Zinc in PDB 4qbq: Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide

All present enzymatic activity of Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide:
2.1.1.37;

The structure of Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide, PDB code: 4qbq was solved by H.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.56 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.557, 56.424, 57.301, 90.00, 90.27, 90.00
R / Rfree (%)	17.4 / 23

The binding sites of Zinc atom in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide (pdb code 4qbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide, PDB code: 4qbq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


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 DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:24.1 occ:1.00 SG A:CYS549 2.5 23.4 1.0 SG A:CYS586 2.5 31.1 1.0 SG A:CYS554 2.5 22.0 1.0 SG A:CYS583 2.5 25.2 1.0 CB A:CYS554 3.1 25.6 1.0 CB A:CYS549 3.2 29.0 1.0 CB A:CYS586 3.3 29.2 1.0 CB A:CYS583 3.4 26.1 1.0 N A:CYS583 3.9 29.8 1.0 CA A:CYS583 4.2 28.2 1.0 N A:CYS586 4.2 25.3 1.0 OD1 A:ASN551 4.2 40.7 1.0 CA A:CYS586 4.4 28.0 1.0 ND2 A:ASN551 4.5 37.1 1.0 CA A:CYS554 4.5 28.9 1.0 C A:CYS583 4.7 25.7 1.0 CA A:CYS549 4.7 31.6 1.0 O A:HOH821 4.7 24.9 1.0 CG A:ASN551 4.7 40.8 1.0 O A:CYS583 4.8 27.6 1.0 CB A:MET585 4.8 24.0 1.0 CB A:ARG556 4.9 23.1 1.0 N A:CYS555 4.9 26.8 1.0 C A:MET585 4.9 26.1 1.0 C A:CYS554 5.0 22.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


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 DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:20.7 occ:1.00 SG A:CYS562 2.4 23.4 1.0 SG A:CYS540 2.5 15.5 1.0 SG A:CYS537 2.5 19.3 1.0 SG A:CYS559 2.5 17.5 1.0 CB A:CYS540 3.2 16.1 1.0 CB A:CYS537 3.3 19.9 1.0 CB A:CYS562 3.4 18.4 1.0 CB A:CYS559 3.5 19.8 1.0 O C:HOH810 3.6 26.3 1.0 N A:CYS540 3.7 20.0 1.0 CA A:CYS540 4.0 19.6 1.0 N A:CYS559 4.1 20.4 1.0 ND2 C:ASN516 4.2 24.3 1.0 CA A:CYS559 4.3 21.6 1.0 N A:CYS562 4.4 22.0 1.0 CA A:CYS562 4.5 20.4 1.0 CB A:ILE539 4.6 25.1 1.0 CA A:CYS537 4.7 18.7 1.0 CA A:GLY543 4.8 19.3 1.0 C A:ILE539 4.8 20.3 1.0 O A:CYS559 4.8 16.8 1.0 C A:CYS559 4.9 20.7 1.0 C A:CYS540 4.9 20.2 1.0 N A:GLY543 5.0 20.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


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 DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:27.1 occ:1.00 SG A:CYS517 2.4 21.0 1.0 SG A:CYS494 2.5 21.3 1.0 SG A:CYS514 2.5 26.5 1.0 SG A:CYS497 2.5 24.0 1.0 CB A:CYS497 3.2 26.8 1.0 CB A:CYS517 3.3 22.1 1.0 CB A:CYS514 3.5 24.3 1.0 CB A:CYS494 3.6 23.6 1.0 N A:CYS497 3.7 24.4 1.0 O C:HOH826 3.8 27.1 1.0 N A:CYS514 3.9 23.4 1.0 CA A:CYS497 4.0 24.7 1.0 O C:HOH832 4.1 26.9 1.0 CA A:CYS514 4.2 24.9 1.0 N A:CYS517 4.2 21.8 1.0 CA A:CYS517 4.3 21.8 1.0 CB A:SER496 4.5 25.5 1.0 C A:SER496 4.5 22.2 1.0 CB A:SER499 4.5 29.1 1.0 C A:CYS497 4.6 25.3 1.0 N A:GLY498 4.6 26.6 1.0 O A:CYS514 4.8 22.7 1.0 C A:CYS514 4.8 24.0 1.0 N A:SER499 4.8 28.4 1.0 CA A:CYS494 4.9 24.8 1.0 CA A:SER496 4.9 21.7 1.0 N A:SER496 5.0 21.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


