Zinc in PDB 5wg6: Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor

All present enzymatic activity of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor:
2.1.1.43;

The structure of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor, PDB code: 5wg6 was solved by M.A.Bratkowski, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.65 / 3.90
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	243.880, 243.880, 243.699, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 30

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor (pdb code 5wg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor, PDB code: 5wg6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9001 b:100.0 occ:1.00 SG A:CYS452 2.4 0.1 1.0 SG A:CYS463 2.4 87.4 1.0 CB A:CYS452 3.0 0.1 1.0 CB A:CYS463 3.7 88.2 1.0 CA A:CYS452 3.8 0.1 1.0 NH2 A:ARG464 4.3 73.9 1.0 CZ A:ARG464 4.4 74.3 1.0 N A:CYS452 4.4 0.5 1.0 NE A:ARG464 4.5 75.5 1.0 CG A:ARG464 4.6 75.3 1.0 NH1 A:ARG464 4.9 73.6 1.0

Zinc binding site 2 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9002 b:48.0 occ:1.00 SG A:CYS530 2.3 39.0 1.0 SG A:CYS549 2.3 39.1 1.0 SG A:CYS543 2.4 36.7 1.0 SG A:CYS553 2.5 37.5 1.0 CB A:CYS549 3.0 40.1 1.0 CB A:CYS530 3.1 38.2 1.0 CB A:CYS543 3.4 36.4 1.0 CB A:CYS553 3.6 38.1 1.0 ZN A:ZN9004 3.7 41.0 1.0 SG A:CYS523 3.7 54.5 1.0 ZN A:ZN9003 3.9 37.5 1.0 CB A:ASN555 4.1 35.1 1.0 CA A:CYS549 4.5 41.2 1.0 CA A:CYS530 4.6 38.8 1.0 ND2 A:ASN555 4.7 34.6 1.0 CB A:CYS547 4.8 38.8 1.0 CA A:CYS543 4.8 35.5 1.0 SG A:CYS547 4.9 37.9 1.0 N A:CYS549 4.9 41.3 1.0 CA A:ASN555 4.9 34.6 1.0 CG A:ASN555 4.9 34.4 1.0 CG A:ARG556 5.0 36.8 1.0 CE1 A:HIS525 5.0 40.9 1.0

Zinc binding site 3 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9003 b:37.5 occ:1.00 SG A:CYS547 2.2 37.9 1.0 SG A:CYS536 2.3 36.4 1.0 SG A:CYS523 2.3 54.5 1.0 SG A:CYS543 2.4 36.7 1.0 CB A:CYS523 2.6 54.3 1.0 CB A:CYS543 3.2 36.4 1.0 N A:CYS523 3.5 46.5 1.0 CB A:CYS547 3.6 38.8 1.0 CA A:CYS523 3.6 47.0 1.0 CB A:CYS536 3.6 35.4 1.0 CA A:CYS543 3.7 35.5 1.0 ZN A:ZN9004 3.8 41.0 1.0 ZN A:ZN9002 3.9 48.0 1.0 SG A:CYS534 4.1 37.6 1.0 N A:CYS543 4.5 34.7 1.0 C A:CYS523 4.5 48.1 1.0 C A:PRO522 4.6 39.3 1.0 SG A:CYS530 4.7 39.0 1.0 CE2 A:TYR520 4.7 35.8 1.0 O A:CYS523 4.7 48.3 1.0 CA A:CYS547 4.7 39.6 1.0 O A:GLN521 4.9 45.8 1.0 CA A:CYS536 4.9 35.1 1.0 N A:CYS536 4.9 36.0 1.0 C A:CYS543 4.9 35.4 1.0 ND2 A:ASN555 5.0 34.6 1.0

