Zinc in PDB 4mi5: Crystal Structure of the EZH2 Set Domain

All present enzymatic activity of Crystal Structure of the EZH2 Set Domain:
2.1.1.43;

The structure of Crystal Structure of the EZH2 Set Domain, PDB code: 4mi5 was solved by S.Antonysamy, B.Condon, Z.Druzina, J.Bonanno, T.Gheyi, I.Macewan, A.Zhang, S.Ashok, M.Russell, J.G.Luz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.02 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.134, 57.674, 75.501, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.7

The binding sites of Zinc atom in the Crystal Structure of the EZH2 Set Domain (pdb code 4mi5). 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 the EZH2 Set Domain, PDB code: 4mi5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:24.4 occ:1.00 SG A:CYS590 2.2 14.3 1.0 SG A:CYS578 2.3 13.7 1.0 SG A:CYS585 2.4 14.9 1.0 SG A:CYS565 2.5 13.6 1.0 CB A:CYS585 3.2 14.7 1.0 CB A:CYS590 3.3 15.3 1.0 CB A:CYS565 3.3 14.9 1.0 CB A:CYS578 3.3 11.6 1.0 CA A:CYS585 3.5 17.0 1.0 N A:CYS565 3.6 18.3 1.0 ZN A:ZN803 3.8 25.0 1.0 ZN A:ZN804 4.0 26.8 1.0 CA A:CYS565 4.0 15.9 1.0 C A:GLY564 4.3 21.5 1.0 SG A:CYS576 4.3 15.6 1.0 N A:ASP586 4.5 22.8 1.0 CA A:CYS590 4.5 18.6 1.0 N A:CYS585 4.5 16.6 1.0 CA A:GLY564 4.6 24.1 1.0 SG A:CYS593 4.6 21.9 1.0 C A:CYS585 4.6 17.2 1.0 O A:HOH918 4.6 17.8 1.0 CA A:CYS578 4.7 14.3 1.0 C A:CYS565 4.8 14.3 1.0 O A:CYS565 4.8 13.2 1.0 SG A:CYS571 4.8 18.3 1.0 O A:HOH902 4.9 16.7 1.0 N A:CYS578 4.9 13.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:25.0 occ:1.00 SG A:CYS576 2.3 15.6 1.0 SG A:CYS571 2.3 18.3 1.0 SG A:CYS565 2.4 13.6 1.0 SG A:CYS567 2.4 16.2 1.0 CB A:CYS565 3.2 14.9 1.0 CB A:CYS567 3.2 13.9 1.0 CB A:CYS571 3.2 16.9 1.0 CB A:CYS576 3.3 15.8 1.0 ZN A:ZN804 3.8 26.8 1.0 ZN A:ZN802 3.8 24.4 1.0 CA A:CYS571 3.9 21.3 1.0 SG A:CYS585 4.0 14.9 1.0 CA A:CYS576 4.1 17.4 1.0 N A:CYS567 4.3 16.1 1.0 CA A:CYS567 4.4 18.1 1.0 O A:HOH1014 4.4 33.4 1.0 CB A:CYS593 4.6 20.7 1.0 CA A:CYS565 4.6 15.9 1.0 CD A:PRO577 4.7 21.1 1.0 N A:CYS571 4.7 16.2 1.0 SG A:CYS593 4.8 21.9 1.0 C A:CYS576 4.8 17.8 1.0 SG A:CYS578 4.9 13.7 1.0 N A:PRO577 4.9 17.3 1.0 CB A:CYS578 5.0 11.6 1.0 C A:CYS571 5.0 21.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:26.8 occ:1.00 SG A:CYS593 2.3 21.9 1.0 SG A:CYS606 2.3 19.3 1.0 SG A:CYS571 2.4 18.3 1.0 SG A:CYS585 2.4 14.9 1.0 CB A:CYS593 3.2 20.7 1.0 CB A:CYS571 3.2 16.9 1.0 CB A:CYS606 3.3 18.9 1.0 CB A:CYS585 3.4 14.7 1.0 ZN A:ZN803 3.8 25.0 1.0 ZN A:ZN802 4.0 24.4 1.0 SG A:CYS565 4.0 13.6 1.0 CA A:CYS606 4.3 17.4 1.0 CB A:ALA595 4.4 27.6 1.0 CB A:ASN608 4.5 16.6 1.0 CA A:CYS593 4.5 23.1 1.0 CA A:CYS571 4.7 21.3 1.0 C A:CYS593 4.7 23.7 1.0 N A:ALA595 4.8 28.7 1.0 CB A:CYS590 4.8 15.3 1.0 CA A:CYS585 4.8 17.0 1.0 O A:CYS593 4.8 23.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:24.6 occ:1.00 SG A:CYS541 2.3 15.6 1.0 SG A:CYS552 2.4 17.7 1.0 SG A:CYS548 2.4 12.4 1.0 SG A:CYS528 2.5 14.7 1.0 CB A:CYS548 3.2 15.2 1.0 CB A:CYS552 3.2 22.3 1.0 CB A:CYS528 3.3 14.3 1.0 CB A:CYS541 3.3 13.8 1.0 CA A:CYS548 3.6 16.1 1.0 N A:CYS528 3.7 17.2 1.0 ZN A:ZN806 3.7 27.3 1.0 ZN A:ZN807 3.9 24.8 1.0 CA A:CYS528 4.1 16.5 1.0 SG A:CYS539 4.2 18.8 1.0 O A:HOH974 4.3 36.3 1.0 SG A:CYS554 4.4 17.5 1.0 CA A:CYS552 4.5 20.2 1.0 N A:CYS548 4.5 15.6 1.0 SG A:CYS535 4.6 15.0 1.0 C A:CYS548 4.6 20.7 1.0 N A:GLU549 4.7 22.4 1.0 CA A:CYS541 4.7 16.2 1.0 C A:PRO527 4.8 23.8 1.0 C A:CYS528 5.0 21.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:27.3 occ:1.00 SG A:CYS539 2.2 18.8 1.0 SG A:CYS528 2.3 14.7 1.0 NE2 A:HIS530 2.3 27.4 1.0 SG A:CYS535 2.3 15.0 1.0 CB A:CYS528 3.0 14.3 1.0 CE1 A:HIS530 3.1 28.7 1.0 CB A:CYS539 3.2 17.7 1.0 CB A:CYS535 3.3 14.3 1.0 CD2 A:HIS530 3.3 24.2 1.0 ZN A:ZN805 3.7 24.6 1.0 CA A:CYS535 3.9 18.5 1.0 ZN A:ZN807 3.9 24.8 1.0 SG A:CYS548 4.1 12.4 1.0 ND1 A:HIS530 4.3 26.3 1.0 CA A:CYS539 4.3 18.4 1.0 CG A:HIS530 4.4 26.6 1.0 CA A:CYS528 4.5 16.5 1.0 N A:CYS535 4.6 18.4 1.0 SG A:CYS541 4.7 15.6 1.0 CB A:CYS554 4.8 19.5 1.0 O A:HOH948 4.8 28.0 1.0 CB A:CYS541 4.8 13.8 1.0 CD A:PRO540 4.8 14.3 1.0 SG A:CYS554 4.9 17.5 1.0 O A:HOH1031 4.9 32.7 1.0 C A:CYS528 5.0 21.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the EZH2 Set Domain


