Zinc in PDB 7kso: Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2

All present enzymatic activity of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2:
2.1.1.356;

The binding sites of Zinc atom in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 (pdb code 7kso). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2, PDB code: 7kso:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:131.4 occ:1.00 SG A:CYS302 1.8 112.7 1.0 ND1 A:HIS310 2.3 105.9 1.0 CE1 A:HIS310 2.5 105.9 1.0 SG A:CYS307 2.5 109.3 0.9 CB A:CYS302 2.5 112.7 1.0 CB A:CYS307 3.2 109.3 1.0 SG A:CYS299 3.3 118.2 1.0 CD2 A:LEU309 3.6 102.5 1.0 CG A:HIS310 3.6 105.9 1.0 CA A:CYS302 3.7 112.7 1.0 NE2 A:HIS310 3.8 105.9 1.0 N A:CYS302 3.9 112.7 1.0 CB A:CYS299 4.1 118.2 1.0 CD2 A:HIS310 4.3 105.9 1.0 CG A:LEU309 4.4 102.5 1.0 CB A:HIS310 4.5 105.9 1.0 C A:ARG301 4.6 114.0 1.0 C A:CYS302 4.6 112.7 1.0 CA A:CYS307 4.7 109.3 1.0

Zinc binding site 2 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:173.8 occ:1.00 SG A:CYS550 2.3 138.7 1.0 ZN A:ZN803 2.5 180.2 1.0 SG A:CYS531 2.5 147.4 1.0 SG A:CYS544 3.0 127.2 1.0 CB A:CYS550 3.3 138.7 1.0 CB A:CYS544 3.4 127.2 1.0 ZN A:ZN804 3.7 160.3 1.0 SG A:CYS554 3.7 129.5 1.0 CG A:ARG557 3.9 123.3 1.0 CB A:CYS531 4.1 147.4 1.0 CB A:CYS554 4.2 129.5 1.0 SG A:CYS548 4.5 132.9 1.0 CD A:ARG557 4.5 123.3 1.0 CB A:ASN556 4.6 129.3 1.0 CA A:CYS550 4.7 138.7 1.0 N A:ARG557 4.8 123.3 1.0 CE1 A:HIS526 4.8 146.7 1.0 ND2 A:ASN556 4.9 129.3 1.0 CA A:CYS544 4.9 127.2 1.0

Zinc binding site 3 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:180.2 occ:1.00 SG A:CYS544 2.3 127.2 1.0 ZN A:ZN804 2.3 160.3 1.0 ZN A:ZN802 2.5 173.8 1.0 SG A:CYS531 2.7 147.4 1.0 SG A:CYS535 3.5 145.3 1.0 CB A:CYS531 3.7 147.4 1.0 ND2 A:ASN556 3.7 129.3 1.0 CB A:CYS544 3.8 127.2 1.0 NE2 A:HIS526 3.9 146.7 1.0 CE1 A:HIS526 4.0 146.7 1.0 SG A:CYS537 4.0 140.9 0.9 CB A:CYS537 4.2 140.9 1.0 SG A:CYS550 4.3 138.7 1.0 CB A:CYS550 4.5 138.7 1.0 SG A:CYS548 4.5 132.9 1.0 SG A:CYS524 4.5 139.6 1.0 CA A:CYS531 4.6 147.4 1.0 CB A:ASN556 4.6 129.3 1.0 CG A:ASN556 4.7 129.3 1.0 CB A:CYS535 4.7 145.3 1.0

Zinc binding site 4 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:160.3 occ:1.00 ZN A:ZN803 2.3 180.2 1.0 SG A:CYS548 2.6 132.9 1.0 SG A:CYS524 2.6 139.6 1.0 SG A:CYS537 3.1 140.9 0.9 SG A:CYS544 3.2 127.2 1.0 NE2 A:HIS526 3.5 146.7 1.0 SG A:CYS535 3.6 145.3 1.0 ZN A:ZN802 3.7 173.8 1.0 CB A:CYS548 3.7 132.9 1.0 CE1 A:HIS526 3.7 146.7 1.0 CB A:CYS537 4.3 140.9 1.0 CB A:CYS544 4.3 127.2 1.0 CB A:CYS550 4.3 138.7 1.0 CB A:CYS524 4.4 139.6 1.0 SG A:CYS531 4.4 147.4 1.0 SG A:CYS550 4.5 138.7 1.0 CD2 A:HIS526 4.7 146.7 1.0 N A:CYS524 4.9 139.6 1.0 ND1 A:HIS526 5.0 146.7 1.0

