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Zinc in PDB 4qbr: Crystal Structure of DNMT3A Add Domain G550D Mutant Bound to H3 Peptide

Enzymatic activity of Crystal Structure of DNMT3A Add Domain G550D Mutant Bound to H3 Peptide

All present enzymatic activity of Crystal Structure of DNMT3A Add Domain G550D Mutant Bound to H3 Peptide:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of DNMT3A Add Domain G550D Mutant Bound to H3 Peptide, PDB code: 4qbr 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) 36.14 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.057, 37.161, 50.125, 78.70, 83.89, 81.56
R / Rfree (%) 17.8 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DNMT3A Add Domain G550D Mutant Bound to H3 Peptide (pdb code 4qbr). 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 G550D Mutant Bound to H3 Peptide, PDB code: 4qbr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4qbr

Go back to Zinc Binding Sites List in 4qbr
Zinc binding site 1 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:20.1
occ:1.00
SG A:CYS549 2.2 19.6 1.0
SG A:CYS583 2.3 17.5 1.0
SG A:CYS586 2.3 22.8 1.0
SG A:CYS554 2.4 18.1 1.0
CB A:CYS549 3.1 16.5 1.0
CB A:CYS554 3.1 22.2 1.0
CB A:CYS583 3.5 15.7 1.0
CB A:CYS586 3.5 29.8 1.0
N A:CYS583 3.7 18.2 1.0
CA A:CYS583 4.1 19.1 1.0
N A:CYS586 4.2 25.6 1.0
CB A:ASN551 4.3 21.5 1.0
CA A:CYS586 4.4 32.5 1.0
CA A:CYS549 4.5 17.8 1.0
C A:CYS583 4.5 18.8 1.0
CA A:CYS554 4.6 20.0 1.0
O A:CYS583 4.6 14.9 1.0
C A:MET585 4.7 24.6 1.0
CB A:ARG556 4.8 19.4 1.0
C A:ASN582 4.8 19.1 1.0
N A:ARG556 4.9 18.0 1.0
CB A:MET585 4.9 21.5 1.0
N A:MET585 5.0 17.9 1.0
ND2 A:ASN551 5.0 25.9 1.0

Zinc binding site 2 out of 6 in 4qbr

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Zinc binding site 2 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:18.0
occ:1.00
SG A:CYS559 2.2 16.9 1.0
SG A:CYS562 2.3 17.2 1.0
SG A:CYS537 2.4 17.0 1.0
SG A:CYS540 2.4 18.8 1.0
CB A:CYS537 3.2 16.9 1.0
CB A:CYS562 3.2 14.4 1.0
CB A:CYS540 3.2 22.7 1.0
CB A:CYS559 3.5 18.8 1.0
N A:CYS540 3.7 17.8 1.0
N A:CYS559 4.0 14.8 1.0
CA A:CYS540 4.1 19.7 1.0
N A:CYS562 4.1 15.9 1.0
CA A:CYS562 4.2 14.3 1.0
CA A:CYS559 4.3 15.5 1.0
CB A:ILE539 4.6 14.3 1.0
CA A:CYS537 4.7 17.5 1.0
O A:CYS559 4.7 16.7 1.0
CA A:GLY543 4.8 24.6 1.0
NH2 A:ARG476 4.8 21.8 1.0
N A:GLY543 4.8 21.6 1.0
C A:ILE539 4.8 19.6 1.0
C A:CYS559 4.8 16.9 1.0
C A:CYS540 4.9 22.6 1.0
C A:GLY542 5.0 23.0 1.0

Zinc binding site 3 out of 6 in 4qbr

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Zinc binding site 3 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:22.2
occ:1.00
SG A:CYS497 2.3 20.5 1.0
SG A:CYS494 2.4 17.9 1.0
SG A:CYS514 2.4 18.5 1.0
SG A:CYS517 2.4 20.4 1.0
CB A:CYS497 3.2 26.2 1.0
CB A:CYS494 3.3 17.9 1.0
CB A:CYS517 3.3 23.6 1.0
CB A:CYS514 3.5 17.7 1.0
N A:CYS497 3.8 18.9 1.0
N A:CYS514 4.0 17.8 1.0
CA A:CYS497 4.0 20.5 1.0
CB A:SER499 4.1 27.2 1.0
N A:CYS517 4.3 16.8 1.0
CA A:CYS514 4.3 18.0 1.0
CA A:CYS517 4.4 21.1 1.0
CB A:SER496 4.5 18.5 1.0
N A:SER499 4.6 23.4 1.0
O A:HOH840 4.6 36.6 1.0
C A:SER496 4.6 21.8 1.0
C A:CYS497 4.7 23.7 1.0
N A:GLY498 4.7 20.1 1.0
CA A:CYS494 4.7 21.9 1.0
OG A:SER496 4.7 25.9 1.0
O A:CYS514 4.8 15.9 1.0
C A:CYS514 4.8 22.6 1.0
O A:HOH904 4.9 33.7 1.0
CA A:SER496 5.0 17.5 1.0
CA A:SER499 5.0 23.1 1.0

