Zinc in PDB 5hyn: Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide

All present enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide:
2.1.1.43;

The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide, PDB code: 5hyn was solved by Y.Zhang, N.Justin, J.R.Wilson, S.J.Gamblin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.01 / 2.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	131.640, 171.510, 274.550, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide (pdb code 5hyn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide, PDB code: 5hyn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:54.8 occ:1.00 ND1 A:HIS297 2.0 64.7 1.0 SG A:CYS289 2.1 41.5 1.0 SG A:CYS294 2.1 56.1 0.9 SG A:CYS286 2.3 49.4 1.0 CE1 A:HIS297 2.9 54.5 1.0 CB A:CYS294 3.0 49.9 1.0 CG A:HIS297 3.1 44.1 1.0 CB A:CYS286 3.3 54.3 1.0 CB A:HIS297 3.5 38.1 1.0 CB A:CYS289 3.8 49.8 1.0 N A:CYS289 4.0 62.9 1.0 NE2 A:HIS297 4.0 66.5 1.0 N A:HIS297 4.1 54.5 1.0 CD2 A:HIS297 4.1 42.4 1.0 CA A:HIS297 4.4 52.6 1.0 CA A:CYS289 4.4 66.2 1.0 CA A:CYS294 4.4 55.8 1.0 CB A:ARG288 4.7 45.5 1.0 CA A:CYS286 4.8 50.9 1.0 CB A:LEU296 4.9 42.6 1.0 O A:HIS297 4.9 63.1 1.0 C A:LEU296 4.9 45.2 1.0 C A:ARG288 4.9 55.3 1.0 N A:LEU296 5.0 66.9 1.0

Zinc binding site 2 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:64.4 occ:1.00 SG A:CYS463 2.2 61.6 1.0 CB A:CYS320 2.2 94.4 1.0 SG A:CYS452 2.3 60.5 0.9 SG A:CYS320 2.5 77.9 1.0 SG A:CYS324 2.9 82.7 1.0 CB A:CYS463 3.1 49.7 1.0 CA A:CYS320 3.2 99.0 1.0 CB A:CYS452 3.3 70.2 1.0 CA A:CYS452 3.4 60.8 1.0 CB A:CYS324 3.7 72.7 1.0 N A:CYS320 3.7 0.2 1.0 N A:CYS452 4.0 57.4 1.0 CD1 A:TYR325 4.1 79.5 1.0 CA A:CYS324 4.2 81.9 1.0 N A:TYR325 4.4 85.8 1.0 CE1 A:TYR325 4.5 72.1 1.0 C A:CYS320 4.5 95.8 1.0 CA A:CYS463 4.5 51.9 1.0 C A:CYS452 4.7 58.0 1.0 C A:CYS324 4.9 93.7 1.0 C A:PHE451 4.9 57.3 1.0 C A:PRO319 5.0 94.1 1.0

Zinc binding site 3 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:51.6 occ:1.00 SG A:CYS530 2.2 52.5 1.0 SG A:CYS553 2.3 59.8 1.0 SG A:CYS543 2.4 56.0 1.0 SG A:CYS549 2.6 53.4 1.0 CB A:CYS530 3.1 62.7 1.0 CB A:CYS543 3.2 54.2 1.0 CB A:CYS549 3.2 63.5 1.0 CB A:CYS553 3.3 68.3 1.0 ZN A:ZN1004 3.7 63.6 1.0 ZN A:ZN1005 3.9 56.4 1.0 SG A:CYS523 4.2 52.0 1.0 CG A:ARG556 4.5 65.7 1.0 CA A:CYS530 4.6 70.1 1.0 CB A:ASN555 4.7 48.0 1.0 CA A:CYS543 4.7 41.0 1.0 CA A:CYS549 4.7 59.2 1.0 CA A:CYS553 4.7 68.4 1.0 CB A:CYS547 4.9 64.1 1.0 N A:ARG556 4.9 49.6 1.0 NE A:ARG556 5.0 56.0 1.0 SG A:CYS534 5.0 52.1 1.0 N A:CYS530 5.0 72.5 1.0

