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Zinc in PDB 4mi0: Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)

Enzymatic activity of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)

All present enzymatic activity of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2):
2.1.1.43;

Protein crystallography data

The structure of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2), PDB code: 4mi0 was solved by A.Dong, H.Zeng, H.He, A.Wernimont, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, H.Wu, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.06 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.010, 57.796, 74.542, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) (pdb code 4mi0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2), PDB code: 4mi0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4mi0

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Zinc binding site 1 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:26.3
occ:1.00
 SG A:CYS566 2.2 28.5 1.0
SG A:CYS601 2.3 33.2 1.0
SG A:CYS580 2.4 26.8 1.0
SG A:CYS588 2.4 32.6 1.0
CB A:CYS566 3.1 25.6 1.0
CB A:CYS588 3.1 29.7 1.0
CB A:CYS601 3.3 30.5 1.0
CB A:CYS580 3.4 23.7 1.0
ZN A:ZN803 3.8 30.3 1.0
ZN A:ZN802 4.0 26.8 1.0
SG A:CYS560 4.0 27.7 1.0
CA A:CYS601 4.3 31.4 1.0
CB A:ALA590 4.4 37.0 1.0
CA A:CYS588 4.5 31.1 1.0
CA A:CYS566 4.6 26.4 1.0
CB A:ASN603 4.6 23.8 1.0
CB A:CYS585 4.7 24.9 1.0
CA A:CYS580 4.8 24.5 1.0
N A:ALA590 4.8 36.1 1.0
C A:CYS588 4.8 35.5 1.0
O A:HOH906 4.9 33.4 1.0
O A:CYS588 5.0 34.1 1.0
N A:CYS566 5.0 27.7 1.0

Zinc binding site 2 out of 6 in 4mi0

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Zinc binding site 2 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:26.8
occ:1.00
 SG A:CYS585 2.3 26.4 1.0
SG A:CYS573 2.3 26.1 1.0
SG A:CYS560 2.4 27.7 1.0
SG A:CYS580 2.5 26.8 1.0
CB A:CYS580 3.3 23.7 1.0
CB A:CYS573 3.3 22.7 1.0
CB A:CYS585 3.3 24.9 1.0
CB A:CYS560 3.3 24.2 1.0
N A:CYS560 3.5 25.7 1.0
CA A:CYS580 3.6 24.5 1.0
ZN A:ZN803 3.8 30.3 1.0
ZN A:ZN801 4.0 26.3 1.0
CA A:CYS560 4.0 24.4 1.0
C A:GLY559 4.3 28.9 1.0
SG A:CYS571 4.4 29.4 1.0
O A:HOH948 4.4 32.4 1.0
CA A:CYS585 4.5 28.6 1.0
N A:CYS580 4.6 25.4 1.0
CA A:GLY559 4.6 23.6 1.0
CA A:CYS573 4.6 23.9 1.0
N A:ASP581 4.6 31.2 1.0
SG A:CYS588 4.7 32.6 1.0
C A:CYS580 4.7 31.8 1.0
C A:CYS560 4.7 27.2 1.0
O A:CYS560 4.7 25.1 1.0
SG A:CYS566 4.8 28.5 1.0
N A:CYS573 4.8 26.2 1.0
O A:HOH906 4.8 33.4 1.0

Zinc binding site 3 out of 6 in 4mi0

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Zinc binding site 3 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:30.3
occ:1.00
 SG A:CYS571 2.3 29.4 1.0
SG A:CYS562 2.3 33.9 1.0
SG A:CYS560 2.3 27.7 1.0
SG A:CYS566 2.5 28.5 1.0
CB A:CYS560 3.2 24.2 1.0
CB A:CYS562 3.2 30.6 1.0
CB A:CYS566 3.2 25.6 1.0
CB A:CYS571 3.3 27.7 1.0
CA A:CYS566 3.8 26.4 1.0
ZN A:ZN801 3.8 26.3 1.0
ZN A:ZN802 3.8 26.8 1.0
SG A:CYS580 4.0 26.8 1.0
CA A:CYS571 4.1 28.3 1.0
N A:CYS562 4.4 32.7 1.0
CA A:CYS562 4.4 31.7 1.0
N A:CYS566 4.6 27.7 1.0
CB A:CYS588 4.6 29.7 1.0
CA A:CYS560 4.6 24.4 1.0
CD A:PRO572 4.7 28.1 1.0
C A:CYS571 4.8 31.7 1.0
SG A:CYS573 4.9 26.1 1.0
CB A:CYS573 4.9 22.7 1.0
N A:PRO572 4.9 27.4 1.0
SG A:CYS588 5.0 32.6 1.0
C A:CYS566 5.0 32.1 1.0

