Zinc in PDB 5oqd: PHD2 and Winged-Helix Domain of Polycomblike

The structure of PHD2 and Winged-Helix Domain of Polycomblike, PDB code: 5oqd was solved by J.Choi, C.Benda, J.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.69 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	307.423, 53.119, 86.839, 90.00, 105.47, 90.00
R / Rfree (%)	23.7 / 27.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the PHD2 and Winged-Helix Domain of Polycomblike (pdb code 5oqd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the PHD2 and Winged-Helix Domain of Polycomblike, PDB code: 5oqd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:53.9 occ:1.00 ND1 B:HIS538 2.1 51.1 1.0 SG B:CYS541 2.3 50.6 1.0 SG B:CYS517 2.3 59.0 1.0 SG B:CYS515 2.4 50.9 1.0 CB B:CYS515 2.5 43.0 1.0 CG B:HIS538 3.0 48.5 1.0 CE1 B:HIS538 3.0 52.0 1.0 CB B:CYS541 3.2 50.2 1.0 CB B:HIS538 3.3 47.1 1.0 CB B:CYS517 3.3 58.5 1.0 CA B:CYS515 3.9 53.4 1.0 N B:HIS538 4.0 49.2 1.0 N B:CYS517 4.0 55.1 1.0 CD2 B:HIS538 4.1 47.7 1.0 NE2 B:HIS538 4.1 57.5 1.0 CA B:HIS538 4.2 51.2 1.0 CA B:CYS517 4.3 58.8 1.0 N B:TYR516 4.4 59.4 1.0 C B:CYS515 4.5 57.2 1.0 CA B:CYS541 4.6 56.2 1.0 N B:CYS515 4.7 59.7 1.0 N B:CYS541 5.0 55.7 1.0

Zinc binding site 2 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:35.7 occ:1.00 SG B:CYS560 2.3 33.9 1.0 SG B:CYS533 2.3 38.3 1.0 SG B:CYS563 2.3 35.3 1.0 SG B:CYS530 2.4 37.6 1.0 CB B:CYS533 3.1 27.9 1.0 CB B:CYS530 3.2 31.8 1.0 CB B:CYS563 3.3 37.9 1.0 CB B:CYS560 3.6 42.0 1.0 N B:CYS533 3.6 38.4 1.0 N B:CYS560 4.0 43.9 1.0 CA B:CYS533 4.0 37.0 1.0 N B:CYS563 4.2 32.2 1.0 CA B:CYS560 4.3 35.6 1.0 CA B:CYS563 4.4 40.0 1.0 CZ B:PHE537 4.6 34.9 1.0 CE1 B:PHE537 4.6 37.4 1.0 C B:LYS532 4.7 35.9 1.0 CA B:CYS530 4.7 41.5 1.0 CB B:LYS532 4.8 40.4 1.0 O B:CYS560 4.8 38.0 1.0 C B:CYS560 4.8 31.2 1.0 C B:CYS533 4.9 38.9 1.0 CA B:LYS532 5.0 34.0 1.0 CB B:VAL562 5.0 40.5 1.0 N B:ARG534 5.0 39.0 1.0

Zinc binding site 3 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:61.6 occ:1.00 ND1 A:HIS538 2.0 67.4 1.0 SG A:CYS541 2.3 56.5 1.0 SG A:CYS517 2.3 78.3 1.0 SG A:CYS515 2.3 65.8 1.0 CB A:CYS515 2.8 51.5 1.0 CG A:HIS538 3.0 69.5 1.0 CE1 A:HIS538 3.0 69.6 1.0 CB A:CYS541 3.0 50.8 1.0 CB A:CYS517 3.2 68.4 1.0 CB A:HIS538 3.3 61.6 1.0 N A:HIS538 3.8 72.9 1.0 N A:CYS517 4.1 70.2 1.0 NE2 A:HIS538 4.1 77.7 1.0 CD2 A:HIS538 4.1 72.0 1.0 CA A:HIS538 4.2 61.2 1.0 CA A:CYS515 4.2 59.8 1.0 CA A:CYS517 4.3 74.7 1.0 CA A:CYS541 4.5 59.6 1.0 C A:CYS515 4.6 62.6 1.0 N A:TYR516 4.6 64.0 1.0 O A:LYS519 4.8 82.1 1.0 N A:CYS541 4.9 62.7 1.0 C A:PHE537 4.9 66.4 1.0 N A:CYS515 5.0 60.1 1.0 O A:HIS538 5.0 68.8 1.0

