Zinc in PDB 3a1b: Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3

All present enzymatic activity of Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3:
2.1.1.37;

The structure of Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3, PDB code: 3a1b was solved by J.Otani, K.Arita, M.Ariyoshi, M.Shirakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.72 / 2.29
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.547, 68.547, 109.950, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.4

The binding sites of Zinc atom in the Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3 (pdb code 3a1b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3, PDB code: 3a1b:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3


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 the DNMT3A Add Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:53.5 occ:1.00 SG A:CYS494 2.3 38.7 1.0 SG A:CYS497 2.3 39.2 1.0 SG A:CYS514 2.3 40.1 1.0 SG A:CYS517 2.4 41.0 1.0 CB A:CYS517 3.2 39.3 1.0 CB A:CYS494 3.3 38.3 1.0 CB A:CYS497 3.3 41.1 1.0 CB A:CYS514 3.6 37.6 1.0 N A:CYS497 3.7 41.2 1.0 N A:CYS514 4.0 37.6 1.0 CA A:CYS497 4.0 40.7 1.0 N A:CYS517 4.2 40.7 1.0 CA A:CYS517 4.2 40.3 1.0 CA A:CYS514 4.3 38.0 1.0 CB A:SER499 4.3 40.9 1.0 CB A:SER496 4.4 40.9 0.3 CB A:SER496 4.5 41.8 0.7 OG A:SER496 4.5 44.2 0.7 C A:SER496 4.6 41.5 1.0 CA A:CYS494 4.7 39.1 1.0 C A:CYS497 4.7 41.2 1.0 N A:SER499 4.7 40.9 1.0 N A:GLY498 4.8 41.3 1.0 O A:CYS514 4.8 37.2 1.0 C A:CYS514 4.9 38.3 1.0 CA A:SER496 4.9 40.9 0.3 CA A:SER496 5.0 41.5 0.7

Zinc binding site 2 out of 3 in the Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3


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 the DNMT3A Add Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:54.0 occ:1.00 SG A:CYS540 2.3 44.1 1.0 SG A:CYS559 2.3 39.3 1.0 SG A:CYS562 2.4 42.9 1.0 SG A:CYS537 2.4 39.4 1.0 CB A:CYS537 3.1 38.1 1.0 CB A:CYS540 3.2 44.5 1.0 CB A:CYS562 3.2 41.4 1.0 CB A:CYS559 3.6 35.8 1.0 N A:CYS540 3.7 44.9 1.0 N A:CYS559 4.1 36.7 1.0 CA A:CYS540 4.1 44.9 1.0 O A:HOH43 4.1 73.9 1.0 N A:CYS562 4.1 41.6 1.0 CA A:CYS562 4.3 41.2 1.0 CA A:CYS559 4.3 37.0 1.0 CB A:ILE539 4.6 43.8 1.0 CA A:CYS537 4.6 38.5 1.0 O A:CYS559 4.7 36.3 1.0 C A:ILE539 4.7 43.9 1.0 C A:CYS559 4.8 37.1 1.0 C A:CYS540 4.9 45.8 1.0 NH1 A:ARG476 4.9 39.3 1.0 CA A:GLY543 4.9 43.5 1.0 N A:ILE539 5.0 42.9 1.0 N A:GLY543 5.0 44.3 1.0 CA A:ILE539 5.0 43.6 1.0 O A:GLY542 5.0 45.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the DNMT3A Add Domain in Complex with Histone H3


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 the DNMT3A Add Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:64.6 occ:1.00 SG A:CYS549 2.2 37.2 1.0 SG A:CYS586 2.2 41.9 1.0 SG A:CYS554 2.3 45.8 1.0 SG A:CYS583 2.4 40.0 1.0 CB A:CYS549 3.1 39.8 1.0 CB A:CYS554 3.2 45.6 1.0 CB A:CYS583 3.4 38.6 1.0 CB A:CYS586 3.4 42.4 1.0 ND2 A:ASN551 3.7 53.0 1.0 N A:CYS583 3.8 38.0 1.0 N A:CYS586 3.9 42.1 1.0 CA A:CYS583 4.1 38.3 1.0 CA A:CYS586 4.3 42.3 1.0 CA A:CYS549 4.5 39.5 1.0 C A:CYS583 4.5 37.8 1.0 CA A:CYS554 4.6 46.1 1.0 CB A:MET585 4.7 40.8 1.0 O A:CYS583 4.7 37.8 1.0 C A:MET585 4.7 41.8 1.0 CB A:ARG556 4.8 38.9 1.0 O A:HOH31 4.8 68.1 1.0 CG A:ASN551 4.9 51.3 1.0 C A:ASN582 4.9 37.9 1.0 N A:MET585 4.9 39.6 1.0

J.Otani, T.Nankumo, K.Arita, S.Inamoto, M.Ariyoshi, M.Shirakawa. Structural Basis For Recognition of H3K4 Methylation Status By the Dna Methyltransferase 3A Atrx-DNMT3-DNMT3L Domain Embo Rep. V. 10 1235 2009.
ISSN: ISSN 1469-221X
PubMed: 19834512
DOI: 10.1038/EMBOR.2009.218