Iodine in PDB 5zbb: Crystal Structure of RTT109-ASF1-H3-H4 Complex

The structure of Crystal Structure of RTT109-ASF1-H3-H4 Complex, PDB code: 5zbb was solved by L.Zhang, A.Serra-Cardona, H.Zhou, M.Wang, N.Yang, Z.Zhang, R.M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.92 / 3.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.251, 112.251, 333.057, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 26.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of RTT109-ASF1-H3-H4 Complex (pdb code 5zbb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 23 binding sites of Iodine where determined in the Crystal Structure of RTT109-ASF1-H3-H4 Complex, PDB code: 5zbb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:42.9 occ:1.00 NE1 A:TRP168 3.5 33.2 1.0 NZ C:LYS56 3.8 38.2 1.0 CE1 A:TYR145 3.9 37.9 1.0 CE C:LYS56 4.1 34.8 1.0 CZ2 A:TRP168 4.2 34.8 1.0 O A:ALA93 4.2 37.9 1.0 CE2 A:TRP168 4.2 33.5 1.0 CD2 A:LEU164 4.3 42.5 1.0 CD1 A:TYR145 4.3 37.3 1.0 N A:ALA93 4.4 35.3 1.0 O A:PHE138 4.6 40.1 1.0 CD1 A:TRP168 4.6 34.1 1.0 CB A:ALA93 4.7 28.9 1.0 CA A:ALA139 4.9 33.1 1.0 O A:ARG140 4.9 26.2 1.0 CA A:ALA93 4.9 28.2 1.0 CD1 A:LEU164 5.0 35.4 1.0 CZ A:TYR145 5.0 35.6 1.0

Iodine binding site 2 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I602 b:64.3 occ:1.00 CB A:ASP410 3.9 49.0 1.0 CE1 A:HIS54 3.9 36.4 1.0 CE1 A:HIS26 4.0 34.5 1.0 CE2 A:PHE121 4.1 51.3 1.0 N A:ASP410 4.2 56.9 1.0 CE1 A:HIS415 4.3 54.7 1.0 NE2 A:HIS126 4.3 51.2 1.0 CD A:PRO409 4.3 62.0 1.0 CE3 A:TRP408 4.5 84.0 1.0 OG1 A:THR125 4.6 54.1 1.0 ND1 A:HIS54 4.7 32.7 1.0 CZ A:PHE121 4.7 53.1 1.0 CA A:ASP410 4.7 54.0 1.0 NE2 A:HIS415 4.8 46.1 1.0 CG A:PRO409 4.8 62.6 1.0 CB A:PRO409 4.8 66.3 1.0 NE2 A:HIS54 4.8 37.3 1.0 NE2 A:HIS26 4.9 35.3 1.0 N A:PRO409 4.9 58.7 1.0 ND1 A:HIS26 4.9 36.8 1.0 ND1 A:HIS415 4.9 47.9 1.0 CD2 A:LEU122 5.0 43.4 1.0

Iodine binding site 3 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:72.8 occ:0.60 N A:ASN236 3.7 45.3 1.0 CB A:ASN236 4.0 40.9 1.0 CE A:LYS213 4.1 81.9 1.0 CG A:ARG217 4.3 61.2 1.0 NE A:ARG217 4.3 80.3 1.0 CD A:ARG217 4.4 61.7 1.0 CA A:ASN236 4.5 40.3 1.0 NZ A:LYS213 4.5 80.4 1.0 CA A:LEU235 4.5 43.3 1.0 C A:LEU235 4.6 45.6 1.0 CB A:LYS213 4.7 58.0 1.0 CE2 A:PHE220 4.8 54.4 1.0 O A:TRP234 4.8 51.2 1.0 CD2 A:LEU235 4.9 47.7 1.0

Iodine binding site 4 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I604 b:57.6 occ:0.40 N A:LEU296 3.5 41.2 1.0 CB A:LEU296 3.9 38.9 1.0 CD1 A:LEU254 4.1 59.2 1.0 CA A:SER295 4.2 45.6 1.0 C A:SER295 4.3 44.3 1.0 CA A:LEU296 4.3 42.4 1.0 CG A:PRO251 4.5 51.2 1.0 CB A:SER295 4.5 55.2 1.0 O A:PRO247 4.8 0.5 1.0 CB A:PRO251 4.9 41.0 1.0 CD2 A:LEU240 4.9 78.2 1.0 CG A:LEU296 5.0 39.0 1.0

Iodine binding site 5 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I605 b:62.0 occ:0.50 CD2 A:LEU296 4.0 49.8 1.0 CB A:TYR238 4.0 44.9 1.0 CB A:LEU296 4.3 38.9 1.0 CD1 A:TRP300 4.3 40.2 1.0 CG A:LEU296 4.4 39.0 1.0 N A:ALA297 4.5 46.5 1.0 C A:LEU296 4.7 45.5 1.0 CA A:ALA297 4.7 46.0 1.0 NE1 A:TRP300 4.7 38.2 1.0 CG A:TYR238 4.8 48.2 1.0 CD2 A:TYR238 4.8 49.3 1.0 N A:TYR238 4.9 37.8 1.0 O A:LEU296 4.9 42.0 1.0 O A:TYR238 4.9 58.1 1.0 CA A:TYR238 5.0 45.1 1.0

