Zinc in PDB 3swr: Structure of Human DNMT1 (601-1600) in Complex with Sinefungin

All present enzymatic activity of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin:
2.1.1.37;

The structure of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin, PDB code: 3swr was solved by H.Hashimoto, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.000, 110.770, 201.260, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 27.2

The binding sites of Zinc atom in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin (pdb code 3swr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin, PDB code: 3swr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1601 b:70.5 occ:1.00 SG A:CYS656 2.5 77.4 1.0 SG A:CYS659 2.5 79.0 1.0 SG A:CYS691 2.6 91.5 1.0 O A:CYS653 2.7 87.7 1.0 SG A:CYS653 2.9 87.9 1.0 CB A:CYS656 3.4 78.7 1.0 C A:CYS653 3.7 86.9 1.0 CB A:CYS691 3.8 92.0 1.0 CB A:CYS659 3.8 82.6 1.0 N A:CYS656 3.9 80.7 1.0 N A:CYS653 4.0 87.2 1.0 CA A:CYS653 4.1 87.0 1.0 CB A:CYS653 4.2 87.7 1.0 CA A:CYS656 4.2 79.9 1.0 N A:CYS659 4.4 82.3 1.0 CB A:ASN693 4.4 86.8 1.0 CA A:CYS691 4.4 92.4 1.0 ND2 A:ASN693 4.4 84.7 1.0 N A:VAL655 4.5 83.6 1.0 CA A:CYS659 4.7 83.8 1.0 N A:GLY654 4.7 86.1 1.0 CD A:PRO692 4.8 90.0 1.0 O A:CYS656 4.8 79.7 1.0 C A:CYS656 4.8 80.3 1.0 CG A:ASN693 4.8 86.0 1.0 N A:ASN693 4.9 88.4 1.0 C A:ARG652 4.9 87.9 1.0 CB A:ARG652 4.9 90.1 1.0 C A:VAL655 5.0 81.7 1.0

Zinc binding site 2 out of 4 in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1602 b:0.9 occ:1.00 SG A:CYS686 2.7 0.1 1.0 SG A:CYS664 2.8 0.4 1.0 SG A:CYS670 2.8 0.3 1.0 SG A:CYS667 2.8 0.3 1.0 CB A:CYS670 3.1 0.1 1.0 N A:GLY665 3.5 0.8 1.0 CB A:CYS686 3.8 0.1 1.0 N A:CYS670 3.9 0.8 1.0 N A:CYS664 3.9 0.3 1.0 N A:LYS666 4.1 0.7 1.0 CA A:CYS670 4.1 0.7 1.0 CB A:CYS667 4.1 0.9 1.0 CB A:CYS664 4.2 0.5 1.0 CA A:CYS686 4.2 0.9 1.0 N A:GLN687 4.2 1.0 1.0 N A:CYS667 4.2 0.5 1.0 CA A:GLY665 4.2 0.9 1.0 CA A:CYS664 4.4 0.1 1.0 C A:CYS664 4.4 0.5 1.0 C A:GLY665 4.7 0.7 1.0 CA A:CYS667 4.7 1.0 1.0 C A:CYS686 4.7 0.4 1.0 C A:GLU663 4.7 0.1 1.0 CG A:GLU688 4.8 0.1 1.0 O A:CYS667 4.8 0.9 1.0 CB A:ALA669 4.8 1.0 1.0 C A:LYS666 4.9 0.9 1.0 N A:GLU688 4.9 0.1 1.0 CA A:GLU663 5.0 0.8 1.0

Zinc binding site 3 out of 4 in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:50.5 occ:1.00 NE2 A:HIS793 2.1 43.7 1.0 SG A:CYS893 2.3 48.8 1.0 SG A:CYS896 2.5 53.1 1.0 SG A:CYS820 2.5 48.0 1.0 CB A:CYS820 3.0 49.1 1.0 CE1 A:HIS793 3.1 43.9 1.0 CD2 A:HIS793 3.1 44.9 1.0 CB A:CYS893 3.3 53.2 1.0 N A:CYS896 3.4 52.1 1.0 CB A:CYS896 3.4 53.5 1.0 CA A:CYS896 3.8 53.1 1.0 CB A:SER895 3.9 50.1 1.0 ND1 A:HIS793 4.2 45.8 1.0 CG A:HIS793 4.2 46.9 1.0 OG A:SER895 4.3 46.7 1.0 C A:SER895 4.3 51.6 1.0 CA A:CYS820 4.5 48.9 1.0 CA A:SER895 4.6 50.7 1.0 CA A:CYS893 4.7 54.8 1.0 O A:CYS893 4.9 54.9 1.0 N A:SER895 4.9 51.3 1.0 C A:CYS820 4.9 49.7 1.0 C A:CYS893 5.0 54.7 1.0

Zinc binding site 4 out of 4 in the Structure of Human DNMT1 (601-1600) in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human DNMT1 (601-1600) in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:62.7 occ:1.00 NE2 A:HIS1502 2.3 49.8 1.0 SG A:CYS1478 2.3 65.2 1.0 SG A:CYS1476 2.5 65.0 1.0 SG A:CYS1485 2.6 76.6 1.0 CD2 A:HIS1502 3.2 51.2 1.0 CB A:CYS1476 3.2 61.7 1.0 CE1 A:HIS1502 3.3 50.8 1.0 CB A:CYS1485 3.3 73.2 1.0 CB A:CYS1478 3.4 66.2 1.0 CA A:CYS1485 3.9 72.4 1.0 N A:CYS1478 4.1 66.2 1.0 CG A:HIS1502 4.3 52.7 1.0 ND1 A:HIS1502 4.4 52.0 1.0 CA A:CYS1478 4.4 66.3 1.0 CA A:CYS1476 4.6 61.9 1.0 N A:SER1477 4.7 65.0 1.0 N A:CYS1485 4.8 72.7 1.0 C A:CYS1476 4.8 63.9 1.0 O A:HOH239 4.9 60.3 1.0

H.Hashimoto, X.Cheng. Structure of Human DNMT1 (Residues 600-1600) in Complex with Sinefungin To Be Published.