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Zinc in PDB 4u7p: Crystal Structure of DNMT3A-DNMT3L Complex

Enzymatic activity of Crystal Structure of DNMT3A-DNMT3L Complex

All present enzymatic activity of Crystal Structure of DNMT3A-DNMT3L Complex:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of DNMT3A-DNMT3L Complex, PDB code: 4u7p was solved by L.Wang, X.Guo, J.Li, J.Xiao, X.Yin, 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) 42.01 / 3.82
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 252.031, 252.031, 75.336, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DNMT3A-DNMT3L Complex (pdb code 4u7p). 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-DNMT3L Complex, PDB code: 4u7p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4u7p

Go back to Zinc Binding Sites List in 4u7p
Zinc binding site 1 out of 3 in the Crystal Structure of DNMT3A-DNMT3L Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.2
occ:1.00
SG A:CYS540 2.2 0.2 1.0
SG A:CYS559 2.3 0.4 1.0
SG A:CYS562 2.4 0.1 1.0
SG A:CYS537 2.4 0.1 1.0
CB A:CYS537 3.3 0.0 1.0
CB A:CYS540 3.5 0.5 1.0
CB A:CYS562 3.5 0.5 1.0
N A:CYS540 3.6 0.3 1.0
CB A:CYS559 3.8 0.5 1.0
CB A:ILE539 4.1 0.3 1.0
CA A:CYS540 4.1 0.2 1.0
CG2 A:ILE539 4.6 0.1 1.0
C A:ILE539 4.6 0.3 1.0
CA A:CYS562 4.6 0.6 1.0
N A:CYS562 4.6 0.2 1.0
NH2 A:ARG476 4.6 0.5 1.0
CA A:ILE539 4.7 0.7 1.0
CA A:CYS537 4.8 0.5 1.0
NH1 A:ARG476 4.8 0.0 1.0
N A:CYS559 4.8 0.5 1.0
N A:ILE539 4.8 0.2 1.0
C A:CYS540 4.8 0.0 1.0
CA A:CYS559 4.9 0.7 1.0
N A:CYS541 4.9 0.0 1.0
N A:GLY542 5.0 1.0 1.0
C A:GLY542 5.0 0.0 1.0

Zinc binding site 2 out of 3 in 4u7p

Go back to Zinc Binding Sites List in 4u7p
Zinc binding site 2 out of 3 in the Crystal Structure of DNMT3A-DNMT3L Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:0.9
occ:1.00
SG A:CYS517 2.2 0.1 1.0
SG A:CYS514 2.3 0.5 1.0
SG A:CYS497 2.4 0.5 1.0
SG A:CYS494 2.4 0.2 1.0
CB A:CYS494 3.3 0.7 1.0
CB A:CYS517 3.4 0.9 1.0
CB A:CYS514 3.4 0.7 1.0
CB A:CYS497 3.7 0.2 1.0
N A:CYS497 3.8 0.9 1.0
N A:CYS514 3.9 0.9 1.0
CA A:CYS514 4.3 0.6 1.0
CB A:SER499 4.3 0.4 1.0
N A:CYS517 4.3 0.8 1.0
CA A:CYS497 4.3 0.3 1.0
CB A:SER496 4.4 0.5 1.0
CA A:CYS517 4.4 0.7 1.0
N A:SER499 4.7 0.4 1.0
CA A:CYS494 4.7 1.0 1.0
N A:GLY498 4.9 0.9 1.0
C A:CYS497 4.9 0.5 1.0
C A:SER496 4.9 0.1 1.0
C A:CYS514 4.9 0.6 1.0

Zinc binding site 3 out of 3 in 4u7p

Go back to Zinc Binding Sites List in 4u7p
Zinc binding site 3 out of 3 in the Crystal Structure of DNMT3A-DNMT3L Complex


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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:0.6
occ:1.00
SG A:CYS583 2.3 0.5 1.0
SG A:CYS586 2.3 0.2 1.0
SG A:CYS554 2.4 0.1 1.0
SG A:CYS549 2.4 0.4 1.0
CB A:CYS554 3.3 0.1 1.0
CB A:CYS586 3.3 0.2 1.0
CB A:CYS549 3.5 0.8 1.0
CB A:CYS583 3.6 0.4 1.0
N A:CYS583 3.9 0.3 1.0
N A:CYS586 4.0 0.7 1.0
CA A:CYS586 4.2 0.0 1.0
CA A:CYS583 4.3 0.6 1.0
CB A:ASN551 4.5 0.3 1.0
CB A:ARG556 4.5 0.8 1.0
N A:ARG556 4.5 0.9 1.0
CA A:CYS554 4.7 0.2 1.0
N A:CYS555 4.7 0.1 1.0
CB A:MET585 4.8 0.4 1.0
C A:CYS583 4.8 0.9 1.0
CA A:CYS549 4.9 1.0 1.0
O A:CYS583 4.9 0.3 1.0
C A:MET585 4.9 0.1 1.0
C A:CYS554 5.0 0.0 1.0
C A:ASN582 5.0 0.8 1.0

Reference:

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
Page generated: Wed Dec 16 05:47:54 2020

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