Zinc in PDB 8eij: Cryo-Em Structure of Human DNMT3B Homo-Trimer

All present enzymatic activity of Cryo-Em Structure of Human DNMT3B Homo-Trimer:
2.1.1.37;

The binding sites of Zinc atom in the Cryo-Em Structure of Human DNMT3B Homo-Trimer (pdb code 8eij). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Human DNMT3B Homo-Trimer, PDB code: 8eij:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


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 Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:208.9 occ:1.00 CB A:CYS438 1.8 186.5 1.0 CB A:CYS458 2.2 168.1 1.0 SG A:CYS435 2.3 179.0 1.0 SG A:CYS455 2.3 177.9 1.0 SG A:CYS458 2.3 170.7 1.0 SG A:CYS438 2.3 187.3 1.0 CA A:CYS438 3.3 185.2 1.0 CB A:CYS455 3.6 175.2 1.0 CA A:CYS458 3.7 165.9 1.0 CB A:CYS435 3.7 181.8 1.0 N A:CYS438 3.9 185.0 1.0 N A:CYS455 4.0 174.2 1.0 N A:CYS458 4.2 165.2 1.0 C A:CYS438 4.2 186.2 1.0 CA A:CYS455 4.3 175.0 1.0 C A:SER437 4.6 180.4 1.0 NH2 A:ARG440 4.6 188.4 1.0 OG A:SER437 4.7 181.7 1.0 C A:CYS458 4.7 165.2 1.0 O A:CYS438 4.8 186.7 1.0 O A:CYS455 4.8 174.8 1.0 N A:GLY439 4.9 189.2 1.0 C A:CYS455 4.9 174.5 1.0 O A:SER437 5.0 181.0 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


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 Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:200.8 occ:1.00 CB A:CYS500 2.1 184.1 1.0 SG A:CYS503 2.3 188.7 1.0 SG A:CYS481 2.3 178.8 1.0 SG A:CYS500 2.3 186.5 1.0 SG A:CYS478 2.3 175.2 1.0 O A:GLU483 3.3 176.3 1.0 CB A:CYS478 3.3 172.4 1.0 CB A:CYS481 3.3 177.3 1.0 CA A:CYS500 3.6 184.3 1.0 CB A:CYS503 3.7 189.3 1.0 N A:CYS481 3.7 176.4 1.0 CA A:CYS481 4.0 176.5 1.0 N A:CYS500 4.1 183.6 1.0 C A:GLU483 4.4 176.3 1.0 C A:CYS481 4.6 175.9 1.0 C A:CYS500 4.6 185.1 1.0 N A:GLU483 4.6 176.0 1.0 N A:CYS482 4.7 174.4 1.0 CB A:VAL480 4.7 170.0 1.0 N A:CYS503 4.8 188.9 1.0 CA A:CYS478 4.8 170.8 1.0 CA A:CYS503 4.8 189.3 1.0 C A:VAL480 4.9 169.7 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


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 Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:186.1 occ:1.00 SG A:CYS527 2.3 186.7 1.0 SG A:CYS495 2.3 179.2 1.0 SG A:CYS524 2.3 185.2 1.0 SG A:CYS490 2.3 184.0 1.0 CB A:CYS495 3.3 179.2 1.0 CB A:CYS490 3.4 183.7 1.0 CB A:CYS524 3.6 185.9 1.0 CB A:CYS527 3.8 186.4 1.0 N A:CYS524 4.0 186.8 1.0 CB A:ASN492 4.1 187.5 1.0 CA A:CYS524 4.3 186.3 1.0 N A:CYS527 4.6 186.1 1.0 CG A:ARG497 4.6 161.7 1.0 CA A:CYS495 4.7 178.9 1.0 CA A:CYS527 4.7 186.0 1.0 CA A:CYS490 4.8 184.0 1.0 C A:CYS524 4.9 186.1 1.0 C A:CYS495 4.9 178.2 1.0 CG A:ASN492 4.9 187.0 1.0 O A:CYS524 5.0 186.7 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


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 Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:165.2 occ:1.00 SG B:CYS458 2.3 135.8 1.0 SG B:CYS438 2.3 153.6 1.0 SG B:CYS455 2.3 139.4 1.0 SG B:CYS435 2.3 149.1 1.0 CB B:CYS458 3.1 131.2 1.0 CB B:CYS435 3.2 144.8 1.0 CB B:CYS438 3.6 151.3 1.0 CB B:CYS455 3.6 135.6 1.0 N B:CYS455 4.0 133.7 1.0 N B:CYS438 4.2 150.9 1.0 CA B:CYS458 4.3 129.7 1.0 CA B:CYS455 4.3 135.2 1.0 CA B:CYS438 4.4 151.6 1.0 N B:CYS458 4.4 131.0 1.0 CA B:CYS435 4.7 145.4 1.0 CB B:ARG440 4.7 158.9 1.0 CG2 B:THR457 4.9 132.4 1.0 N B:ARG440 5.0 159.1 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


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 Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:200.3 occ:1.00 SG B:CYS481 2.3 161.0 1.0 SG B:CYS503 2.3 155.4 1.0 SG B:CYS478 2.3 146.4 1.0 SG B:CYS500 2.3 161.2 1.0 CB B:CYS481 2.9 156.7 1.0 CB B:CYS503 3.2 154.2 1.0 CB B:CYS500 3.2 159.6 1.0 N B:CYS481 3.4 154.2 1.0 CA B:CYS481 3.6 155.7 1.0 CB B:CYS478 3.8 145.8 1.0 N B:CYS503 4.2 156.0 1.0 CA B:CYS503 4.3 155.6 1.0 C B:CYS481 4.3 155.8 1.0 N B:CYS482 4.3 156.5 1.0 CA B:CYS500 4.3 161.7 1.0 N B:CYS500 4.3 161.2 1.0 C B:VAL480 4.6 140.0 1.0 O B:GLU483 4.6 165.3 1.0 CB B:VAL480 4.9 138.8 1.0 N B:VAL480 4.9 140.1 1.0 N B:GLU483 4.9 165.9 1.0 C B:CYS500 5.0 162.8 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of Human DNMT3B Homo-Trimer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human DNMT3B Homo-Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn904 b:211.3 occ:1.00 SG B:CYS524 2.3 153.7 1.0 SG B:CYS527 2.3 159.2 1.0 SG B:CYS495 2.3 159.4 1.0 SG B:CYS490 2.3 154.0 1.0 CB B:CYS495 3.3 156.3 1.0 CB B:CYS524 3.3 155.5 1.0 CB B:CYS527 3.4 153.0 1.0 CB B:CYS490 3.5 152.9 1.0 N B:CYS524 3.9 158.3 1.0 CA B:CYS524 4.1 157.2 1.0 N B:CYS527 4.2 151.7 1.0 CA B:CYS527 4.3 152.5 1.0 O B:ARG497 4.6 139.3 1.0 CA B:CYS495 4.6 156.0 1.0 O B:CYS524 4.6 157.1 1.0 C B:CYS524 4.7 156.6 1.0 C B:CYS495 4.8 156.8 1.0 CA B:CYS490 4.9 150.5 1.0 OG B:SER523 4.9 160.1 1.0 CB B:ASN492 5.0 169.0 1.0

J.W.Lu, J.K.Song. Cryo-Em Structure of Human DNMT3B Homo-Trimer To Be Published.