Zinc in PDB 4da4: Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna

All present enzymatic activity of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna:
2.1.1.37;

The structure of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna, PDB code: 4da4 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)	39.47 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.680, 152.042, 96.053, 90.00, 94.54, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna (pdb code 4da4). 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 Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna, PDB code: 4da4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:30.3 occ:1.00 SG A:CYS1479 2.2 31.1 1.0 SG A:CYS1487 2.3 38.1 1.0 SG A:CYS1481 2.3 30.1 1.0 NE2 A:HIS1504 2.4 28.9 1.0 CB A:CYS1479 3.1 30.3 1.0 CD2 A:HIS1504 3.2 25.5 1.0 CB A:CYS1481 3.3 34.0 1.0 CB A:CYS1487 3.4 31.1 1.0 CE1 A:HIS1504 3.6 30.3 1.0 O A:HOH1986 3.6 34.9 1.0 CA A:CYS1487 3.8 35.0 1.0 N A:CYS1481 4.0 34.4 1.0 CA A:CYS1481 4.3 34.8 1.0 CG A:HIS1504 4.4 32.2 1.0 CA A:CYS1479 4.5 31.9 1.0 ND1 A:HIS1504 4.6 34.4 1.0 N A:CYS1487 4.7 36.2 1.0 O C:HOH103 4.7 30.1 1.0 C A:CYS1479 4.8 32.6 1.0 N A:SER1480 4.8 32.2 1.0 C A:CYS1487 5.0 41.0 1.0

Zinc binding site 2 out of 4 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:43.5 occ:1.00 NE2 A:HIS796 2.0 52.7 1.0 SG A:CYS900 2.0 52.9 1.0 SG A:CYS823 2.2 45.2 1.0 SG A:CYS897 2.3 44.3 1.0 CD2 A:HIS796 3.0 50.3 1.0 CB A:CYS823 3.0 44.4 1.0 CE1 A:HIS796 3.0 48.0 1.0 CB A:CYS900 3.3 45.4 1.0 CB A:CYS897 3.4 48.4 1.0 N A:CYS900 3.5 44.1 1.0 CA A:CYS900 3.8 48.1 1.0 ND1 A:HIS796 4.1 50.4 1.0 CB A:SER899 4.1 41.6 1.0 CG A:HIS796 4.1 52.7 1.0 CA A:CYS823 4.4 45.1 1.0 OG A:SER899 4.5 41.6 1.0 C A:SER899 4.5 46.8 1.0 C A:CYS823 4.7 47.0 1.0 CA A:CYS897 4.7 51.0 1.0 CA A:SER899 4.8 42.8 1.0 N A:GLU824 4.8 50.1 1.0 N A:SER899 4.9 41.1 1.0 O A:CYS897 5.0 53.3 1.0

Zinc binding site 3 out of 4 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1702 b:36.4 occ:1.00 SG B:CYS1479 2.3 34.3 1.0 SG B:CYS1487 2.3 35.5 1.0 SG B:CYS1481 2.3 36.3 1.0 NE2 B:HIS1504 2.4 32.5 1.0 CB B:CYS1479 3.1 33.0 1.0 CD2 B:HIS1504 3.2 29.4 1.0 CB B:CYS1481 3.2 36.3 1.0 CB B:CYS1487 3.3 42.1 1.0 CE1 B:HIS1504 3.5 32.1 1.0 CA B:CYS1487 3.8 43.4 1.0 O B:HOH1899 4.0 31.2 1.0 N B:CYS1481 4.0 39.6 1.0 CA B:CYS1481 4.2 40.8 1.0 CG B:HIS1504 4.4 30.7 1.0 CA B:CYS1479 4.5 34.8 1.0 ND1 B:HIS1504 4.5 35.0 1.0 N B:CYS1487 4.6 42.2 1.0 C B:CYS1479 4.7 36.1 1.0 N B:SER1480 4.8 37.8 1.0 O B:HOH1861 4.8 28.2 1.0 C B:CYS1487 4.9 45.0 1.0

Zinc binding site 4 out of 4 in the Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Mouse DNMT1 (731-1602) Bound to Hemimethylated Cpg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1703 b:48.9 occ:1.00 SG B:CYS900 2.0 62.1 1.0 NE2 B:HIS796 2.1 64.5 1.0 SG B:CYS897 2.3 52.7 1.0 SG B:CYS823 2.3 45.7 1.0 CB B:CYS823 3.0 55.6 1.0 CD2 B:HIS796 3.0 64.6 1.0 CE1 B:HIS796 3.1 61.1 1.0 CB B:CYS897 3.3 55.9 1.0 O B:HOH1999 3.5 48.4 1.0 CB B:CYS900 3.5 52.6 1.0 N B:CYS900 3.6 50.7 1.0 CA B:CYS900 4.0 52.2 1.0 CB B:SER899 4.0 48.7 1.0 ND1 B:HIS796 4.2 63.2 1.0 CG B:HIS796 4.2 66.2 1.0 C B:SER899 4.4 51.4 1.0 CA B:CYS823 4.4 58.6 1.0 OG B:SER899 4.5 47.2 1.0 CA B:SER899 4.6 47.7 1.0 CA B:CYS897 4.7 59.4 1.0 C B:CYS823 4.8 62.6 1.0 N B:SER899 4.8 46.4 1.0 C B:CYS897 5.0 57.8 1.0

J.Song, M.Teplova, S.Ishibe-Murakami, D.J.Patel. Structure-Based Mechanistic Insights Into DNMT1-Mediated Maintenance Dna Methylation. Science V. 335 709 2012.
ISSN: ISSN 0036-8075
PubMed: 22323818
DOI: 10.1126/SCIENCE.1214453