Zinc binding site 4 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:46.8 occ:1.00 SG A:CYS560 2.2 44.2 1.0 SG A:CYS533 2.3 51.5 1.0 SG A:CYS563 2.3 44.8 1.0 SG A:CYS530 2.5 45.8 1.0 CB A:CYS533 2.9 43.4 1.0 CB A:CYS563 3.3 44.3 1.0 CB A:CYS530 3.3 37.5 1.0 CB A:CYS560 3.6 56.1 1.0 N A:CYS533 3.7 55.9 1.0 O D:HOH828 3.7 53.6 1.0 CA A:CYS533 3.9 45.9 1.0 N A:CYS560 4.0 49.8 1.0 N A:CYS563 4.1 53.7 1.0 CA A:CYS563 4.3 46.7 1.0 CA A:CYS560 4.3 53.6 1.0 CZ A:PHE537 4.6 43.2 1.0 CE1 A:PHE537 4.7 51.5 1.0 C A:LYS532 4.8 46.6 1.0 CA A:CYS530 4.8 52.9 1.0 C A:CYS533 4.8 48.0 1.0 C A:CYS560 4.8 47.7 1.0 CB A:VAL562 4.9 54.4 1.0 O A:CYS560 4.9 41.7 1.0 CB A:LYS532 4.9 46.8 1.0 N A:ARG534 5.0 46.3 1.0

Zinc binding site 5 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:0.5 occ:1.00 ND1 C:HIS538 1.9 0.4 1.0 SG C:CYS541 2.3 98.0 1.0 SG C:CYS515 2.3 97.6 1.0 SG C:CYS517 2.3 0.1 1.0 CB C:CYS515 2.6 98.6 1.0 CE1 C:HIS538 2.8 0.9 1.0 CG C:HIS538 3.0 93.5 1.0 CB C:CYS541 3.2 0.5 1.0 CB C:CYS517 3.2 0.9 1.0 CB C:HIS538 3.4 96.4 1.0 N C:CYS517 3.9 0.3 1.0 NE2 C:HIS538 4.0 1.0 1.0 N C:HIS538 4.0 91.1 1.0 CA C:CYS515 4.1 0.2 1.0 CD2 C:HIS538 4.1 96.5 1.0 CA C:CYS517 4.2 0.3 1.0 CA C:HIS538 4.4 93.9 1.0 N C:TYR516 4.4 1.0 1.0 C C:CYS515 4.5 0.8 1.0 CA C:CYS541 4.6 0.1 1.0 O C:LYS519 4.7 0.0 1.0 N C:CYS515 4.9 0.9 1.0 CD1 C:TYR516 5.0 0.9 1.0 N C:CYS541 5.0 0.0 1.0

Zinc binding site 6 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn702 b:95.2 occ:1.00 SG C:CYS563 1.7 0.7 1.0 SG C:CYS560 2.2 92.4 1.0 CB C:CYS563 2.6 1.0 1.0 SG C:CYS530 2.7 0.4 1.0 SG C:CYS533 2.7 0.5 1.0 CB C:CYS533 2.8 0.9 1.0 N C:CYS533 3.1 92.5 1.0 CB C:CYS530 3.4 98.6 1.0 CA C:CYS533 3.5 0.6 1.0 CA C:CYS563 3.7 0.3 1.0 N C:CYS563 3.8 0.5 1.0 CB C:CYS560 3.9 0.6 1.0 C C:LYS532 4.1 94.4 1.0 CB C:LYS532 4.2 0.8 1.0 N C:CYS560 4.3 0.9 1.0 C C:CYS533 4.4 0.1 1.0 CA C:LYS532 4.5 98.8 1.0 CA C:CYS560 4.6 0.3 1.0 N C:ARG534 4.6 0.9 1.0 O C:CYS560 4.7 0.4 1.0 N C:LYS532 4.8 0.9 1.0 CE1 C:PHE537 4.8 0.9 1.0 CA C:CYS530 4.9 98.4 1.0 CZ C:PHE537 4.9 0.4 1.0 C C:VAL562 5.0 0.1 1.0 C C:CYS560 5.0 0.1 1.0 O C:LYS532 5.0 0.9 1.0 C C:CYS563 5.0 0.6 1.0

Zinc binding site 7 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:0.7 occ:1.00 ND1 D:HIS538 2.0 99.5 1.0 SG D:CYS515 2.2 0.1 1.0 CB D:CYS515 2.3 0.2 1.0 SG D:CYS541 2.4 91.3 1.0 SG D:CYS517 2.8 99.0 1.0 CE1 D:HIS538 2.9 99.0 1.0 CG D:HIS538 3.0 89.2 1.0 CB D:CYS541 3.1 83.6 1.0 CB D:CYS517 3.4 0.4 1.0 CB D:HIS538 3.4 87.2 1.0 CA D:CYS515 3.7 93.5 1.0 N D:HIS538 3.9 90.1 1.0 NE2 D:HIS538 4.0 96.4 1.0 CD2 D:HIS538 4.1 97.8 1.0 C D:CYS515 4.1 0.6 1.0 N D:CYS517 4.2 0.8 1.0 CA D:HIS538 4.3 95.2 1.0 N D:TYR516 4.4 0.0 1.0 CA D:CYS517 4.5 0.0 1.0 CA D:CYS541 4.5 98.3 1.0 N D:CYS515 4.5 99.2 1.0 O D:CYS515 4.6 0.6 1.0 N D:CYS541 4.8 0.2 1.0

