Zinc in PDB 8ge0: Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3

The structure of Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3, PDB code: 8ge0 was solved by B.J.Klein, J.Liu, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.51 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.16, 78.16, 222.88, 90, 90, 90
R / Rfree (%)	20.7 / 24.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3 (pdb code 8ge0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3, PDB code: 8ge0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:49.8 occ:1.00 ND1 A:HIS48 2.1 40.6 1.0 SG A:CYS51 2.3 38.9 1.0 SG A:CYS23 2.3 38.0 1.0 SG A:CYS26 2.3 42.3 1.0 CB A:CYS23 3.0 34.3 1.0 CE1 A:HIS48 3.1 39.8 1.0 CG A:HIS48 3.1 37.2 1.0 CB A:CYS26 3.4 34.2 1.0 CB A:HIS48 3.4 38.9 1.0 CB A:CYS51 3.5 43.2 1.0 N A:CYS26 3.7 35.3 1.0 N A:HIS48 4.1 37.9 1.0 CA A:CYS26 4.1 39.1 1.0 NE2 A:HIS48 4.2 36.4 1.0 CD2 A:HIS48 4.2 37.2 1.0 CA A:HIS48 4.4 37.7 1.0 CA A:CYS23 4.5 36.6 1.0 CB A:VAL25 4.5 37.5 1.0 C A:CYS26 4.8 40.0 1.0 C A:VAL25 4.8 45.4 1.0 CA A:CYS51 4.8 35.5 1.0 N A:GLN27 4.9 38.1 1.0 N A:VAL25 4.9 38.3 1.0 C A:CYS23 5.0 34.3 1.0 N A:SER28 5.0 49.6 1.0 CA A:VAL25 5.0 39.5 1.0

Zinc binding site 2 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:75.3 occ:1.00 SG A:CYS43 2.3 63.5 1.0 SG A:CYS40 2.3 54.8 1.0 SG A:CYS67 2.3 61.0 1.0 SG A:CYS64 2.3 57.3 1.0 CB A:CYS67 3.2 49.2 1.0 CB A:CYS43 3.2 57.6 1.0 CB A:CYS40 3.3 50.4 1.0 CB A:CYS64 3.6 52.3 1.0 N A:CYS43 3.6 51.3 1.0 N A:CYS64 3.9 47.1 1.0 CA A:CYS43 4.0 50.0 1.0 CA A:CYS64 4.3 47.4 1.0 CA A:CYS67 4.4 47.3 1.0 N A:CYS67 4.4 54.5 1.0 CG1 A:ILE45 4.6 39.1 1.0 CB A:LYS42 4.6 66.6 1.0 CD1 A:ILE45 4.7 57.7 1.0 CA A:CYS40 4.7 54.1 1.0 C A:CYS43 4.7 58.0 1.0 C A:LYS42 4.7 61.5 1.0 N A:ASN44 4.8 63.4 1.0 C A:CYS64 4.9 55.3 1.0 O A:CYS64 4.9 56.7 1.0 OG1 A:THR66 4.9 58.1 1.0 N A:LYS42 5.0 66.2 1.0

Zinc binding site 3 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:51.4 occ:1.00 ND1 A:HIS96 2.1 40.6 1.0 SG A:CYS99 2.3 39.7 1.0 SG A:CYS75 2.3 39.1 1.0 SG A:CYS78 2.3 40.7 1.0 CB A:CYS75 3.0 36.5 1.0 CG A:HIS96 3.0 44.0 1.0 CE1 A:HIS96 3.1 35.6 1.0 CB A:CYS78 3.2 35.6 1.0 CB A:HIS96 3.3 37.1 1.0 CB A:CYS99 3.5 36.0 1.0 N A:CYS78 3.8 38.6 1.0 CG2 A:THR157 3.9 34.3 1.0 N A:HIS96 4.0 40.3 1.0 CA A:CYS78 4.1 41.1 1.0 CD2 A:HIS96 4.2 39.5 1.0 NE2 A:HIS96 4.2 39.8 1.0 C A:LEU77 4.3 44.8 1.0 CA A:HIS96 4.3 32.9 1.0 OG1 A:THR157 4.3 37.5 1.0 CA A:CYS75 4.5 43.2 1.0 CB A:LEU77 4.6 35.0 1.0 N A:LEU77 4.7 36.8 1.0 C A:CYS78 4.7 44.5 1.0 O A:CYS78 4.7 53.8 1.0 CA A:LEU77 4.7 40.1 1.0 O A:LEU77 4.8 51.6 1.0 CB A:THR157 4.8 39.7 1.0 CA A:CYS99 4.8 36.9 1.0 O A:HOH327 5.0 44.6 1.0 C A:CYS75 5.0 40.3 1.0

