Zinc in PDB 3av4: Crystal Structure of Mouse Dna Methyltransferase 1

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

The structure of Crystal Structure of Mouse Dna Methyltransferase 1, PDB code: 3av4 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)	43.42 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	135.780, 97.865, 130.636, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 26.7

The binding sites of Zinc atom in the Crystal Structure of Mouse Dna Methyltransferase 1 (pdb code 3av4). 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, PDB code: 3av4:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:35.3 occ:1.00 SG A:CYS362 2.1 67.3 1.0 SG A:CYS359 2.2 63.2 1.0 ND1 A:HIS424 2.2 59.3 1.0 SG A:CYS420 2.3 47.2 1.0 CB A:CYS359 3.0 60.2 1.0 CE1 A:HIS424 3.1 58.8 1.0 CB A:CYS362 3.2 63.8 1.0 CG A:HIS424 3.3 56.7 1.0 CB A:CYS420 3.5 43.8 1.0 CB A:HIS424 3.7 52.6 1.0 N A:CYS362 3.7 63.6 1.0 CA A:CYS362 4.0 63.7 1.0 CB A:ARG422 4.2 47.6 1.0 NE2 A:HIS424 4.3 58.5 1.0 CD2 A:HIS424 4.4 58.2 1.0 CA A:CYS359 4.5 61.7 1.0 N A:HIS424 4.6 50.4 1.0 CB A:GLU361 4.7 62.3 1.0 CA A:HIS424 4.7 51.3 1.0 C A:CYS362 4.7 70.8 1.0 C A:GLU361 4.7 66.1 1.0 CG A:ARG422 4.8 49.0 1.0 N A:GLY363 4.8 69.7 1.0 CA A:CYS420 4.9 43.6 1.0 N A:GLU361 5.0 61.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:37.0 occ:1.00 SG A:CYS659 2.2 58.2 1.0 SG A:CYS662 2.2 69.4 1.0 SG A:CYS656 2.2 65.3 1.0 SG A:CYS694 2.2 57.2 1.0 CB A:CYS694 3.3 54.0 1.0 CB A:CYS659 3.4 54.4 1.0 CB A:CYS656 3.4 61.2 1.0 CB A:CYS662 3.7 66.2 1.0 N A:GLY657 3.8 60.3 1.0 N A:CYS659 3.9 56.6 1.0 N A:CYS656 4.0 62.1 1.0 CA A:CYS694 4.0 53.8 1.0 CA A:CYS656 4.1 61.4 1.0 CA A:CYS659 4.1 55.3 1.0 OD1 A:ASN696 4.2 46.1 1.0 N A:CYS662 4.3 65.2 1.0 C A:CYS656 4.4 64.6 1.0 CD A:PRO695 4.4 51.2 1.0 CA A:CYS662 4.6 66.6 1.0 CG A:ARG655 4.6 72.8 1.0 C A:CYS694 4.7 55.5 1.0 C A:GLY657 4.7 61.5 1.0 CA A:GLY657 4.7 59.4 1.0 C A:CYS659 4.7 61.5 1.0 N A:PRO695 4.8 50.0 1.0 CB A:ASN696 4.8 44.0 1.0 O A:CYS659 4.8 61.9 1.0 CG A:ASN696 4.9 61.7 1.0 N A:VAL658 4.9 58.0 1.0 C A:ARG655 5.0 68.2 1.0 O A:GLY657 5.0 60.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:32.8 occ:1.00 SG A:CYS900 2.1 56.8 1.0 SG A:CYS823 2.2 53.1 1.0 SG A:CYS897 2.2 59.4 1.0 NE2 A:HIS796 2.3 54.2 1.0 CB A:CYS897 2.9 56.7 1.0 CD2 A:HIS796 3.2 55.1 1.0 CB A:CYS900 3.2 53.0 1.0 CB A:CYS823 3.2 48.8 1.0 CE1 A:HIS796 3.3 53.6 1.0 N A:CYS900 3.6 51.6 1.0 CA A:CYS900 3.8 51.9 1.0 CG A:HIS796 4.3 53.4 1.0 CA A:CYS897 4.3 57.1 1.0 CB A:SER899 4.4 43.7 1.0 ND1 A:HIS796 4.4 54.7 1.0 C A:SER899 4.4 53.0 1.0 OG A:SER899 4.6 41.0 1.0 CA A:CYS823 4.6 47.6 1.0 O A:CYS897 4.6 56.5 1.0 C A:CYS897 4.7 58.2 1.0 CA A:SER899 4.8 44.8 1.0 C A:CYS823 4.9 51.2 1.0 N A:SER899 5.0 46.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2005 b:9.4 occ:1.00 NE2 A:HIS1504 2.0 35.6 1.0 SG A:CYS1479 2.1 32.1 1.0 SG A:CYS1487 2.1 38.3 1.0 SG A:CYS1481 2.1 30.0 1.0 CD2 A:HIS1504 3.0 35.8 1.0 CE1 A:HIS1504 3.0 35.2 1.0 CB A:CYS1479 3.2 28.0 1.0 CB A:CYS1481 3.3 26.8 1.0 CB A:CYS1487 3.4 35.7 1.0 CA A:CYS1487 3.9 36.7 1.0 N A:CYS1481 4.1 27.4 1.0 CG A:HIS1504 4.1 32.1 1.0 ND1 A:HIS1504 4.2 35.0 1.0 CA A:CYS1481 4.3 27.0 1.0 CA A:CYS1479 4.5 26.2 1.0 N A:CYS1487 4.7 36.1 1.0 N A:SER1480 4.7 22.9 1.0 C A:CYS1479 4.7 25.0 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