Zinc in PDB 5ye4: Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment

The structure of Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment, PDB code: 5ye4 was solved by T.Matsuda, T.Ito, M.Wakamori, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.76 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.346, 164.093, 73.700, 90.00, 104.50, 90.00
R / Rfree (%)	19.4 / 22.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment (pdb code 5ye4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 26 binding sites of Zinc where determined in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment, PDB code: 5ye4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.2 occ:1.00 OD2 B:ASP166 2.0 20.9 1.0 NE2 A:HIS162 2.1 19.4 1.0 O B:HOH552 2.2 19.4 1.0 O B:HOH517 2.3 22.4 1.0 CG B:ASP166 2.8 21.6 1.0 OD1 B:ASP166 3.0 17.6 1.0 CD2 A:HIS162 3.0 19.6 1.0 CE1 A:HIS162 3.1 19.5 1.0 ND2 B:ASN137 4.2 23.5 1.0 CG A:HIS162 4.2 14.4 1.0 O B:HOH453 4.2 17.9 1.0 ND1 A:HIS162 4.2 14.9 1.0 CB B:ASP166 4.2 16.1 1.0 CD B:LYS168 4.4 37.0 1.0 O B:HOH574 4.5 43.8 1.0 NZ B:LYS168 4.7 50.3 1.0 OD1 B:ASN137 4.8 18.9 1.0 O B:HOH413 4.8 37.0 1.0 CB B:LYS168 4.9 21.6 1.0 CG B:ASN137 4.9 19.7 1.0 CG B:LYS168 4.9 26.2 1.0

Zinc binding site 2 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:43.8 occ:1.00 OE2 A:GLU16 2.2 32.5 1.0 O A:HOH547 2.3 32.3 1.0 O A:HOH564 2.6 39.5 1.0 CD A:GLU16 3.1 32.5 1.0 CG A:GLU16 3.3 28.4 1.0 NZ A:LYS13 4.3 36.0 1.0 OE1 A:GLU16 4.3 27.2 1.0 CD A:LYS13 4.4 31.4 1.0 CB A:GLU16 4.8 23.0 1.0 CE A:LYS13 4.8 30.6 1.0 CG A:LYS13 4.9 17.7 1.0 CB A:LYS13 5.0 19.9 1.0

Zinc binding site 3 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:50.7 occ:1.00 O A:HOH451 2.3 49.1 1.0 OE1 A:GLU89 2.4 24.1 1.0 OE2 A:GLU89 2.9 35.5 1.0 CD A:GLU89 3.0 33.8 1.0 N A:ASN88 4.1 20.9 1.0 CB A:LYS87 4.1 18.7 1.0 CB A:ASN88 4.4 25.1 1.0 CD A:LYS87 4.4 30.1 1.0 CG A:GLU89 4.5 36.0 1.0 N A:GLU89 4.6 15.4 1.0 ND2 A:ASN88 4.7 42.5 1.0 CA A:LYS87 4.7 17.7 1.0 CA A:ASN88 4.8 23.3 1.0 CG A:ASN88 4.8 32.0 1.0 CG A:LYS87 4.8 25.5 1.0 C A:LYS87 4.9 20.5 1.0

Zinc binding site 4 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:68.6 occ:1.00 OD2 A:ASP31 2.3 41.3 1.0 OD1 A:ASP31 2.8 35.8 1.0 CG A:ASP31 2.9 32.8 1.0 O A:HOH401 4.0 39.9 1.0 CG2 A:THR28 4.2 30.8 1.0 CB A:ASP31 4.4 28.9 1.0 CB A:THR28 4.7 35.9 1.0 OG1 A:THR28 4.7 35.5 1.0

Zinc binding site 5 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:64.0 occ:1.00 OE2 A:GLU10 2.2 26.0 1.0 O A:HOH430 2.3 51.5 1.0 O A:HOH530 2.3 25.6 1.0 CD A:GLU10 2.9 35.7 1.0 OE1 A:GLU10 3.0 31.8 1.0 O A:LYS19 3.6 19.3 1.0 CG A:GLU10 4.3 29.2 1.0 O A:HOH420 4.4 22.6 1.0 CG2 A:VAL18 4.6 20.3 1.0 N A:LYS19 4.6 21.1 1.0 C A:LYS19 4.7 18.1 1.0 CE A:LYS12 4.7 27.3 1.0 NZ A:LYS12 4.7 24.4 1.0 O A:HOH560 4.9 43.9 1.0 O A:HOH553 4.9 43.7 1.0

Zinc binding site 6 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:79.9 occ:1.00 OD2 A:ASP62 2.1 45.8 1.0 OD1 B:ASP1 2.2 51.7 1.0 OD2 B:ASP1 2.5 47.9 1.0 CG B:ASP1 2.6 48.5 1.0 CG A:ASP62 3.2 32.6 1.0 O A:HOH463 3.2 37.0 1.0 OD1 A:ASP62 3.5 35.0 1.0 CB B:ASP1 4.1 36.8 1.0 O B:HOH483 4.4 27.6 1.0 CB A:ASP62 4.5 32.0 1.0 N B:ASP1 4.6 32.8 1.0 CA B:ASP1 4.8 28.3 1.0 O A:HOH528 5.0 38.7 1.0

