Zinc in PDB 4u7t: Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3

All present enzymatic activity of Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3:
2.1.1.37;

The structure of Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3, PDB code: 4u7t was solved by X.Guo, L.Wang, X.Yin, J.Li, J.Xiao, S.He, J.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.21 / 2.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	183.823, 183.823, 123.265, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.1

The binding sites of Zinc atom in the Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3 (pdb code 4u7t). 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-DNMT3L in Complex with Histone H3, PDB code: 4u7t:
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-DNMT3L 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 DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:80.6 occ:1.00 SG A:CYS494 2.2 78.0 1.0 SG A:CYS497 2.3 90.8 1.0 SG A:CYS517 2.3 77.2 1.0 SG A:CYS514 2.4 72.4 1.0 CB A:CYS517 3.3 77.2 1.0 CB A:CYS494 3.4 85.5 1.0 CB A:CYS497 3.4 87.3 1.0 CB A:CYS514 3.4 77.4 1.0 N A:CYS497 3.6 89.0 1.0 N A:CYS514 3.8 79.8 1.0 CA A:CYS497 4.0 88.8 1.0 CB A:SER499 4.1 84.3 1.0 CB A:SER496 4.1 81.0 1.0 CA A:CYS514 4.1 85.5 1.0 N A:SER499 4.5 94.9 1.0 CA A:CYS517 4.5 81.0 1.0 N A:CYS517 4.5 87.0 1.0 C A:SER496 4.5 88.0 1.0 C A:CYS497 4.6 88.2 1.0 N A:GLY498 4.6 87.0 1.0 O A:CYS514 4.7 85.9 1.0 CA A:CYS494 4.7 86.0 1.0 O A:CYS494 4.7 86.2 1.0 C A:CYS514 4.7 85.4 1.0 CA A:SER496 4.8 80.5 1.0 C A:CYS494 4.9 88.2 1.0 N A:SER496 4.9 77.6 1.0 CA A:SER499 4.9 87.3 1.0 C A:MET513 4.9 86.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of DNMT3A-DNMT3L 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 DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:0.0 occ:1.00 SG A:CYS562 2.2 97.5 1.0 SG A:CYS540 2.2 0.1 1.0 SG A:CYS559 2.4 0.9 1.0 SG A:CYS537 2.6 86.8 1.0 CB A:CYS537 3.2 83.3 1.0 CB A:CYS562 3.2 0.9 1.0 CB A:CYS540 3.3 88.6 1.0 CB A:CYS559 3.7 0.5 1.0 N A:CYS540 3.9 90.8 1.0 CA A:CYS562 4.2 0.4 1.0 N A:CYS562 4.2 0.3 1.0 CA A:CYS540 4.2 86.0 1.0 N A:CYS559 4.2 97.2 1.0 NH2 A:ARG476 4.4 0.3 1.0 CB A:ILE539 4.4 85.1 1.0 CA A:CYS559 4.5 0.9 1.0 CA A:GLY543 4.6 0.6 1.0 CA A:CYS537 4.7 80.5 1.0 O A:CYS559 4.7 0.1 1.0 O A:GLY542 4.7 0.5 1.0 N A:GLY543 4.8 0.7 1.0 C A:GLY542 4.8 96.7 1.0 C A:ILE539 5.0 94.2 1.0 C A:CYS559 5.0 0.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of DNMT3A-DNMT3L 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 DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:99.3 occ:1.00 SG A:CYS583 2.1 86.1 1.0 SG A:CYS554 2.2 75.2 1.0 SG A:CYS586 2.3 86.4 1.0 SG A:CYS549 2.5 95.5 1.0 CB A:CYS583 3.3 0.1 1.0 CB A:CYS554 3.3 80.5 1.0 CB A:CYS586 3.4 0.2 1.0 CB A:CYS549 3.6 95.7 1.0 N A:CYS583 4.1 0.1 1.0 CA A:CYS583 4.1 0.2 1.0 N A:CYS586 4.4 0.7 1.0 O A:CYS583 4.4 0.8 1.0 CA A:CYS586 4.4 0.7 1.0 C A:CYS583 4.5 0.1 1.0 CB A:ASN551 4.6 88.8 1.0 CA A:CYS554 4.7 80.0 1.0 CB A:ARG556 4.8 87.4 1.0 CG A:ARG556 4.9 86.5 1.0 CB A:MET585 4.9 0.6 1.0 C A:MET585 5.0 0.