.0 45.8 1.0

Zinc binding site 3 out of 5 in the Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah


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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2404 b:70.7 occ:1.00 SG A:CYS1200 2.2 61.4 1.0 SG A:CYS1271 2.3 61.5 1.0 CD2 A:HIS1348 2.4 42.4 1.0 SG A:CYS1274 2.4 56.8 1.0 CB A:CYS1271 2.5 61.5 1.0 CG A:HIS1348 3.1 42.4 1.0 CB A:CYS1274 3.2 56.8 1.0 CB A:HIS1348 3.3 42.4 1.0 NE2 A:HIS1348 3.5 42.4 1.0 CB A:CYS1200 3.7 61.4 1.0 CA A:CYS1271 3.9 61.5 1.0 ND1 A:HIS1348 4.2 42.4 1.0 O A:CYS1271 4.3 61.5 1.0 C A:CYS1271 4.3 61.5 1.0 CE1 A:HIS1348 4.4 42.4 1.0 OE2 A:GLU1198 4.5 73.8 1.0 CA A:CYS1274 4.6 56.8 1.0 O A:VAL1344 4.6 43.4 1.0 O A:GLU1272 4.6 62.0 1.0 N A:CYS1271 4.7 61.5 1.0 CA A:SER1345 4.8 41.3 1.0 N A:CYS1274 4.8 56.8 1.0 CA A:HIS1348 4.9 42.4 1.0 CA A:CYS1200 4.9 61.4 1.0

Zinc binding site 4 out of 5 in the Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah


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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2405 b:138.3 occ:1.00 N A:CYS2104 2.2 85.7 1.0 SG A:CYS2081 2.3 97.0 1.0 CB A:CYS2081 2.5 97.0 1.0 CB A:CYS2104 3.0 85.7 1.0 CB A:ALA2103 3.1 83.7 1.0 CA A:CYS2104 3.1 85.7 1.0 C A:ALA2103 3.2 83.7 1.0 CA A:ALA2103 3.2 83.7 1.0 SG A:CYS2107 3.6 81.8 1.0 CB A:CYS2107 3.7 81.8 1.0 O A:CYS2104 3.9 85.7 1.0 CA A:CYS2081 4.0 97.0 1.0 C A:CYS2104 4.0 85.7 1.0 OG A:SER2078 4.1 89.6 1.0 O A:ALA2103 4.3 83.7 1.0 CE1 A:HIS2083 4.3 92.5 1.0 C A:CYS2081 4.5 97.0 1.0 O A:HIS2083 4.6 92.5 1.0 NE2 A:HIS2083 4.7 92.5 1.0 N A:ALA2103 4.7 83.7 1.0 ND1 A:HIS2083 4.8 92.5 1.0 SG A:CYS2104 4.8 85.7 1.0 OG A:SER2079 4.8 87.3 1.0 N A:CYS2081 4.8 97.0 1.0 O A:CYS2081 4.9 97.0 1.0 CG1 A:VAL2118 4.9 77.7 1.0 CA A:CYS2107 4.9 81.8 1.0

Zinc binding site 5 out of 5 in the Cryo-Em Structure of DNMT5 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah


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 Quaternary Complex with Hemimethylated Dna, Amp-Pnp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2406 b:93.3 occ:1.00 CD2 A:HIS2101 2.2 67.1 1.0 SG A:CYS2123 2.3 69.7 1.0 SG A:CYS2117 2.3 76.5 1.0 SG A:CYS2099 2.4 68.2 1.0 CB A:CYS2099 2.6 68.2 1.0 NE2 A:HIS2101 3.0 67.1 1.0 CG A:HIS2101 3.1 67.1 1.0 CB A:CYS2123 3.3 69.7 1.0 CB A:CYS2117 3.6 76.5 1.0 CB A:HIS2101 3.7 67.1 1.0 CA A:CYS2099 4.0 68.2 1.0 CE1 A:HIS2101 4.1 67.1 1.0 ND1 A:HIS2101 4.2 67.1 1.0 C A:CYS2099 4.4 68.2 1.0 O A:CYS2099 4.5 68.2 1.0 N A:HIS2101 4.6 67.1 1.0 CA A:CYS2123 4.7 69.7 1.0 CA A:HIS2101 4.8 67.1 1.0 CA A:CYS2117 4.9 76.5 1.0 CB A:ALA2125 5.0 57.9 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