Zinc in PDB 6w8w: Crystal Structure of Mouse DNMT1 in Complex with Ccg Dna

All present enzymatic activity of Crystal Structure of Mouse DNMT1 in Complex with Ccg Dna:
2.1.1.37;

The structure of Crystal Structure of Mouse DNMT1 in Complex with Ccg Dna, PDB code: 6w8w was solved by H.Anteneh, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.44 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.794, 152.593, 95.631, 90.00, 94.74, 90.00
R / Rfree (%)	23.8 / 28

The structure of Crystal Structure of Mouse DNMT1 in Complex with Ccg Dna also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Mouse DNMT1 in Complex with Ccg Dna (pdb code 6w8w). 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 Mouse DNMT1 in Complex with Ccg Dna, PDB code: 6w8w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mouse DNMT1 in Complex with Ccg 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 Mouse DNMT1 in Complex with Ccg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:75.8 occ:1.00 NE2 A:HIS1504 2.2 61.7 1.0 SG A:CYS1487 2.3 50.5 1.0 SG A:CYS1479 2.3 60.9 1.0 CB A:CYS1479 2.5 63.0 1.0 O A:HOH1811 2.5 62.2 1.0 CD2 A:HIS1504 2.6 72.5 1.0 SG A:CYS1481 2.9 0.9 1.0 O A:HOH1820 3.4 48.9 1.0 CB A:CYS1481 3.5 71.5 1.0 CE1 A:HIS1504 3.5 65.7 1.0 CB A:CYS1487 3.8 56.3 1.0 N A:CYS1481 3.8 67.0 1.0 CA A:CYS1479 3.8 53.4 1.0 CG A:HIS1504 3.9 63.5 1.0 C A:CYS1479 4.1 65.7 1.0 CA A:CYS1487 4.2 52.2 1.0 N A:SER1480 4.2 71.4 1.0 CA A:CYS1481 4.3 68.2 1.0 ND1 A:HIS1504 4.3 60.5 1.0 N A:CYS1479 4.7 53.3 1.0 O A:CYS1479 4.8 68.4 1.0 C A:SER1480 4.9 80.4 1.0 CZ2 A:TRP1500 5.0 48.9 1.0 N A:ALA1482 5.0 66.2 1.0 O A:HIS1504 5.0 64.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mouse DNMT1 in Complex with Ccg 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 Mouse DNMT1 in Complex with Ccg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:0.7 occ:1.00 NE2 A:HIS796 2.2 0.1 1.0 SG A:CYS897 2.3 88.1 1.0 CE1 A:HIS796 2.4 0.1 1.0 SG A:CYS900 2.5 0.9 1.0 CB A:CYS823 2.5 0.5 1.0 SG A:CYS823 2.6 0.4 1.0 CD2 A:HIS796 3.5 0.3 1.0 N A:CYS900 3.6 0.8 1.0 CB A:CYS897 3.6 86.6 1.0 ND1 A:HIS796 3.7 0.8 1.0 CB A:CYS900 3.7 0.5 1.0 CA A:CYS823 3.9 0.5 1.0 CA A:CYS900 4.0 0.4 1.0 CB A:SER899 4.1 93.8 1.0 CG A:HIS796 4.2 0.3 1.0 C A:SER899 4.3 0.0 1.0 C A:CYS823 4.5 97.7 1.0 OG A:SER899 4.6 93.0 1.0 CA A:SER899 4.7 88.7 1.0 N A:GLU824 4.8 0.7 1.0 N A:CYS823 4.9 0.3 1.0 CA A:CYS897 4.9 92.4 1.0 N A:SER899 4.9 83.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mouse DNMT1 in Complex with Ccg 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 Mouse DNMT1 in Complex with Ccg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1702 b:68.9 occ:1.00 NE2 B:HIS1504 2.1 67.6 1.0 SG B:CYS1479 2.3 83.0 1.0 SG B:CYS1487 2.3 71.7 1.0 SG B:CYS1481 2.7 89.9 1.0 CB B:CYS1479 2.8 61.2 1.0 CD2 B:HIS1504 2.9 62.6 1.0 CE1 B:HIS1504 3.2 62.9 1.0 CB B:CYS1481 3.3 63.5 1.0 CB B:CYS1487 3.4 72.3 1.0 CA B:CYS1487 3.8 79.2 1.0 N B:CYS1481 3.8 68.8 1.0 CA B:CYS1479 4.1 59.2 1.0 CG B:HIS1504 4.2 60.6 1.0 CA B:CYS1481 4.2 60.9 1.0 ND1 B:HIS1504 4.3 62.6 1.0 N B:SER1480 4.3 89.4 1.0 C B:CYS1479 4.4 82.8 1.0 N B:ASP1488 4.6 70.7 1.0 C B:CYS1487 4.6 75.3 1.0 N B:CYS1487 4.9 66.4 1.0 C B:SER1480 4.9 80.3 1.0 OG B:SER1480 5.0 80.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse DNMT1 in Complex with Ccg 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 Mouse DNMT1 in Complex with Ccg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1703 b:0.4 occ:1.00 NE2 B:HIS796 2.1 0.6 1.0 SG B:CYS897 2.3 0.2 1.0 SG B:CYS900 2.4 96.0 1.0 SG B:CYS823 2.4 99.7 1.0 CE1 B:HIS796 2.9 0.6 1.0 CB B:CYS823 3.0 82.6 1.0 CD2 B:HIS796 3.2 0.9 1.0 CB B:CYS897 3.3 0.3 1.0 CB B:CYS900 3.4 96.4 1.0 N B:CYS900 3.6 91.4 1.0 CA B:CYS900 3.9 93.6 1.0 ND1 B:HIS796 4.1 0.4 1.0 CB B:SER899 4.1 83.1 1.0 OG B:SER899 4.1 86.0 1.0 CG B:HIS796 4.3 0.2 1.0 C B:SER899 4.3 92.6 1.0 CA B:CYS823 4.5 81.7 1.0 CA B:SER899 4.7 84.3 1.0 CA B:CYS897 4.7 0.9 1.0 C B:CYS823 4.9 76.9 1.0 O B:CYS897 4.9 0.5 1.0 N B:SER899 4.9 95.5 1.0 C B:CYS897 5.0 0.9 1.0

S.Adam, H.Anteneh, M.Hornisch, V.Wagner, J.Lu, N.E.Radde, P.Bashtrykov, J.Song, A.Jeltsch. DNMT1 Activity, Base Flipping Mechanism and Genome-Wide Dna Methylation Are Regulated By the Dna Sequence Context Nat Commun 2020.
ISSN: ESSN 2041-1723