Zinc binding site 4 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9004 b:41.0 occ:1.00 NE2 A:HIS525 2.0 40.4 1.0 SG A:CYS530 2.3 39.0 1.0 SG A:CYS534 2.3 37.6 1.0 SG A:CYS523 2.4 54.5 1.0 CE1 A:HIS525 2.8 40.9 1.0 CB A:CYS534 3.1 37.9 1.0 CB A:CYS523 3.2 54.3 1.0 CD2 A:HIS525 3.2 41.0 1.0 CB A:CYS530 3.2 38.2 1.0 CA A:CYS530 3.7 38.8 1.0 ZN A:ZN9002 3.7 48.0 1.0 ZN A:ZN9003 3.8 37.5 1.0 ND1 A:HIS525 4.0 41.9 1.0 SG A:CYS543 4.2 36.7 1.0 CG A:HIS525 4.2 42.0 1.0 CA A:CYS534 4.2 38.1 1.0 CB A:CYS549 4.4 40.1 1.0 CA A:CYS523 4.5 47.0 1.0 N A:CYS530 4.7 39.6 1.0 C A:CYS530 4.7 38.1 1.0 C A:CYS523 4.8 48.1 1.0 CD A:PRO535 4.8 38.7 1.0 SG A:CYS536 4.8 36.4 1.0 N A:ASP524 4.9 46.4 1.0 C A:CYS534 5.0 37.4 1.0

Zinc binding site 5 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9005 b:30.2 occ:1.00 SG A:CYS573 2.3 29.7 1.0 SG A:CYS585 2.3 31.7 1.0 SG A:CYS560 2.4 43.5 1.0 SG A:CYS580 2.5 29.5 1.0 CB A:CYS580 2.8 30.6 1.0 CB A:CYS573 3.2 28.7 1.0 CB A:CYS585 3.2 32.1 1.0 CA A:CYS580 3.4 30.6 1.0 CB A:CYS560 3.5 45.5 1.0 ZN A:ZN9006 3.7 29.4 1.0 N A:CYS560 3.8 39.3 1.0 ZN A:ZN9007 3.9 28.1 1.0 CA A:CYS560 4.2 38.6 1.0 N A:CYS580 4.4 29.9 1.0 SG A:CYS588 4.4 30.6 1.0 N A:ASP581 4.4 32.2 1.0 C A:CYS580 4.5 31.6 1.0 SG A:CYS571 4.5 27.4 1.0 SG A:CYS566 4.6 28.2 1.0 C A:GLY559 4.6 31.2 1.0 CA A:CYS585 4.6 33.0 1.0 CA A:CYS573 4.7 28.2 1.0 CA A:GLY559 4.7 31.9 1.0 C A:CYS560 5.0 38.9 1.0 O A:CYS560 5.0 39.7 1.0

Zinc binding site 6 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9006 b:29.4 occ:1.00 SG A:CYS601 2.2 29.1 1.0 SG A:CYS588 2.2 30.6 1.0 SG A:CYS566 2.3 28.2 1.0 SG A:CYS580 2.3 29.5 1.0 CB A:CYS588 3.0 30.0 1.0 CB A:CYS566 3.3 27.2 1.0 CB A:CYS601 3.4 29.5 1.0 CB A:CYS580 3.5 30.6 1.0 ZN A:ZN9005 3.7 30.2 1.0 ZN A:ZN9007 3.7 28.1 1.0 SG A:CYS560 3.9 43.5 1.0 CA A:CYS588 4.5 30.6 1.0 CA A:CYS601 4.5 28.8 1.0 CB A:CYS585 4.5 32.1 1.0 CA A:CYS566 4.8 26.4 1.0 CB A:ALA590 4.8 32.2 1.0 CA A:CYS580 4.9 30.6 1.0 C A:CYS588 4.9 30.9 1.0