Zinc binding site 4 out of 6 in 4qbr

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Zinc binding site 4 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:19.0
occ:1.00
SG C:CYS549 2.2 19.0 1.0
SG C:CYS583 2.3 16.5 1.0
SG C:CYS586 2.4 20.2 1.0
SG C:CYS554 2.5 19.6 1.0
CB C:CYS549 3.1 19.4 1.0
CB C:CYS554 3.1 19.3 1.0
CB C:CYS586 3.4 22.0 1.0
CB C:CYS583 3.5 15.6 1.0
N C:CYS583 3.8 15.6 1.0
N C:CYS586 4.1 20.5 1.0
CA C:CYS583 4.1 19.1 1.0
CA C:CYS586 4.3 23.9 1.0
CB C:ASN551 4.5 22.1 1.0
CA C:CYS549 4.5 16.2 1.0
C C:CYS583 4.6 19.0 1.0
CA C:CYS554 4.6 17.2 1.0
O C:CYS583 4.6 16.0 1.0
CB C:ARG556 4.7 14.3 1.0
C C:MET585 4.8 22.8 1.0
CB C:MET585 4.8 18.9 1.0
N C:ARG556 4.9 17.2 1.0
C C:ASN582 4.9 14.1 1.0
CD C:ARG556 4.9 19.8 1.0
N C:CYS555 4.9 12.7 1.0
N C:MET585 5.0 19.2 1.0
ND2 C:ASN551 5.0 30.8 1.0
C C:CYS554 5.0 16.1 1.0

Zinc binding site 5 out of 6 in 4qbr

Go back to Zinc Binding Sites List in 4qbr
Zinc binding site 5 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:17.8
occ:1.00
SG C:CYS559 2.3 18.8 1.0
SG C:CYS540 2.3 18.5 1.0
SG C:CYS562 2.4 18.5 1.0
SG C:CYS537 2.4 15.9 1.0
CB C:CYS537 3.1 17.7 1.0
CB C:CYS562 3.2 18.3 1.0
CB C:CYS540 3.2 22.1 1.0
CB C:CYS559 3.5 19.8 1.0
N C:CYS540 3.8 18.1 1.0
N C:CYS559 4.0 15.8 1.0
CA C:CYS540 4.1 21.0 1.0
N C:CYS562 4.2 16.4 1.0
CA C:CYS559 4.3 16.5 1.0
CA C:CYS562 4.3 12.4 1.0
O C:HOH886 4.4 36.1 1.0
CB C:ILE539 4.5 17.3 1.0
CA C:CYS537 4.6 12.8 1.0
O C:CYS559 4.7 18.5 1.0
C C:ILE539 4.8 18.7 1.0
O C:HOH845 4.8 38.4 1.0
C C:CYS540 4.8 20.3 1.0
C C:CYS559 4.8 17.9 1.0
CA C:GLY543 4.8 21.8 1.0
NH2 C:ARG476 4.8 19.7 1.0
N C:GLY543 4.9 23.6 1.0

Zinc binding site 6 out of 6 in 4qbr

Go back to Zinc Binding Sites List in 4qbr
Zinc binding site 6 out of 6 in the Crystal Structure of DNMT3A Add Domain G550D Mutant 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 G550D Mutant Bound to H3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:20.2
occ:1.00
SG C:CYS497 2.3 20.1 1.0
SG C:CYS517 2.4 17.4 1.0
SG C:CYS494 2.4 17.6 1.0
SG C:CYS514 2.4 18.2 1.0
CB C:CYS517 3.2 19.5 1.0
CB C:CYS497 3.3 23.5 1.0
CB C:CYS494 3.3 16.9 1.0
CB C:CYS514 3.6 16.8 1.0
N C:CYS497 3.7 18.3 1.0
N C:CYS514 4.0 15.5 1.0
CA C:CYS497 4.0 17.8 1.0
O C:HOH888 4.2 34.0 1.0
N C:CYS517 4.2 18.3 1.0
CB C:SER499 4.3 24.4 1.0
CB C:SER496 4.3 20.1 1.0
CA C:CYS517 4.3 21.5 1.0
CA C:CYS514 4.3 17.7 1.0
C C:SER496 4.5 17.1 1.0
N C:SER499 4.6 19.2 1.0
C C:CYS497 4.7 21.7 1.0
N C:GLY498 4.7 18.3 1.0
CA C:CYS494 4.7 19.9 1.0
O C:HOH840 4.8 34.5 1.0
O C:CYS514 4.8 15.9 1.0
C C:CYS514 4.8 18.9 1.0
CA C:SER496 4.8 20.0 1.0

Reference:

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.
Page generated: Wed Dec 16 05:43:15 2020

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