Iodine binding site 6 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I606 b:71.8 occ:0.50 OE1 A:GLN242 3.3 74.0 1.0 CD A:GLN242 3.5 77.6 1.0 CG A:GLN242 4.0 79.0 1.0 NE2 A:GLN242 4.0 79.0 1.0 CA A:PRO239 4.2 52.8 1.0 N A:LEU240 4.2 58.5 1.0 N A:HIS241 4.3 87.5 1.0 CZ A:PHE205 4.3 50.1 1.0 N A:GLN242 4.4 82.5 1.0 CE2 A:PHE205 4.4 51.4 1.0 C A:PRO239 4.5 56.8 1.0 CB A:GLN242 4.5 70.8 1.0 CB A:HIS241 4.6 84.1 1.0 O A:TYR238 4.8 58.1 1.0 CA A:HIS241 4.8 87.8 1.0 ND1 A:HIS241 4.8 88.6 1.0 C A:HIS241 4.9 85.5 1.0 CB A:PRO239 4.9 54.9 1.0

Iodine binding site 7 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:63.6 occ:0.50 O A:ALA224 3.9 63.5 1.0 CA A:ARG225 4.1 62.0 1.0 C A:ALA224 4.2 59.7 1.0 CD A:ARG217 4.2 61.7 1.0 N A:ARG225 4.3 59.8 1.0 CG A:ARG225 4.4 68.1 1.0 CD2 A:PHE220 4.5 53.4 1.0 CB A:ARG217 4.6 62.5 1.0 CB A:ALA224 4.6 67.3 1.0 CG A:ARG217 4.7 61.2 1.0 O A:ARG217 4.8 56.6 1.0 CB A:ARG225 4.8 59.3 1.0

Iodine binding site 8 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I608 b:68.7 occ:0.70 CB A:SER109 3.6 68.9 1.0 NE1 A:TRP167 3.7 45.1 1.0 CA A:SER109 3.8 72.4 1.0 CB A:LEU111 3.8 43.4 1.0 N A:ARG112 3.9 45.1 1.0 N A:LEU111 4.0 54.7 1.0 C A:SER109 4.0 69.8 1.0 OG A:SER109 4.1 64.2 1.0 N A:LEU110 4.2 67.4 1.0 CA A:LEU111 4.3 53.8 1.0 CG A:LEU111 4.4 41.0 1.0 CB A:ARG112 4.4 50.1 1.0 CD1 A:TRP167 4.5 44.1 1.0 C A:LEU111 4.6 51.7 1.0 O A:SER109 4.6 66.5 1.0 CE2 A:TRP167 4.7 42.6 1.0 CA A:ARG112 4.7 44.5 1.0 CD1 A:LEU111 4.8 46.9 1.0 O1 A:PEG612 4.8 32.6 1.0 I A:IOD611 4.9 72.6 0.4 C A:LEU110 4.9 57.5 1.0

Iodine binding site 9 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I609 b:75.8 occ:0.50 NH2 A:ARG464 3.3 93.7 1.0 CE2 A:TRP460 4.3 45.0 1.0 CZ A:ARG464 4.3 83.1 1.0 CZ2 A:TRP460 4.4 53.9 1.0 CD2 A:TRP460 4.5 46.5 1.0 NE1 A:TRP460 4.6 44.6 1.0 CH2 A:TRP460 4.7 55.4 1.0 NE A:ARG464 4.8 73.4 1.0 CE3 A:TRP460 4.8 53.2 1.0 CZ3 A:TRP460 4.9 50.3 1.0 CG A:TRP460 5.0 43.8 1.0 CD1 A:TRP460 5.0 44.9 1.0

Iodine binding site 10 out of 23 in the Crystal Structure of RTT109-ASF1-H3-H4 Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of RTT109-ASF1-H3-H4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I610 b:73.5 occ:0.50 NH1 A:ARG162 3.2 43.7 1.0 OE1 A:GLU215 3.5 53.2 1.0 NH1 D:ARG95 3.8 56.7 1.0 CD A:GLU215 3.9 69.3 1.0 NH2 D:ARG95 3.9 59.7 1.0 CZ A:ARG162 4.1 51.3 1.0 NH2 A:ARG162 4.2 52.3 1.0 OE2 A:GLU215 4.2 83.2 1.0 SG A:CYS211 4.2 52.4 1.0 CZ D:ARG95 4.2 54.0 1.0 CD1 D:LEU97 4.6 35.9 1.0 CD1 A:LEU314 4.6 47.2 1.0 CB A:GLU215 4.6 56.4 1.0 CG A:GLU215 4.6 67.8 1.0 O D:PHE100 4.7 40.2 1.0

L.Zhang, A.Serra-Cardona, H.Zhou, M.Wang, N.Yang, Z.Zhang, R.M.Xu. Multisite Substrate Recognition in ASF1-Dependent Acetylation of Histone H3 K56 By RTT109. Cell V. 174 818 2018.
ISSN: ISSN 1097-4172
PubMed: 30057113
DOI: 10.1016/J.CELL.2018.07.005