Zinc in PDB 3av5: Crystal Structure of Mouse Dna Methyltransferase 1 with Adohcy

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

The structure of Crystal Structure of Mouse Dna Methyltransferase 1 with Adohcy, PDB code: 3av5 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)	38.66 / 3.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.993, 96.920, 130.615, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 26.4

The binding sites of Zinc atom in the Crystal Structure of Mouse Dna Methyltransferase 1 with Adohcy (pdb code 3av5). 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 Adohcy, PDB code: 3av5:
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 Adohcy


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 Adohcy within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:56.2 occ:1.00 ND1 A:HIS424 2.0 46.8 1.0 SG A:CYS359 2.2 71.9 1.0 SG A:CYS362 2.3 55.7 1.0 SG A:CYS420 2.5 44.4 1.0 CB A:CYS359 2.8 67.6 1.0 CE1 A:HIS424 2.9 46.7 1.0 CG A:HIS424 2.9 44.3 1.0 CB A:HIS424 3.3 40.8 1.0 CB A:CYS362 3.5 52.2 1.0 CB A:CYS420 3.6 40.9 1.0 N A:CYS362 3.6 54.6 1.0 NE2 A:HIS424 3.9 46.7 1.0 CD2 A:HIS424 3.9 46.2 1.0 CA A:CYS362 4.0 52.7 1.0 CA A:CYS359 4.3 67.5 1.0 N A:HIS424 4.5 42.1 1.0 CA A:HIS424 4.5 40.6 1.0 CB A:ARG422 4.5 41.2 1.0 N A:GLY363 4.5 54.0 1.0 CB A:GLU361 4.6 63.9 1.0 C A:CYS362 4.7 56.8 1.0 C A:GLU361 4.8 61.4 1.0 CD A:ARG422 4.9 64.5 1.0 C A:CYS359 5.0 65.9 1.0 CG A:ARG422 5.0 48.8 1.0 SG A:CYS426 5.0 44.8 1.0 CA A:CYS420 5.0 40.9 1.0

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


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 Adohcy within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:65.3 occ:1.00 SG A:CYS662 2.2 66.3 1.0 SG A:CYS694 2.3 61.1 1.0 SG A:CYS659 2.3 56.1 1.0 SG A:CYS656 2.5 64.2 1.0 CB A:CYS694 3.1 58.0 1.0 CB A:CYS656 3.1 60.7 1.0 CB A:CYS659 3.3 52.6 1.0 CB A:CYS662 3.4 62.8 1.0 N A:CYS656 3.8 62.7 1.0 CA A:CYS656 3.9 61.6 1.0 CA A:CYS694 3.9 58.0 1.0 N A:GLY657 4.1 63.7 1.0 N A:CYS659 4.1 55.3 1.0 CD A:PRO695 4.2 54.3 1.0 OD1 A:ASN696 4.2 62.5 1.0 CA A:CYS659 4.2 53.6 1.0 N A:CYS662 4.2 61.2 1.0 CA A:CYS662 4.3 63.0 1.0 C A:CYS656 4.4 66.7 1.0 C A:CYS694 4.6 59.1 1.0 N A:PRO695 4.6 52.8 1.0 CB A:ASN696 4.8 38.0 1.0 N A:ASN696 4.8 42.9 1.0 CG A:ARG655 4.9 65.6 1.0 C A:CYS659 4.9 58.1 1.0 CG A:ASN696 4.9 64.8 1.0

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


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 Adohcy within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:58.8 occ:1.00 SG A:CYS823 2.2 45.6 1.0 NE2 A:HIS796 2.2 54.5 1.0 SG A:CYS897 2.3 63.5 1.0 SG A:CYS900 2.3 60.0 1.0 CB A:CYS897 3.0 60.1 1.0 CB A:CYS900 3.1 56.2 1.0 CE1 A:HIS796 3.1 54.1 1.0 CB A:CYS823 3.3 41.8 1.0 CD2 A:HIS796 3.3 55.2 1.0 N A:CYS900 3.5 55.5 1.0 CA A:CYS900 3.7 55.6 1.0 ND1 A:HIS796 4.3 54.9 1.0 C A:SER899 4.3 58.0 1.0 CB A:SER899 4.3 56.2 1.0 CG A:HIS796 4.4 53.4 1.0 CA A:CYS897 4.4 59.9 1.0 O A:CYS897 4.6 57.9 1.0 CA A:CYS823 4.6 41.6 1.0 OG A:SER899 4.6 64.7 1.0 C A:CYS897 4.7 59.5 1.0 CA A:SER899 4.7 53.2 1.0 N A:SER899 4.9 53.7 1.0 C A:CYS823 4.9 46.2 1.0

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


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 Adohcy within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:34.2 occ:1.00 NE2 A:HIS1504 2.0 29.2 1.0 SG A:CYS1487 2.1 35.8 1.0 SG A:CYS1481 2.2 27.9 1.0 SG A:CYS1479 2.3 25.6 1.0 CD2 A:HIS1504 2.8 29.5 1.0 CB A:CYS1487 3.1 32.0 1.0 CB A:CYS1481 3.1 24.3 1.0 CE1 A:HIS1504 3.2 28.8 1.0 CB A:CYS1479 3.2 21.5 1.0 CA A:CYS1487 3.6 31.7 1.0 N A:CYS1481 3.9 25.0 1.0 CG A:HIS1504 4.0 27.8 1.0 CA A:CYS1481 4.1 24.4 1.0 ND1 A:HIS1504 4.2 29.6 1.0 N A:CYS1487 4.4 31.0 1.0 CA A:CYS1479 4.5 21.4 1.0 C A:CYS1479 4.6 26.7 1.0 N A:SER1480 4.7 25.4 1.0 C A:CYS1487 4.8 38.1 1.0 C A:CYS1481 5.0 24.9 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