Zinc binding site 4 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:49.8 occ:1.00 ND1 A:HIS185 2.0 42.3 1.0 SG A:CYS150 2.3 41.6 1.0 SG A:CYS182 2.3 41.6 1.0 SG A:CYS145 2.3 40.4 1.0 CE1 A:HIS185 2.9 45.5 1.0 CB A:CYS145 3.0 42.8 1.0 CG A:HIS185 3.1 49.6 1.0 CB A:CYS150 3.2 30.3 1.0 CB A:CYS182 3.4 28.4 1.0 CB A:HIS185 3.5 38.9 1.0 N A:CYS182 4.0 44.0 1.0 NE2 A:HIS185 4.1 42.6 1.0 CD2 A:HIS185 4.2 47.5 1.0 CB A:VAL147 4.2 39.2 1.0 CA A:CYS182 4.3 42.5 1.0 O A:HOH309 4.3 41.2 1.0 CG2 A:VAL147 4.4 31.5 1.0 CA A:CYS145 4.5 45.9 1.0 N A:HIS185 4.6 62.9 1.0 CA A:CYS150 4.7 36.7 1.0 CA A:HIS185 4.7 53.0 1.0 CG1 A:VAL147 4.9 35.6 1.0 C A:CYS182 4.9 41.9 1.0 O A:CYS182 5.0 43.6 1.0

Zinc binding site 5 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:52.2 occ:1.00 ND1 A:HIS155 2.1 40.5 1.0 SG A:CYS135 2.3 49.6 1.0 SG A:CYS158 2.3 45.6 1.0 SG A:CYS132 2.3 38.5 1.0 CB A:CYS132 3.0 39.0 1.0 CE1 A:HIS155 3.0 40.8 1.0 CG A:HIS155 3.1 50.0 1.0 CB A:CYS135 3.3 31.1 1.0 CB A:CYS158 3.3 43.5 1.0 CB A:HIS155 3.4 33.3 1.0 N A:CYS135 3.8 45.1 1.0 N A:HIS155 4.0 38.3 1.0 CA A:CYS135 4.1 38.6 1.0 NE2 A:HIS155 4.2 43.4 1.0 CD2 A:HIS155 4.2 44.1 1.0 CA A:HIS155 4.4 32.6 1.0 CA A:CYS132 4.5 44.2 1.0 CD A:PRO79 4.6 49.7 1.0 CA A:CYS158 4.7 39.5 1.0 CB A:LEU134 4.7 29.6 1.0 C A:LEU134 4.8 52.1 1.0 C A:CYS135 4.9 42.1 1.0 N A:ASN136 4.9 52.3 1.0 CG A:PRO79 4.9 40.8 1.0 C A:CYS132 5.0 49.5 1.0

Zinc binding site 6 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


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 JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:67.5 occ:1.00 SG B:CYS64 2.3 54.3 1.0 SG B:CYS67 2.3 64.4 1.0 SG B:CYS40 2.3 57.8 1.0 SG B:CYS43 2.3 57.5 1.0 CB B:CYS67 3.1 50.2 1.0 CB B:CYS43 3.2 60.3 1.0 CB B:CYS40 3.3 63.6 1.0 N B:CYS43 3.6 57.5 1.0 CB B:CYS64 3.6 53.7 1.0 CA B:CYS43 4.0 65.4 1.0 N B:CYS64 4.0 47.5 1.0 CA B:CYS67 4.3 68.6 1.0 N B:CYS67 4.3 55.4 1.0 CA B:CYS64 4.4 58.4 1.0 CB B:LYS42 4.5 67.4 1.0 CG1 B:ILE45 4.7 52.2 1.0 C B:LYS42 4.7 65.4 1.0 O B:HOH321 4.7 58.5 1.0 C B:CYS43 4.7 58.9 1.0 CA B:CYS40 4.8 61.9 1.0 CD1 B:ILE45 4.8 65.6 1.0 OG1 B:THR66 4.8 60.2 1.0 N B:ASN44 4.9 42.3 1.0 O B:CYS64 4.9 58.8 1.0 C B:CYS64 4.9 59.7 1.0 N B:LYS42 5.0 60.2 1.0 CA B:LYS42 5.0 56.6 1.0

Zinc binding site 7 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:57.5 occ:1.00 ND1 B:HIS96 2.1 50.1 1.0 SG B:CYS78 2.3 52.5 1.0 SG B:CYS99 2.3 47.8 1.0 SG B:CYS75 2.3 49.2 1.0 CG B:HIS96 3.1 41.5 1.0 CE1 B:HIS96 3.1 52.1 1.0 CB B:CYS75 3.1 39.9 1.0 CB B:CYS78 3.3 47.9 1.0 CB B:HIS96 3.4 33.3 1.0 CB B:CYS99 3.5 39.5 1.0 CG2 B:THR157 3.8 36.2 1.0 N B:CYS78 3.9 46.6 1.0 N B:HIS96 4.0 51.2 1.0 CA B:CYS78 4.1 53.1 1.0 NE2 B:HIS96 4.2 48.4 1.0 CD2 B:HIS96 4.2 44.5 1.0 C B:LEU77 4.3 56.1 1.0 CA B:HIS96 4.3 42.3 1.0 OG1 B:THR157 4.4 43.5 1.0 CB B:LEU77 4.5 52.4 1.0 CA B:CYS75 4.6 50.3 1.0 N B:LEU77 4.7 55.9 1.0 CA B:LEU77 4.7 54.5 1.0 O B:HOH320 4.7 42.8 1.0 O B:LEU77 4.8 49.6 1.0 C B:CYS78 4.8 51.9 1.0 CA B:CYS99 4.8 42.6 1.0 CB B:THR157 4.8 41.7 1.0 O B:CYS78 4.8 47.0 1.0