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 DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:27.8 occ:1.00 SG C:CYS554 2.4 29.5 1.0 SG C:CYS549 2.4 34.0 1.0 SG C:CYS583 2.6 26.9 1.0 SG C:CYS586 2.6 42.5 1.0 CB C:CYS549 3.1 31.8 1.0 CB C:CYS554 3.2 34.4 1.0 CB C:CYS583 3.4 25.9 1.0 CB C:CYS586 3.4 29.8 1.0 N C:CYS583 3.8 30.2 1.0 CA C:CYS583 4.1 31.3 1.0 N C:CYS586 4.2 25.9 1.0 CB C:ASN551 4.2 46.2 1.0 CA C:CYS586 4.5 27.6 1.0 O C:CYS583 4.5 27.1 1.0 C C:CYS583 4.6 28.4 1.0 CA C:CYS549 4.6 30.5 1.0 CB C:MET585 4.6 26.1 1.0 CA C:CYS554 4.7 37.2 1.0 C C:MET585 4.9 29.1 1.0 CB C:ARG556 4.9 25.2 1.0 C C:ASN582 5.0 33.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:21.2 occ:1.00 SG C:CYS562 2.5 20.3 1.0 SG C:CYS559 2.5 17.9 1.0 SG C:CYS537 2.5 18.1 1.0 SG C:CYS540 2.6 20.9 1.0 CB C:CYS537 3.1 24.5 1.0 CB C:CYS562 3.2 19.1 1.0 CB C:CYS540 3.4 19.9 1.0 CB C:CYS559 3.7 23.6 1.0 N C:CYS540 3.8 21.3 1.0 N C:CYS559 4.1 23.0 1.0 N C:CYS562 4.2 19.9 1.0 CA C:CYS540 4.2 22.9 1.0 CA C:CYS562 4.3 22.1 1.0 CA C:CYS559 4.3 24.7 1.0 CB C:ILE539 4.6 23.9 1.0 O C:CYS559 4.6 20.7 1.0 CA C:CYS537 4.7 23.6 1.0 C C:ILE539 4.8 24.9 1.0 CA C:GLY543 4.9 36.5 1.0 C C:CYS559 4.9 23.7 1.0 C C:CYS540 5.0 26.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of DNMT3A Add Domain Bound to H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:20.6 occ:1.00 SG C:CYS517 2.4 18.4 1.0 SG C:CYS494 2.4 17.2 1.0 SG C:CYS497 2.5 16.5 1.0 SG C:CYS514 2.6 16.9 1.0 CB C:CYS517 3.2 22.6 1.0 CB C:CYS497 3.3 18.8 1.0 CB C:CYS494 3.4 18.4 1.0 CB C:CYS514 3.7 18.4 1.0 N C:CYS497 3.7 18.9 1.0 O A:HOH814 3.8 21.1 1.0 N C:CYS514 3.9 20.2 1.0 CA C:CYS497 4.1 19.0 1.0 CB C:SER499 4.1 17.1 1.0 N C:CYS517 4.2 21.5 1.0 CA C:CYS517 4.3 23.1 1.0 CB C:SER496 4.3 18.4 1.0 CA C:CYS514 4.3 20.7 1.0 C C:SER496 4.4 18.5 1.0 N C:SER499 4.7 20.3 1.0 N C:GLY498 4.8 17.1 1.0 CA C:SER496 4.8 18.4 1.0 O C:CYS514 4.8 19.1 1.0 C C:CYS497 4.8 19.9 1.0 CA C:CYS494 4.8 18.2 1.0 C C:CYS514 4.9 20.4 1.0 N C:SER496 4.9 16.5 1.0

K.Noh, H.Wang, H.Kim, W.Wenderski, F.Fang, C.Li, S.Dewell, X.Wu, A.Ferris, S.H.Hughes, D.Zheng, A.M.Melnick, D.J.Patel, H.Li, C.D.Allis. Engineering of A Histone-Recognition Domain in A De Novo Dna Methyltransferase Alters the Epigenetic Landscape of Escs To Be Published.