Zinc binding site 7 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9007 b:28.1 occ:1.00 SG A:CYS571 2.2 27.4 1.0 SG A:CYS566 2.2 28.2 1.0 SG A:CYS562 2.3 27.8 1.0 SG A:CYS560 2.4 43.5 1.0 CB A:CYS566 3.1 27.2 1.0 CB A:CYS571 3.2 26.4 1.0 CB A:CYS560 3.2 45.5 1.0 CB A:CYS562 3.4 27.9 1.0 CA A:CYS566 3.7 26.4 1.0 ZN A:ZN9006 3.7 29.4 1.0 ZN A:ZN9005 3.9 30.2 1.0 SG A:CYS580 4.2 29.5 1.0 CA A:CYS571 4.3 26.2 1.0 N A:CYS562 4.4 29.2 1.0 CA A:CYS562 4.5 28.5 1.0 N A:CYS566 4.6 26.3 1.0 CB A:CYS573 4.6 28.7 1.0 CA A:CYS560 4.7 38.6 1.0 SG A:CYS573 4.7 29.7 1.0 CB A:CYS588 4.8 30.0 1.0 SG A:CYS588 4.8 30.6 1.0 C A:CYS566 4.8 25.7 1.0 C A:CYS571 4.9 26.5 1.0 O A:CYS566 5.0 25.8 1.0

Zinc binding site 8 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9008 b:38.8 occ:1.00 ND1 A:HIS297 2.0 48.2 1.0 SG A:CYS286 2.1 39.9 1.0 SG A:CYS289 2.1 38.9 1.0 SG A:CYS294 2.2 39.3 1.0 CE1 A:HIS297 2.5 47.5 1.0 CB A:CYS294 3.0 39.4 1.0 CB A:CYS286 3.1 41.1 1.0 CG A:HIS297 3.3 47.9 1.0 CB A:CYS289 3.3 38.1 1.0 NE2 A:HIS297 3.7 46.8 1.0 N A:CYS289 3.9 38.9 1.0 CB A:HIS297 4.0 48.5 1.0 CD2 A:HIS297 4.1 47.0 1.0 CA A:CYS289 4.2 38.6 1.0 N A:HIS297 4.4 47.7 1.0 CA A:CYS294 4.5 39.8 1.0 CA A:CYS286 4.5 42.1 1.0 CB A:ARG288 4.8 38.1 1.0 CA A:HIS297 4.8 48.1 1.0 C A:ARG288 4.9 38.5 1.0 CB A:LEU296 5.0 35.4 1.0 C A:CYS286 5.0 41.9 1.0 C A:CYS289 5.0 39.5 1.0

Zinc binding site 9 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn9001 b:71.5 occ:1.00 SG C:CYS452 2.2 42.3 1.0 CB C:CYS452 3.9 36.4 1.0 O C:CYS452 4.2 25.8 1.0 CA C:CYS452 4.4 25.8 1.0 CB C:CYS463 4.6 47.7 1.0 C C:CYS452 4.8 26.1 1.0 SG C:CYS463 4.8 50.4 1.0

Zinc binding site 10 out of 16 in the Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Polycomb Repressive Complex 2 in Complex with GSK126 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn9002 b:43.6 occ:1.00 SG C:CYS530 2.3 48.8 1.0 SG C:CYS549 2.4 34.1 1.0 SG C:CYS543 2.5 43.5 1.0 SG C:CYS553 2.5 35.1 1.0 CB C:CYS549 3.2 34.1 1.0 CB C:CYS530 3.4 49.4 1.0 CB C:CYS543 3.5 42.8 1.0 CB C:CYS553 3.7 33.8 1.0 ZN C:ZN9004 3.8 48.2 1.0 CB C:ASN555 4.1 37.5 1.0 ZN C:ZN9003 4.1 37.2 1.0 SG C:CYS523 4.4 40.9 1.0 CA C:CYS549 4.7 33.2 1.0 ND2 C:ASN555 4.8 38.8 1.0 CA C:CYS530 4.8 49.6 1.0 CA C:ASN555 4.9 37.0 1.0 CA C:CYS543 4.9 43.5 1.0 N C:ASN555 5.0 36.2 1.0 CG C:ASN555 5.0 38.6 1.0 C C:ASN555 5.0 36.7 1.0

M.Bratkowski, X.Yang, X.Liu. An Evolutionarily Conserved Structural Platform For PRC2 Inhibition By A Class of EZH2 Inhibitors. Sci Rep V. 8 9092 2018.
ISSN: ESSN 2045-2322
PubMed: 29904056
DOI: 10.1038/S41598-018-27175-W