Zinc binding site 8 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:64.9 occ:1.00 ND1 B:HIS155 2.1 50.3 1.0 SG B:CYS132 2.3 53.2 1.0 SG B:CYS158 2.3 49.2 1.0 SG B:CYS135 2.3 56.1 1.0 CB B:CYS132 3.0 42.1 1.0 CE1 B:HIS155 3.1 55.8 1.0 CG B:HIS155 3.1 47.0 1.0 CB B:CYS135 3.2 43.1 1.0 CB B:CYS158 3.4 37.0 1.0 CB B:HIS155 3.4 46.9 1.0 N B:CYS135 3.8 47.1 1.0 N B:HIS155 4.0 46.3 1.0 CA B:CYS135 4.1 50.5 1.0 NE2 B:HIS155 4.2 43.9 1.0 CD2 B:HIS155 4.2 46.7 1.0 CA B:HIS155 4.4 42.0 1.0 CG B:PRO79 4.5 50.9 1.0 CA B:CYS132 4.5 50.8 1.0 CD B:PRO79 4.5 57.3 1.0 CB B:LEU134 4.7 53.1 1.0 CA B:CYS158 4.7 35.1 1.0 C B:LEU134 4.8 56.5 1.0 C B:CYS135 4.8 64.4 1.0 N B:ASN136 4.9 66.2 1.0 C B:CYS132 5.0 50.2 1.0

Zinc binding site 9 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:52.2 occ:1.00 ND1 B:HIS48 2.1 45.7 1.0 SG B:CYS51 2.3 45.1 1.0 SG B:CYS23 2.3 32.0 1.0 SG B:CYS26 2.3 46.6 1.0 CE1 B:HIS48 3.1 51.5 1.0 CG B:HIS48 3.1 42.1 1.0 CB B:CYS23 3.1 31.4 1.0 CB B:CYS26 3.4 34.6 1.0 CB B:CYS51 3.4 37.9 1.0 CB B:HIS48 3.4 45.8 1.0 N B:CYS26 3.8 48.1 1.0 N B:HIS48 4.0 35.8 1.0 CA B:CYS26 4.1 42.2 1.0 NE2 B:HIS48 4.2 48.6 1.0 CD2 B:HIS48 4.2 47.7 1.0 CA B:HIS48 4.3 44.2 1.0 CA B:CYS23 4.6 35.0 1.0 CB B:VAL25 4.6 39.3 1.0 CA B:CYS51 4.7 47.9 1.0 C B:CYS26 4.9 35.9 1.0 C B:VAL25 4.9 56.4 1.0

Zinc binding site 10 out of 15 in the Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of JADE1 Pzp Domain in Complex with Histone H3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:51.0 occ:1.00 ND1 B:HIS185 2.1 59.5 1.0 SG B:CYS150 2.3 44.2 1.0 SG B:CYS182 2.3 47.5 1.0 SG B:CYS145 2.3 41.8 1.0 CE1 B:HIS185 2.9 55.4 1.0 CB B:CYS145 3.1 33.3 1.0 CG B:HIS185 3.2 57.2 1.0 CB B:CYS150 3.2 36.3 1.0 CB B:CYS182 3.4 51.9 1.0 CB B:HIS185 3.6 51.4 1.0 N B:CYS182 4.0 40.0 1.0 NE2 B:HIS185 4.1 53.2 1.0 CD2 B:HIS185 4.2 53.1 1.0 CB B:VAL147 4.2 41.2 1.0 CA B:CYS182 4.3 43.7 1.0 O B:HOH306 4.3 51.8 1.0 CG2 B:VAL147 4.4 35.5 1.0 CA B:CYS145 4.5 38.9 1.0 CA B:CYS150 4.7 40.7 1.0 N B:HIS185 4.7 54.1 1.0 CA B:HIS185 4.8 58.8 1.0 OG1 B:THR152 4.8 38.2 1.0 CB B:THR152 4.8 37.6 1.0 CG1 B:VAL147 5.0 34.3 1.0 C B:CYS182 5.0 46.6 1.0

N.Gaurav, A.Kanai, C.Lachance, K.L.Cox, J.Liu, A.T.Grzybowski, N.Saksouk, B.J.Klein, Y.Komata, S.Asada, A.J.Ruthenburg, M.G.Poirier, J.Cote, A.Yokoyama, T.G.Kutateladze. Guiding the HBO1 Complex Function Through the Jade Subunit Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01245-2