Zinc binding site 4 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:63.6 occ:1.00 NE2 A:HIS525 2.0 49.7 1.0 SG A:CYS534 2.1 52.1 1.0 SG A:CYS530 2.2 52.5 1.0 SG A:CYS523 2.4 52.0 1.0 CE1 A:HIS525 2.6 55.3 1.0 CB A:CYS530 3.2 62.7 1.0 CD2 A:HIS525 3.3 58.3 1.0 CB A:CYS534 3.3 64.0 1.0 CB A:CYS523 3.3 56.2 1.0 CA A:CYS530 3.7 70.1 1.0 ZN A:ZN1003 3.7 51.6 1.0 ND1 A:HIS525 3.8 51.1 1.0 ZN A:ZN1005 3.8 56.4 1.0 SG A:CYS543 3.9 56.0 1.0 CG A:HIS525 4.2 53.7 1.0 CB A:CYS549 4.3 63.5 1.0 CA A:CYS534 4.5 68.3 1.0 N A:CYS530 4.5 72.5 1.0 CA A:CYS523 4.7 64.2 1.0 SG A:CYS536 4.8 54.0 0.9 C A:CYS523 4.8 74.4 1.0 CB A:CYS536 4.9 57.0 1.0 SG A:CYS549 5.0 53.4 1.0 C A:CYS530 5.0 55.2 1.0

Zinc binding site 5 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:56.4 occ:1.00 SG A:CYS543 2.0 56.0 1.0 SG A:CYS523 2.2 52.0 1.0 SG A:CYS536 2.3 54.0 0.9 SG A:CYS547 2.4 66.1 1.0 CB A:CYS543 2.8 54.2 1.0 CA A:CYS543 3.3 41.0 1.0 CB A:CYS536 3.3 57.0 1.0 CB A:CYS547 3.4 64.1 1.0 CB A:CYS523 3.5 56.2 1.0 ZN A:ZN1004 3.8 63.6 1.0 ZN A:ZN1003 3.9 51.6 1.0 N A:CYS523 3.9 67.0 1.0 N A:CYS543 4.2 61.2 1.0 CA A:CYS523 4.2 64.2 1.0 SG A:CYS534 4.3 52.1 1.0 SG A:CYS530 4.5 52.5 1.0 C A:CYS543 4.5 50.2 1.0 N A:GLU544 4.6 45.2 1.0 CA A:CYS547 4.7 47.0 1.0 CA A:CYS536 4.7 69.1 1.0 O A:CYS523 4.7 62.8 1.0 SG A:CYS549 4.8 53.4 1.0 C A:PRO522 4.8 60.1 1.0 C A:CYS523 4.9 74.4 1.0 CE1 A:TYR520 4.9 63.7 1.0 O A:PHE542 5.0 63.4 1.0 N A:CYS536 5.0 61.8 1.0 C A:PHE542 5.0 64.4 1.0

Zinc binding site 6 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:58.6 occ:1.00 SG A:CYS580 2.1 44.1 1.0 SG A:CYS566 2.3 66.5 1.0 SG A:CYS601 2.3 53.8 1.0 SG A:CYS588 2.3 66.8 1.0 CB A:CYS588 3.1 62.0 1.0 ZN A:ZN1008 3.3 58.0 1.0 CB A:CYS580 3.4 56.5 1.0 ZN A:ZN1007 3.6 52.7 1.0 SG A:CYS560 3.6 50.0 1.0 CB A:CYS601 3.7 66.0 1.0 CB A:CYS566 4.0 73.4 1.0 CB A:CYS585 4.4 43.9 1.0 CA A:CYS588 4.6 63.9 1.0 CB A:ASN603 4.6 58.9 1.0 CB A:ALA590 4.6 59.5 1.0 CA A:CYS601 4.7 66.2 1.0 CA A:CYS580 4.7 58.2 1.0 O A:ALA564 4.8 90.7 1.0 N A:ALA590 4.9 60.9 1.0 SG A:CYS585 4.9 41.5 1.0 SG A:CYS571 4.9 50.4 1.0 O A:GLN565 5.0 66.8 1.0 C A:CYS588 5.0 66.3 1.0

Zinc binding site 7 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:52.7 occ:1.00 SG A:CYS585 2.2 41.5 1.0 SG A:CYS560 2.2 50.0 1.0 SG A:CYS573 2.3 59.2 1.0 SG A:CYS580 2.6 44.1 1.0 CB A:CYS560 2.9 66.5 1.0 CB A:CYS585 3.1 43.9 1.0 ZN A:ZN1008 3.3 58.0 1.0 CB A:CYS573 3.4 51.6 1.0 N A:CYS560 3.4 43.1 1.0 CB A:CYS580 3.6 56.5 1.0 ZN A:ZN1006 3.6 58.6 1.0 CA A:CYS560 3.7 61.2 1.0 CA A:CYS580 3.8 58.2 1.0 SG A:CYS571 4.0 50.4 1.0 C A:GLY559 4.3 40.5 1.0 CA A:CYS585 4.4 47.3 1.0 C A:CYS560 4.5 62.6 1.0 SG A:CYS588 4.6 66.8 1.0 O A:CYS560 4.6 69.8 1.0 N A:ASP581 4.7 48.1 1.0 CA A:CYS573 4.7 47.3 1.0 N A:CYS580 4.8 72.0 1.0 CA A:GLY559 4.8 57.4 1.0 SG A:CYS566 4.8 66.5 1.0 C A:CYS580 4.8 49.9 1.0 N A:CYS573 4.8 44.3 1.0

