Zinc in PDB 4qbs: Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH Peptide

All present enzymatic activity of Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH Peptide:
2.1.1.37;

The structure of Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH Peptide, PDB code: 4qbs was solved by H.Wang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.84 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.286, 57.286, 71.923, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Zinc atom in the Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH Peptide (pdb code 4qbs). 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 DNMT3A Add Domain E545R Mutant Bound to H3T3PH Peptide, PDB code: 4qbs:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH 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 E545R Mutant Bound to H3T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:18.0 occ:1.00 SG A:CYS549 2.3 18.5 1.0 SG A:CYS554 2.3 22.2 1.0 SG A:CYS586 2.3 23.1 1.0 SG A:CYS583 2.3 17.0 1.0 CB A:CYS554 3.1 24.7 1.0 CB A:CYS586 3.1 15.5 1.0 CB A:CYS549 3.2 18.9 1.0 CB A:CYS583 3.3 14.6 1.0 N A:CYS583 3.7 14.9 1.0 N A:CYS586 4.0 16.5 1.0 CA A:CYS583 4.0 15.7 1.0 CA A:CYS586 4.1 16.4 1.0 CB A:ASN551 4.3 25.2 1.0 CA A:CYS554 4.5 31.6 1.0 C A:CYS583 4.5 17.9 1.0 CA A:CYS549 4.6 19.0 1.0 CB A:ARG556 4.6 17.6 1.0 O A:CYS583 4.7 19.7 1.0 ND2 A:ASN551 4.8 31.8 1.0 CD A:ARG556 4.8 22.3 1.0 C A:MET585 4.8 21.5 1.0 CB A:MET585 4.9 20.2 1.0 C A:ASN582 4.9 20.9 1.0 CG A:ARG556 4.9 20.4 1.0 C A:CYS554 5.0 33.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH 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 E545R Mutant Bound to H3T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:21.2 occ:1.00 SG A:CYS559 2.3 22.4 1.0 SG A:CYS562 2.3 18.5 1.0 SG A:CYS540 2.3 20.4 1.0 SG A:CYS537 2.4 18.6 1.0 CB A:CYS537 3.1 18.3 1.0 CB A:CYS562 3.2 18.6 1.0 CB A:CYS540 3.2 20.2 1.0 CB A:CYS559 3.4 19.9 1.0 N A:CYS540 3.8 16.9 1.0 O A:HOH877 4.0 30.8 1.0 N A:CYS559 4.0 16.5 1.0 CA A:CYS540 4.1 21.1 1.0 N A:CYS562 4.2 17.6 1.0 CA A:CYS559 4.2 19.2 1.0 CA A:CYS562 4.3 15.4 1.0 CA A:CYS537 4.6 20.0 1.0 CB A:ILE539 4.6 19.2 1.0 O A:CYS559 4.6 17.9 1.0 C A:CYS559 4.8 20.3 1.0 C A:ILE539 4.8 22.9 1.0 O A:HOH902 4.9 36.4 1.0 C A:CYS540 4.9 23.9 1.0 O A:GLY542 5.0 24.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of DNMT3A Add Domain E545R Mutant Bound to H3T3PH 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 E545R Mutant Bound to H3T3PH Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:17.9 occ:1.00 SG A:CYS497 2.3 19.3 1.0 SG A:CYS494 2.3 14.7 1.0 SG A:CYS517 2.4 17.1 1.0 SG A:CYS514 2.4 19.3 1.0 CB A:CYS497 3.3 17.0 1.0 CB A:CYS517 3.3 21.0 1.0 CB A:CYS494 3.3 16.9 1.0 CB A:CYS514 3.5 16.3 1.0 N A:CYS497 3.7 15.8 1.0 OG A:SER496 3.8 16.8 0.5 N A:CYS514 3.9 16.1 1.0 CA A:CYS497 4.0 17.0 1.0 N A:CYS517 4.2 19.8 1.0 CA A:CYS514 4.2 19.5 1.0 O A:HOH804 4.3 16.5 1.0 CB A:SER499 4.3 19.6 1.0 CA A:CYS517 4.3 17.5 1.0 CB A:SER496 4.6 17.9 0.5 C A:SER496 4.6 18.0 1.0 C A:CYS497 4.7 18.9 1.0 N A:SER499 4.7 19.1 1.0 CA A:CYS494 4.7 14.1 1.0 N A:GLY498 4.7 18.8 1.0 C A:CYS514 4.8 20.3 1.0 O A:CYS514 4.8 18.1 1.0 CB A:SER496 4.8 18.0 0.5 CA A:SER496 5.0 16.9 0.5

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.