Zinc in PDB 3pta: Crystal Structure of Human DNMT1(646-1600) in Complex with Dna

All present enzymatic activity of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna:
2.1.1.37;

The structure of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna, PDB code: 3pta was solved by J.Song, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.800, 87.900, 113.900, 90.00, 97.20, 90.00
R / Rfree (%)	25.7 / 29.1

The binding sites of Zinc atom in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna (pdb code 3pta). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna, PDB code: 3pta:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:0.2 occ:0.78 NE2 A:HIS1502 2.2 0.6 1.0 SG A:CYS1476 2.4 0.3 1.0 SG A:CYS1478 2.5 0.8 1.0 CE1 A:HIS1502 2.9 0.6 1.0 SG A:CYS1485 2.9 0.2 1.0 CB A:CYS1476 3.1 0.3 1.0 CD2 A:HIS1502 3.2 0.6 1.0 CB A:CYS1485 3.3 0.2 1.0 CB A:CYS1478 3.6 0.8 1.0 CA A:CYS1485 3.6 0.6 1.0 ND1 A:HIS1502 3.9 0.6 1.0 CG A:HIS1502 4.1 0.6 1.0 N A:CYS1485 4.5 0.6 1.0 CA A:CYS1476 4.6 0.3 1.0 N A:CYS1478 4.6 0.7 1.0 CA A:CYS1478 4.7 0.7 1.0 CH2 A:TRP1498 4.8 0.7 1.0 C A:CYS1485 4.8 0.6 1.0 N A:ASP1486 4.8 0.6 1.0 C A:CYS1476 4.9 0.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:0.2 occ:1.00 SG A:CYS656 2.3 0.1 1.0 SG A:CYS653 2.3 0.9 1.0 SG A:CYS691 2.4 0.2 1.0 SG A:CYS659 2.4 0.2 1.0 O A:CYS653 3.2 0.1 1.0 CB A:CYS691 3.5 0.2 1.0 N A:CYS653 3.5 0.1 1.0 CB A:CYS653 3.6 0.9 1.0 C A:CYS653 3.7 0.1 1.0 CB A:CYS659 3.8 0.2 1.0 CB A:CYS656 3.8 0.1 1.0 CA A:CYS653 3.8 0.1 1.0 CA A:CYS691 4.3 0.7 1.0 N A:CYS656 4.5 0.1 1.0 ND2 A:ASN693 4.5 0.7 1.0 C A:ARG652 4.6 0.4 1.0 CD A:PRO692 4.6 0.8 1.0 CA A:CYS656 4.6 0.1 1.0 CB A:ASN693 4.6 0.7 1.0 N A:CYS659 4.6 0.5 1.0 N A:GLY654 4.7 99.0 1.0 CA A:CYS659 4.8 0.5 1.0 O A:CYS656 4.8 0.1 1.0 CB A:ARG652 4.8 0.1 1.0 N A:ASN693 4.8 0.3 1.0 N A:VAL655 4.9 0.1 1.0 C A:CYS691 4.9 0.7 1.0 N A:PRO692 4.9 0.9 1.0 CA A:ARG652 5.0 0.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:0.2 occ:1.00 NE2 A:HIS793 2.3 0.5 1.0 SG A:CYS896 2.3 0.6 1.0 SG A:CYS820 2.4 0.9 1.0 SG A:CYS893 2.4 0.6 1.0 CE1 A:HIS793 2.6 0.5 1.0 CB A:CYS820 3.2 0.9 1.0 CD2 A:HIS793 3.2 0.5 1.0 ND1 A:HIS793 3.5 0.5 1.0 CB A:CYS893 3.6 0.6 1.0 N A:CYS896 3.8 77.0 1.0 CB A:CYS896 3.8 0.6 1.0 CG A:HIS793 3.9 0.5 1.0 CB A:SER895 3.9 0.3 1.0 OG A:SER895 4.1 0.3 1.0 CA A:CYS896 4.3 77.0 1.0 CA A:CYS820 4.6 0.5 1.0 C A:SER895 4.8 95.1 1.0 C A:CYS820 4.8 0.5 1.0 CA A:SER895 4.9 95.1 1.0 O A:CYS820 4.9 0.5 1.0 CA A:CYS893 5.0 0.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human DNMT1(646-1600) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human DNMT1(646-1600) in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:0.2 occ:0.61 CB A:CYS670 2.3 0.1 1.0 SG A:CYS667 2.3 0.6 1.0 SG A:CYS686 2.7 0.5 1.0 SG A:CYS670 3.1 0.1 1.0 SG A:CYS664 3.2 0.1 1.0 N A:GLN687 3.5 0.4 1.0 CB A:CYS686 3.5 0.5 1.0 CA A:CYS686 3.5 0.1 1.0 CA A:CYS670 3.6 0.5 1.0 CB A:CYS667 3.7 0.6 1.0 N A:CYS670 3.9 0.5 1.0 CG A:GLN687 3.9 0.0 1.0 C A:CYS686 4.0 0.1 1.0 N A:CYS667 4.1 0.7 1.0 N A:GLY665 4.3 1.0 1.0 CA A:CYS667 4.4 0.7 1.0 CB A:GLN687 4.5 0.0 1.0 CA A:GLN687 4.5 0.4 1.0 C A:CYS670 4.6 0.5 1.0 N A:LYS666 4.6 0.1 1.0 O A:CYS667 4.7 0.7 1.0 N A:GLU688 4.7 0.8 1.0 C A:CYS667 4.8 0.7 1.0 CA A:GLY665 4.8 1.0 1.0 CB A:CYS664 4.8 0.1 1.0 N A:CYS686 4.8 0.1 1.0 N A:LYS671 4.9 0.6 1.0 CD A:GLN687 5.0 0.0 1.0 N A:CYS664 5.0 0.6 1.0

J.Song, O.Rechkoblit, T.H.Bestor, D.J.Patel. Structure of DNMT1-Dna Complex Reveals A Role For Autoinhibition in Maintenance Dna Methylation. Science V. 331 1036 2011.
ISSN: ISSN 0036-8075
PubMed: 21163962
DOI: 10.1126/SCIENCE.1195380