Zinc binding site 4 out of 6 in 4mi0

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Zinc binding site 4 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:27.2
occ:1.00
 SG A:CYS549 2.2 28.4 1.0
SG A:CYS553 2.3 28.2 1.0
SG A:CYS530 2.3 27.9 1.0
SG A:CYS543 2.4 25.0 1.0
CB A:CYS549 3.0 26.8 1.0
CB A:CYS553 3.3 24.6 1.0
CB A:CYS543 3.3 21.5 1.0
CB A:CYS530 3.4 25.1 1.0
ZN A:ZN805 3.9 27.6 1.0
ZN A:ZN806 3.9 27.9 1.0
SG A:CYS523 4.1 28.8 1.0
O A:HOH918 4.3 35.4 1.0
CA A:CYS549 4.5 29.3 1.0
CB A:ASN555 4.5 26.6 1.0
CA A:CYS553 4.7 25.6 1.0
CA A:CYS543 4.7 22.5 1.0
CA A:CYS530 4.8 26.3 1.0
CB A:CYS547 4.8 26.0 1.0
NE A:ARG556 4.9 28.2 1.0
CG A:ARG556 4.9 22.7 1.0
N A:CYS549 4.9 31.8 1.0

Zinc binding site 5 out of 6 in 4mi0

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Zinc binding site 5 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:27.6
occ:1.00
 NE2 A:HIS525 2.0 36.4 1.0
SG A:CYS523 2.3 28.8 1.0
SG A:CYS534 2.3 26.8 1.0
SG A:CYS530 2.3 27.9 1.0
CE1 A:HIS525 2.8 36.1 1.0
CB A:CYS523 3.1 26.4 1.0
CD2 A:HIS525 3.1 36.9 1.0
CB A:CYS534 3.2 23.4 1.0
CB A:CYS530 3.4 25.1 1.0
ZN A:ZN806 3.7 27.9 1.0
CA A:CYS530 3.9 26.3 1.0
ZN A:ZN804 3.9 27.2 1.0
ND1 A:HIS525 4.0 37.4 1.0
SG A:CYS543 4.1 25.0 1.0
CG A:HIS525 4.1 36.2 1.0
CA A:CYS534 4.3 24.2 1.0
CA A:CYS523 4.5 27.6 1.0
CB A:CYS549 4.6 26.8 1.0
N A:CYS530 4.7 27.2 1.0
SG A:CYS536 4.8 27.6 1.0
SG A:CYS549 4.8 28.4 1.0
CB A:CYS536 4.9 24.1 1.0
C A:CYS523 4.9 35.0 1.0
C A:CYS534 4.9 28.0 1.0
CD A:PRO535 5.0 26.0 1.0
O A:PRO529 5.0 33.1 1.0

Zinc binding site 6 out of 6 in 4mi0

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Zinc binding site 6 out of 6 in the Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn806

b:27.9
occ:1.00
 SG A:CYS547 2.3 28.8 1.0
SG A:CYS536 2.4 27.6 1.0
SG A:CYS543 2.4 25.0 1.0
SG A:CYS523 2.4 28.8 1.0
CB A:CYS523 3.2 26.4 1.0
CB A:CYS547 3.2 26.0 1.0
CB A:CYS543 3.3 21.5 1.0
CB A:CYS536 3.3 24.1 1.0
CA A:CYS543 3.6 22.5 1.0
N A:CYS523 3.6 30.0 1.0
ZN A:ZN805 3.7 27.6 1.0
ZN A:ZN804 3.9 27.2 1.0
CA A:CYS523 4.0 27.6 1.0
SG A:CYS534 4.3 26.8 1.0
SG A:CYS549 4.4 28.4 1.0
CA A:CYS547 4.5 27.5 1.0
SG A:CYS530 4.5 27.9 1.0
N A:CYS543 4.5 22.4 1.0
CA A:CYS536 4.7 24.2 1.0
C A:CYS543 4.7 29.1 1.0
N A:GLU544 4.7 26.2 1.0
C A:PRO522 4.8 38.0 1.0
C A:CYS523 4.9 35.0 1.0
N A:CYS536 5.0 24.9 1.0

Reference:

H.Zeng, A.Dong, H.He, A.Wernimont, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, H.Wu, Structural Genomics Consortium (Sgc). Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) To Be Published.
Page generated: Wed Dec 16 05:35:24 2020

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