Zinc binding site 8 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:58.0 occ:1.00 SG A:CYS560 2.0 50.0 1.0 SG A:CYS571 2.2 50.4 1.0 SG A:CYS562 2.4 39.2 1.0 SG A:CYS566 2.7 66.5 1.0 CB A:CYS566 2.7 73.4 1.0 CB A:CYS560 3.0 66.5 1.0 CB A:CYS562 3.2 60.7 1.0 CB A:CYS571 3.3 48.5 1.0 ZN A:ZN1006 3.3 58.6 1.0 ZN A:ZN1007 3.3 52.7 1.0 SG A:CYS580 3.8 44.1 1.0 CA A:CYS571 4.2 49.9 1.0 CA A:CYS566 4.2 74.8 1.0 N A:CYS562 4.4 62.3 1.0 CA A:CYS562 4.4 60.2 1.0 CA A:CYS560 4.4 61.2 1.0 SG A:CYS573 4.6 59.2 1.0 CB A:CYS588 4.6 62.0 1.0 CB A:CYS573 4.7 51.6 1.0 SG A:CYS588 4.7 66.8 1.0 O A:CYS566 4.8 47.9 1.0 C A:CYS560 4.9 62.6 1.0 CD A:PRO572 4.9 43.3 1.0 C A:CYS571 4.9 43.5 1.0

Zinc binding site 9 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:63.9 occ:1.00 CD2 F:HIS297 1.9 81.4 1.0 SG F:CYS289 2.1 59.3 1.0 SG F:CYS286 2.2 75.2 0.9 SG F:CYS294 2.3 68.2 1.0 NE2 F:HIS297 2.7 76.3 1.0 CG F:HIS297 2.8 58.6 1.0 CB F:CYS294 3.2 70.6 1.0 CB F:CYS286 3.3 70.3 1.0 CB F:HIS297 3.5 53.1 1.0 CB F:CYS289 3.5 65.0 1.0 N F:CYS289 3.8 64.2 1.0 CE1 F:HIS297 3.8 67.7 1.0 ND1 F:HIS297 3.8 42.8 1.0 CA F:CYS289 4.2 72.6 1.0 N F:HIS297 4.2 59.4 1.0 CB F:ARG288 4.4 51.2 1.0 CA F:HIS297 4.5 64.9 1.0 C F:ARG288 4.7 49.8 1.0 CA F:CYS294 4.7 66.4 1.0 CA F:CYS286 4.7 62.8 1.0 CB F:LEU296 4.8 47.1 1.0 CA F:ARG288 4.9 50.4 1.0 N F:ARG288 4.9 69.8 1.0 C F:CYS289 5.0 74.7 1.0 C F:LEU296 5.0 55.3 1.0

Zinc binding site 10 out of 32 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Oncogenic Histone H3K27M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1002 b:0.9 occ:1.00 SG F:CYS463 2.2 85.5 1.0 CB F:CYS320 2.4 0.5 1.0 SG F:CYS452 2.6 92.4 1.0 SG F:CYS324 2.7 97.5 1.0 SG F:CYS320 2.7 88.5 1.0 CB F:CYS463 2.9 76.8 1.0 CB F:CYS324 3.4 92.5 1.0 CA F:CYS320 3.5 0.7 1.0 CB F:CYS452 3.6 96.8 1.0 CA F:CYS452 3.6 90.4 1.0 N F:CYS320 3.7 0.6 1.0 CA F:CYS324 3.8 0.4 1.0 N F:CYS452 4.1 85.0 1.0 CD1 F:TYR325 4.1 0.8 1.0 N F:TYR325 4.1 0.5 1.0 CA F:CYS463 4.3 90.7 1.0 C F:CYS324 4.5 0.6 1.0 CE1 F:TYR325 4.5 100.0 1.0 C F:CYS320 4.8 0.3 1.0 C F:PRO319 4.9 0.6 1.0 C F:PHE451 4.9 86.1 1.0 N F:CYS324 5.0 0.8 1.0 C F:CYS452 5.0 87.1 1.0

N.Justin, Y.Zhang, C.Tarricone, S.R.Martin, S.Chen, E.Underwood, V.De Marco, L.F.Haire, P.A.Walker, D.Reinberg, J.R.Wilson, S.J.Gamblin. Structural Basis of Oncogenic Histone H3K27M Inhibition of Human Polycomb Repressive Complex 2. Nat Commun V. 7 11316 2016.
ISSN: ESSN 2041-1723
PubMed: 27121947
DOI: 10.1038/NCOMMS11316