Zinc in PDB 3av6: Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet

All present enzymatic activity of Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet:
2.1.1.37;

The structure of Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet, PDB code: 3av6 was solved by K.Takeshita, I.Suetake, E.Yamashita, M.Suga, H.Narita, A.Nakagawa, S.Tajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.14 / 3.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.995, 97.139, 130.794, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.5

The binding sites of Zinc atom in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet (pdb code 3av6). 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 Dna Methyltransferase 1 with Adomet, PDB code: 3av6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet


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 Dna Methyltransferase 1 with Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:55.5 occ:1.00 ND1 A:HIS424 1.9 47.2 1.0 SG A:CYS359 2.3 67.2 1.0 SG A:CYS362 2.4 56.0 1.0 SG A:CYS420 2.4 47.0 1.0 CE1 A:HIS424 2.9 47.4 1.0 CG A:HIS424 2.9 44.9 1.0 CB A:CYS359 3.0 63.2 1.0 CB A:HIS424 3.3 41.3 1.0 CB A:CYS362 3.3 52.4 1.0 CB A:CYS420 3.4 42.6 1.0 N A:CYS362 3.7 54.8 1.0 NE2 A:HIS424 4.0 47.5 1.0 CD2 A:HIS424 4.0 47.0 1.0 CA A:CYS362 4.0 52.9 1.0 N A:HIS424 4.4 43.4 1.0 CA A:HIS424 4.5 41.2 1.0 CA A:CYS359 4.5 64.0 1.0 CB A:ARG422 4.6 41.2 1.0 CB A:GLU361 4.7 62.4 1.0 N A:GLY363 4.7 53.2 1.0 C A:CYS362 4.8 55.6 1.0 C A:GLU361 4.8 61.2 1.0 CA A:CYS420 4.8 41.5 1.0 SG A:CYS426 5.0 44.5 1.0 NE2 A:GLN364 5.0 64.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet


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 Dna Methyltransferase 1 with Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:58.6 occ:1.00 SG A:CYS662 2.2 69.7 1.0 SG A:CYS659 2.4 59.7 1.0 SG A:CYS656 2.4 61.2 1.0 SG A:CYS694 2.6 56.9 1.0 CB A:CYS656 3.1 57.8 1.0 CB A:CYS694 3.2 54.1 1.0 CB A:CYS662 3.4 66.5 1.0 CB A:CYS659 3.4 56.0 1.0 N A:CYS656 3.7 59.7 1.0 CA A:CYS656 3.8 58.8 1.0 CA A:CYS694 3.9 54.0 1.0 OD1 A:ASN696 4.0 51.5 1.0 N A:CYS659 4.1 59.3 1.0 N A:GLY657 4.1 61.7 1.0 CA A:CYS659 4.2 57.4 1.0 C A:CYS656 4.3 64.4 1.0 N A:CYS662 4.3 64.9 1.0 CD A:PRO695 4.3 48.0 1.0 CA A:CYS662 4.4 66.7 1.0 C A:CYS694 4.6 54.9 1.0 N A:PRO695 4.7 46.8 1.0 CG A:ARG655 4.8 61.5 1.0 CB A:ASN696 4.9 31.7 1.0 CG A:ASN696 4.9 52.3 1.0 C A:CYS659 4.9 62.0 1.0 N A:ASN696 4.9 36.2 1.0 C A:ARG655 4.9 64.8 1.0 O A:CYS659 5.0 61.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet


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 Dna Methyltransferase 1 with Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:48.0 occ:1.00 SG A:CYS823 2.3 42.0 1.0 SG A:CYS897 2.3 54.8 1.0 NE2 A:HIS796 2.3 44.5 1.0 SG A:CYS900 2.5 53.1 1.0 CE1 A:HIS796 3.0 44.1 1.0 CB A:CYS900 3.1 49.3 1.0 CB A:CYS897 3.1 51.9 1.0 CB A:CYS823 3.2 38.6 1.0 CD2 A:HIS796 3.3 45.8 1.0 N A:CYS900 3.5 48.0 1.0 CA A:CYS900 3.7 48.0 1.0 ND1 A:HIS796 4.1 45.8 1.0 C A:SER899 4.2 50.2 1.0 CG A:HIS796 4.2 45.1 1.0 CB A:SER899 4.5 48.2 1.0 CA A:CYS897 4.5 52.1 1.0 CA A:CYS823 4.6 38.0 1.0 O A:CYS897 4.7 51.4 1.0 OG A:SER899 4.7 58.0 1.0 CA A:SER899 4.8 44.8 1.0 C A:CYS897 4.8 52.9 1.0 C A:CYS823 4.9 42.2 1.0 O A:SER899 5.0 49.3 1.0 N A:SER899 5.0 45.6 1.0 CG2 A:THR783 5.0 54.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adomet


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 Dna Methyltransferase 1 with Adomet within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:33.3 occ:1.00 SG A:CYS1481 2.1 26.5 1.0 NE2 A:HIS1504 2.1 25.0 1.0 SG A:CYS1487 2.2 35.5 1.0 SG A:CYS1479 2.3 26.7 1.0 CD2 A:HIS1504 3.1 25.4 1.0 CB A:CYS1487 3.1 32.1 1.0 CB A:CYS1481 3.2 23.2 1.0 CE1 A:HIS1504 3.2 24.4 1.0 CB A:CYS1479 3.2 22.5 1.0 CA A:CYS1487 3.6 32.5 1.0 N A:CYS1481 4.0 24.2 1.0 CA A:CYS1481 4.2 23.6 1.0 CG A:HIS1504 4.2 22.8 1.0 ND1 A:HIS1504 4.3 24.7 1.0 N A:CYS1487 4.4 32.8 1.0 CA A:CYS1479 4.6 22.1 1.0 C A:CYS1487 4.8 38.3 1.0 N A:SER1480 4.8 22.7 1.0 C A:CYS1479 4.8 25.8 1.0 N A:ASP1488 5.0 37.8 1.0 CH2 A:TRP1500 5.0 18.8 1.0

K.Takeshita, I.Suetake, E.Yamashita, M.Suga, H.Narita, A.Nakagawa, S.Tajima. Structural Insight Into Maintenance Methylation By Mouse Dna Methyltransferase 1 (DNMT1). Proc.Natl.Acad.Sci.Usa V. 108 9055 2011.
ISSN: ESSN 1091-6490
PubMed: 21518897
DOI: 10.1073/PNAS.1019629108