Zinc binding site 7 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:95.8 occ:1.00 OE1 A:GLN39 2.4 14.8 1.0 O A:HOH489 2.4 25.0 1.0 CE1 B:HIS38 2.8 25.2 1.0 O B:HOH557 2.9 38.3 1.0 CD A:GLN39 3.2 16.1 1.0 NE2 B:HIS38 3.5 18.4 1.0 ND1 B:HIS38 3.6 21.4 1.0 NE2 A:GLN39 3.7 17.3 1.0 O B:HOH446 4.2 14.4 1.0 CA B:PRO40 4.3 36.0 1.0 O B:HOH553 4.4 38.5 1.0 CZ A:PHE95 4.4 11.7 1.0 CG A:GLN39 4.4 12.6 1.0 CD2 B:HIS38 4.6 14.5 1.0 CG B:HIS38 4.6 15.2 1.0 O A:HOH491 4.8 42.6 1.0 N B:GLY41 4.9 35.0 1.0 O A:HOH468 4.9 29.6 1.0 CE2 A:PHE95 4.9 9.2 1.0 CB B:PRO40 4.9 34.8 1.0 N B:PRO40 5.0 29.7 1.0

Zinc binding site 8 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:41.6 occ:1.00 O B:HOH561 2.1 23.6 1.0 O B:HOH548 2.1 34.8 1.0 ND1 B:HIS197 2.3 32.0 1.0 CE1 B:HIS197 3.2 24.8 1.0 CG B:HIS197 3.3 35.2 1.0 O B:HOH408 3.6 50.5 1.0 CB B:HIS197 3.6 39.6 1.0 CB B:THR199 4.2 63.1 1.0 N B:HIS197 4.3 38.1 1.0 NE2 B:HIS197 4.3 22.2 1.0 OG B:SER200 4.4 38.8 1.0 O B:ALA110 4.4 15.2 1.0 CA B:ALA111 4.4 15.7 1.0 CD2 B:HIS197 4.4 27.8 1.0 CB B:ALA111 4.5 25.6 1.0 CA B:HIS197 4.6 36.3 1.0 CB B:SER200 4.7 34.9 1.0 OG1 B:THR199 4.7 66.8 1.0 CG2 B:THR199 4.8 56.8 1.0 C B:ALA110 4.8 17.6 1.0 N B:ALA111 4.8 19.8 1.0 N B:SER200 4.9 75.0 1.0 O B:TYR139 4.9 17.0 1.0 N B:THR199 5.0 67.7 1.0

Zinc binding site 9 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:59.5 occ:1.00 O B:HOH498 2.2 21.4 1.0 OD2 B:ASP92 2.2 26.0 1.0 OD1 B:ASP92 2.3 27.5 1.0 CG B:ASP92 2.6 19.6 1.0 NH1 E:ARG3 3.8 29.8 1.0 O B:ASP28 3.9 17.5 1.0 CB B:ASP92 4.1 10.5 1.0 ND2 B:ASN30 4.4 13.7 1.0 CZ E:ARG3 4.8 35.5 1.0 NH2 E:ARG3 4.8 35.9 1.0 CA B:ILE29 4.8 9.2 1.0 O B:ASP92 4.9 15.8 1.0 C B:ASP92 5.0 21.8 1.0 CA B:ASP92 5.0 14.7 1.0 C B:ASP28 5.0 16.5 1.0

Zinc binding site 10 out of 26 in the Crystal Structure of the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment


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 the Complex of Di-Acetylated Histone H4 and 1A9D7 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:65.9 occ:1.00 O B:ASP1 2.2 31.6 1.0 N B:ASP1 2.2 32.8 1.0 O B:HOH467 2.4 47.9 1.0 O B:HOH405 2.5 46.2 1.0 C B:ASP1 2.9 28.4 1.0 CA B:ASP1 3.0 28.3 1.0 CB B:ASP1 3.7 36.8 1.0 O B:HOH540 3.8 50.9 1.0 NE2 B:GLN3 4.2 47.8 1.0 N B:ILE2 4.2 19.6 1.0 O B:HOH417 4.3 34.7 1.0 CG B:ASP1 4.6 48.5 1.0 OD1 B:ASP1 4.7 51.7 1.0 CA B:ILE2 4.9 13.8 1.0

L.Handoko, B.Kaczkowski, C.C.Hon, M.Lizio, M.Wakamori, T.Matsuda, T.Ito, P.Jeyamohan, Y.Sato, K.Sakamoto, S.Yokoyama, H.Kimura, A.Minoda, T.Umehara. JQ1 Affects BRD2-Dependent and Independent Transcription Regulation Without Disrupting H4-Hyperacetylated Chromatin States. Epigenetics V. 13 410 2018.
ISSN: ESSN 1559-2308
PubMed: 30080437
DOI: 10.1080/15592294.2018.1469891