Zinc binding site 5 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn805 b:162.6 occ:1.00 SG A:CYS561 2.2 123.0 1.0 SG A:CYS581 2.4 110.3 1.0 ZN A:ZN807 2.4 158.2 1.0 SG A:CYS589 2.8 123.1 1.0 CB A:CYS586 3.0 116.5 1.0 SG A:CYS586 3.2 116.5 1.0 ZN A:ZN806 3.2 156.5 1.0 CB A:CYS581 3.3 110.3 1.0 CB A:CYS589 3.6 123.1 1.0 CB A:CYS561 3.9 123.0 1.0 SG A:CYS602 4.2 111.7 1.0 SG A:CYS567 4.2 120.7 1.0 CA A:CYS581 4.2 110.3 1.0 CA A:CYS586 4.3 116.5 1.0 O A:CYS586 4.7 116.5 1.0 N A:CYS561 4.8 123.0 1.0 CA A:CYS561 4.8 123.0 1.0 N A:ASP582 4.8 113.0 1.0 C A:CYS586 4.9 116.5 1.0 CA A:CYS589 5.0 123.1 1.0

Zinc binding site 6 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:156.5 occ:1.00 SG A:CYS567 2.5 120.7 1.0 SG A:CYS561 2.5 123.0 1.0 SG A:CYS572 2.7 117.5 1.0 CB A:CYS561 2.9 123.0 1.0 ZN A:ZN807 3.0 158.2 1.0 SG A:CYS581 3.1 110.3 1.0 ZN A:ZN805 3.2 162.6 1.0 CB A:CYS567 3.3 120.7 1.0 CB A:CYS572 4.2 117.5 1.0 CB A:CYS574 4.2 112.3 1.0 SG A:CYS574 4.3 112.3 1.0 O A:CYS567 4.3 120.7 1.0 CA A:CYS561 4.4 123.0 1.0 CA A:CYS567 4.7 120.7 1.0 CB A:CYS581 4.7 110.3 1.0 N A:CYS561 4.9 123.0 1.0 C A:CYS567 4.9 120.7 1.0

Zinc binding site 7 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn807 b:158.2 occ:1.00 ZN A:ZN805 2.4 162.6 1.0 SG A:CYS567 2.6 120.7 1.0 CB A:CYS589 2.6 123.1 1.0 ZN A:ZN806 3.0 156.5 1.0 SG A:CYS561 3.0 123.0 1.0 SG A:CYS589 3.1 123.1 1.0 CB A:CYS567 3.4 120.7 1.0 SG A:CYS581 3.4 110.3 1.0 SG A:CYS602 3.6 111.7 1.0 CA A:CYS589 4.0 123.1 1.0 O A:CYS563 4.2 123.2 1.0 CB A:CYS602 4.3 111.7 1.0 O A:THR565 4.3 119.3 1.0 CB A:CYS561 4.5 123.0 1.0 O A:GLN566 4.6 117.5 1.0 N A:CYS589 4.7 123.1 1.0 CA A:CYS567 4.7 120.7 1.0 C A:GLN566 4.8 117.5 1.0 CA A:CYS602 4.8 111.7 1.0 CB A:CYS581 4.9 110.3 1.0 N A:CYS567 4.9 120.7 1.0 CB A:CYS563 4.9 123.2 1.0

Zinc binding site 8 out of 8 in the Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of PRC2:EZH1-AEBP2-JARID2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:79.6 occ:1.00 NE2 C:HIS471 2.4 80.0 1.0 CE1 C:HIS466 2.7 79.4 1.0 CB C:CYS453 2.7 90.4 1.0 CD2 C:HIS471 2.9 80.0 1.0 CE1 C:HIS471 3.4 80.0 1.0 ND1 C:HIS466 3.4 79.4 1.0 NE1 C:TRP452 3.5 93.4 1.0 CD1 C:TRP452 3.6 93.4 1.0 SG C:CYS453 3.7 90.4 1.0 NE2 C:HIS466 3.8 79.4 1.0 CA C:CYS453 3.9 90.4 1.0 N C:CYS453 3.9 90.4 1.0 CG C:HIS471 4.0 80.0 1.0 SG C:CYS450 4.0 94.0 1.0 CB C:CYS450 4.2 94.0 1.0 ND1 C:HIS471 4.2 80.0 1.0 CD2 C:LEU467 4.5 82.4 1.0 CE2 C:TRP452 4.6 93.4 1.0 CG C:HIS466 4.7 79.4 1.0 CG C:TRP452 4.8 93.4 1.0 CD2 C:HIS466 4.8 79.4 1.0

D.J.Grau, Y.Zhang, C.H.Lee, M.Valenia-Sanchez, J.Zhang, M.Wang, M.Holder, V.Svetlov, T.Dongyan, E.Nudler, D.Reinberg, T.Walz. Structures of Monomeric and Dimeric PRC2:EZH1 Reveal Flexible Modules Involved in Chromatin Compaction To Be Published.