Zinc binding site 8 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:0.3 occ:1.00 SG D:CYS563 1.8 0.1 1.0 SG D:CYS533 2.3 79.4 1.0 SG D:CYS560 2.3 0.1 1.0 SG D:CYS530 2.3 80.5 1.0 CB D:CYS563 2.7 0.5 1.0 CB D:CYS533 3.0 77.8 1.0 CB D:CYS530 3.3 79.4 1.0 CB D:CYS560 3.4 0.2 1.0 N D:CYS533 3.6 80.7 1.0 N D:CYS560 3.9 96.2 1.0 CA D:CYS533 3.9 76.8 1.0 CA D:CYS563 4.0 1.0 1.0 N D:CYS563 4.1 0.1 1.0 CA D:CYS560 4.2 0.4 1.0 CB D:LYS532 4.7 79.5 1.0 C D:LYS532 4.7 78.5 1.0 CZ D:PHE537 4.8 0.8 1.0 C D:CYS533 4.8 70.5 1.0 CA D:CYS530 4.8 77.9 1.0 CE1 D:PHE537 4.9 93.2 1.0 C D:CYS560 4.9 0.6 1.0 N D:LYS532 4.9 80.7 1.0 N D:ARG534 5.0 79.0 1.0 CA D:LYS532 5.0 79.2 1.0

Zinc binding site 9 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:0.9 occ:1.00 ND1 E:HIS538 2.1 0.7 1.0 SG E:CYS541 2.3 0.7 1.0 SG E:CYS517 2.3 0.4 1.0 SG E:CYS515 2.4 0.7 1.0 CB E:CYS515 2.7 0.5 1.0 CG E:HIS538 3.0 1.0 1.0 CE1 E:HIS538 3.0 0.1 1.0 CB E:CYS517 3.2 0.6 1.0 CB E:HIS538 3.3 1.0 1.0 CB E:CYS541 3.6 96.0 1.0 N E:CYS517 4.0 0.3 1.0 CD2 E:HIS538 4.1 0.0 1.0 NE2 E:HIS538 4.1 0.6 1.0 CA E:CYS515 4.1 0.3 1.0 N E:HIS538 4.2 0.4 1.0 CA E:CYS517 4.2 0.2 1.0 CA E:HIS538 4.4 0.5 1.0 C E:CYS515 4.4 0.3 1.0 N E:TYR516 4.6 0.8 1.0 CA E:CYS541 4.9 0.7 1.0 N E:CYS515 5.0 0.6 1.0

Zinc binding site 10 out of 12 in the PHD2 and Winged-Helix Domain of Polycomblike


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of PHD2 and Winged-Helix Domain of Polycomblike within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn702 b:89.8 occ:1.00 SG E:CYS563 2.2 90.1 1.0 SG E:CYS560 2.3 0.2 1.0 SG E:CYS533 2.3 94.3 1.0 SG E:CYS530 2.4 92.2 1.0 CB E:CYS563 3.0 97.2 1.0 CB E:CYS530 3.1 81.6 1.0 CB E:CYS533 3.2 72.9 1.0 CB E:CYS560 3.5 93.9 1.0 N E:CYS533 3.9 74.6 1.0 N E:CYS563 3.9 100.0 1.0 N E:CYS560 4.0 92.7 1.0 CA E:CYS563 4.0 0.6 1.0 CZ E:PHE537 4.2 92.1 1.0 CA E:CYS533 4.2 77.2 1.0 CE1 E:PHE537 4.2 99.4 1.0 CA E:CYS560 4.2 94.1 1.0 CA E:CYS530 4.6 81.7 1.0 O E:CYS560 4.7 90.7 1.0 C E:CYS560 4.7 94.9 1.0 CB E:LYS532 4.9 85.0 1.0

J.Choi, A.L.Bachmann, K.Tauscher, C.Benda, B.Fierz, J.Muller. Dna Binding By PHF1 Prolongs PRC2 Residence Time on Chromatin and Thereby Promotes H3K27 Methylation. Nat. Struct. Mol. Biol. V. 24 1039 2017.
ISSN: ESSN 1545-9985
PubMed: 29058710
DOI: 10.1038/NSMB.3488