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of DNMT3A-DNMT3L 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 4 of Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:79.7 occ:1.00 SG C:CYS494 2.2 77.5 1.0 SG C:CYS517 2.3 77.5 1.0 SG C:CYS497 2.3 88.9 1.0 SG C:CYS514 2.5 72.4 1.0 CB C:CYS517 3.3 78.1 1.0 CB C:CYS497 3.4 85.0 1.0 CB C:CYS494 3.5 84.3 1.0 N C:CYS497 3.5 89.5 1.0 CB C:CYS514 3.5 78.2 1.0 N C:CYS514 3.9 77.7 1.0 CA C:CYS497 4.0 88.5 1.0 CB C:SER496 4.0 80.8 1.0 CB C:SER499 4.2 86.8 1.0 CA C:CYS514 4.2 84.2 1.0 N C:CYS517 4.4 84.5 1.0 CA C:CYS517 4.4 77.1 1.0 C C:SER496 4.4 87.9 1.0 N C:SER499 4.5 93.3 1.0 C C:CYS497 4.6 86.6 1.0 N C:GLY498 4.6 86.0 1.0 CA C:SER496 4.7 80.8 1.0 O C:CYS514 4.7 81.6 1.0 O C:CYS494 4.7 87.0 1.0 CA C:CYS494 4.8 84.9 1.0 C C:CYS514 4.8 81.2 1.0 N C:SER496 4.9 78.2 1.0 C C:CYS494 4.9 89.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of DNMT3A-DNMT3L 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 5 of Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:0.5 occ:1.00 SG C:CYS562 2.1 0.4 1.0 SG C:CYS559 2.3 0.0 1.0 SG C:CYS540 2.4 98.9 1.0 SG C:CYS537 2.5 90.3 1.0 CB C:CYS562 3.1 0.8 1.0 CB C:CYS537 3.2 82.6 1.0 CB C:CYS540 3.3 87.7 1.0 CB C:CYS559 3.7 0.8 1.0 N C:CYS540 3.7 89.5 1.0 CA C:CYS562 4.1 0.7 1.0 CA C:CYS540 4.1 86.7 1.0 CB C:ILE539 4.2 87.4 1.0 N C:CYS562 4.2 1.0 1.0 N C:CYS559 4.2 96.2 1.0 CA C:CYS559 4.4 0.1 1.0 NH2 C:ARG476 4.5 0.3 1.0 O C:CYS559 4.6 0.7 1.0 CA C:CYS537 4.7 79.8 1.0 C C:ILE539 4.8 96.3 1.0 CG1 C:ILE539 4.8 85.2 1.0 CA C:ILE539 4.9 90.1 1.0 CA C:GLY543 4.9 0.1 1.0 CG2 C:ILE539 4.9 94.0 1.0 C C:CYS559 4.9 0.8 1.0 O C:GLY542 4.9 96.5 1.0 N C:ILE539 5.0 88.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of DNMT3A-DNMT3L 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 6 of Crystal Structure of DNMT3A-DNMT3L in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1003 b:95.0 occ:1.00 SG C:CYS583 2.1 90.8 1.0 SG C:CYS554 2.2 76.4 1.0 SG C:CYS586 2.3 92.7 1.0 SG C:CYS549 2.5 95.2 1.0 CB C:CYS554 3.3 80.2 1.0 CB C:CYS583 3.4 0.7 1.0 CB C:CYS586 3.4 0.8 1.0 CB C:CYS549 3.7 92.3 1.0 N C:CYS583 4.1 0.9 1.0 CA C:CYS583 4.2 0.9 1.0 N C:CYS586 4.4 0.4 1.0 O C:CYS583 4.5 0.3 1.0 CA C:CYS586 4.5 0.8 1.0 CB C:ASN551 4.5 86.5 1.0 C C:CYS583 4.5 0.8 1.0 CA C:CYS554 4.7 77.3 1.0 CB C:MET585 4.8 0.7 1.0 C C:MET585 4.9 0.8 1.0 CB C:ARG556 5.0 86.0 1.0

X.Guo, L.Wang, J.Li, Z.Ding, J.Xiao, X.Yin, S.He, P.Shi, L.Dong, G.Li, C.Tian, J.Wang, Y.Cong, Y.Xu. Structural Insight Into Autoinhibition and Histone H3-Induced Activation of DNMT3A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13899