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 the EZH2 Set Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:24.8 occ:1.00 SG A:CYS554 2.3 17.5 1.0 SG A:CYS558 2.3 18.8 1.0 SG A:CYS535 2.3 15.0 1.0 SG A:CYS548 2.4 12.4 1.0 CB A:CYS554 3.2 19.5 1.0 CB A:CYS548 3.2 15.2 1.0 CB A:CYS558 3.3 19.1 1.0 CB A:CYS535 3.3 14.3 1.0 ZN A:ZN806 3.9 27.3 1.0 ZN A:ZN805 3.9 24.6 1.0 SG A:CYS528 4.1 14.7 1.0 O A:HOH919 4.2 19.8 1.0 CB A:ASN560 4.5 17.7 1.0 CA A:CYS554 4.6 18.9 1.0 CA A:CYS548 4.7 16.1 1.0 CA A:CYS558 4.7 16.8 1.0 CA A:CYS535 4.7 18.5 1.0 CG A:ARG561 4.8 19.2 1.0 CB A:CYS552 4.9 22.3 1.0 NE A:ARG561 4.9 26.0 1.0

S.Antonysamy, B.Condon, Z.Druzina, J.B.Bonanno, T.Gheyi, F.Zhang, I.Macewan, A.Zhang, S.Ashok, L.Rodgers, M.Russell, J.Gately Luz. Structural Context of Disease-Associated Mutations and Putative Mechanism of Autoinhibition Revealed By X-Ray Crystallographic Analysis of the EZH2-Set Domain. Plos One V. 8 84147 2013.
ISSN: ESSN 1932-6203
PubMed: 24367637
DOI: 10.1371/JOURNAL.PONE.0084147