Zinc in PDB 5wy1: Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant)

All present enzymatic activity of Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant):
2.1.1.37;

The structure of Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant), PDB code: 5wy1 was solved by K.Kanada, K.Takeshita, I.Suetake, S.Tajima, A.Nakagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	134.998, 97.804, 130.319, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.3

The binding sites of Zinc atom in the Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant) (pdb code 5wy1). 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 (T1505A Mutant), PDB code: 5wy1:
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 (T1505A Mutant)


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 (T1505A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:73.3 occ:1.00 ND1 A:HIS424 2.0 66.5 1.0 SG A:CYS359 2.1 90.1 1.0 SG A:CYS362 2.1 62.2 1.0 SG A:CYS420 2.3 64.5 1.0 CE1 A:HIS424 2.9 68.3 1.0 CG A:HIS424 3.0 65.2 1.0 CB A:CYS359 3.1 93.5 1.0 CB A:CYS362 3.2 71.0 1.0 CB A:HIS424 3.4 66.6 1.0 CB A:CYS420 3.4 69.9 1.0 N A:CYS362 3.6 76.2 1.0 CA A:CYS362 4.0 73.6 1.0 NE2 A:HIS424 4.0 69.3 1.0 CD2 A:HIS424 4.1 66.0 1.0 CB A:ARG422 4.4 92.0 1.0 N A:HIS424 4.5 72.0 1.0 CB A:GLU361 4.5 93.5 1.0 CA A:HIS424 4.5 68.7 1.0 CA A:CYS359 4.6 91.5 1.0 C A:GLU361 4.6 82.3 1.0 C A:CYS362 4.7 78.3 1.0 N A:GLY363 4.8 85.4 1.0 CA A:CYS420 4.8 73.8 1.0 CA A:GLU361 4.9 88.4 1.0 N A:GLU361 4.9 87.2 1.0 CG A:ARG422 4.9 95.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant)


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 (T1505A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2002 b:88.8 occ:1.00 SG A:CYS656 2.1 79.6 1.0 SG A:CYS694 2.2 85.8 1.0 SG A:CYS659 2.2 86.1 1.0 SG A:CYS662 2.4 87.8 1.0 CB A:CYS659 3.2 89.8 1.0 CB A:CYS656 3.2 83.4 1.0 CB A:CYS694 3.4 90.9 1.0 CB A:CYS662 3.6 97.0 1.0 N A:GLY657 3.7 0.6 1.0 N A:CYS656 3.7 92.5 1.0 N A:CYS659 3.8 92.5 1.0 OD1 A:ASN696 3.9 93.9 1.0 CA A:CYS656 3.9 88.6 1.0 CA A:CYS659 4.0 91.4 1.0 C A:CYS656 4.2 98.3 1.0 CA A:CYS694 4.2 88.9 1.0 N A:CYS662 4.3 96.3 1.0 CA A:CYS662 4.5 0.4 1.0 CD A:PRO695 4.6 91.9 1.0 CB A:ASN696 4.6 86.3 1.0 O A:CYS659 4.7 90.9 1.0 N A:VAL658 4.7 0.5 1.0 C A:CYS659 4.7 92.5 1.0 CA A:GLY657 4.7 0.9 1.0 CG A:ASN696 4.7 91.5 1.0 CB A:ARG655 4.7 0.1 1.0 C A:GLY657 4.8 0.8 1.0 C A:CYS694 4.9 88.6 1.0 C A:ARG655 4.9 0.6 1.0 C A:VAL658 5.0 0.1 1.0 N A:PRO695 5.0 89.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant)


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 (T1505A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:82.1 occ:1.00 SG A:CYS897 2.1 77.4 1.0 SG A:CYS823 2.2 80.6 1.0 SG A:CYS900 2.2 75.2 1.0 NE2 A:HIS796 2.3 83.2 1.0 CB A:CYS897 2.9 83.0 1.0 CB A:CYS900 3.0 79.4 1.0 CE1 A:HIS796 3.1 85.7 1.0 CD2 A:HIS796 3.3 82.8 1.0 N A:CYS900 3.4 83.6 1.0 CB A:CYS823 3.5 72.1 1.0 CA A:CYS900 3.7 82.9 1.0 ND1 A:HIS796 4.2 87.1 1.0 CB A:SER899 4.3 80.1 1.0 CG A:HIS796 4.3 83.8 1.0 C A:SER899 4.3 83.0 1.0 CA A:CYS897 4.4 82.0 1.0 O A:CYS897 4.6 74.8 1.0 C A:CYS897 4.7 80.7 1.0 CA A:SER899 4.7 82.3 1.0 OG A:SER899 4.8 77.9 1.0 CA A:CYS823 4.8 71.0 1.0 N A:SER899 4.8 83.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mouse Dna Methyltransferase 1 (T1505A Mutant)


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 (T1505A Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2004 b:53.1 occ:1.00 SG A:CYS1481 2.0 49.2 1.0 NE2 A:HIS1504 2.1 50.1 1.0 SG A:CYS1487 2.1 57.8 1.0 SG A:CYS1479 2.3 48.2 1.0 CD2 A:HIS1504 3.0 52.2 1.0 CB A:CYS1487 3.0 65.1 1.0 CB A:CYS1481 3.1 55.5 1.0 CE1 A:HIS1504 3.1 51.9 1.0 CB A:CYS1479 3.2 51.1 1.0 CA A:CYS1487 3.8 64.1 1.0 N A:CYS1481 4.0 63.1 1.0 CA A:CYS1481 4.1 59.5 1.0 CG A:HIS1504 4.1 51.8 1.0 ND1 A:HIS1504 4.2 51.1 1.0 N A:CYS1487 4.5 60.6 1.0 CA A:CYS1479 4.6 52.7 1.0 C A:CYS1479 4.8 53.1 1.0 N A:SER1480 4.9 59.4 1.0 CH2 A:TRP1500 5.0 47.9 1.0 C A:CYS1487 5.0 66.8 1.0

K.Kanada, K.Takeshita, I.Suetake, S.Tajima, A.Nakagawa. Conserved Threonine 1505 in the Catalytic Domain Stabilizes Mouse Dna Methyltransferase 1 J. Biochem. V. 162 271 2017.
ISSN: ISSN 1756-2651
PubMed: 28369487
DOI: 10.1093/JB/MVX024