Chlorine in PDB 5cyk: Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E

The structure of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E, PDB code: 5cyk was solved by M.Wegrecki, J.Bravo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.38 / 3.00
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	170.750, 170.750, 155.660, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 26.2

The binding sites of Chlorine atom in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E (pdb code 5cyk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E, PDB code: 5cyk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:83.9 occ:1.00 NH2 A:ARG454 2.9 67.7 1.0 NH2 A:ARG414 3.3 61.5 1.0 NH1 A:ARG414 3.7 66.4 1.0 CZ A:ARG414 3.9 65.3 1.0 CZ A:ARG454 4.1 73.2 1.0 NH1 A:ARG454 4.4 76.4 1.0 O A:GLY386 4.8 73.2 1.0

Chlorine binding site 2 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:82.2 occ:1.00 NH2 A:ARG287 2.6 91.8 1.0 CZ A:ARG287 3.6 95.0 1.0 NH1 A:ARG287 3.9 0.5 1.0 CB A:ALA285 4.2 66.7 1.0 NZ A:LYS256 4.5 0.8 1.0 CA A:ALA285 4.7 74.8 1.0 CE A:LYS256 4.8 0.5 1.0 NE A:ARG287 4.8 75.5 1.0

Chlorine binding site 3 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:93.6 occ:1.00 NH1 B:ARG575 3.3 0.7 1.0 CD B:ARG575 3.7 0.8 1.0 NH2 B:ARG584 4.2 0.6 1.0 CG B:ARG575 4.2 0.9 1.0 CZ B:ARG575 4.3 0.7 1.0 NE B:ARG575 4.4 0.5 1.0 O B:LEU493 4.7 0.6 1.0 CA B:GLY573 5.0 0.8 1.0

Chlorine binding site 4 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl902 b:75.8 occ:1.00 NH2 B:ARG450 3.0 0.4 1.0 NH1 B:ARG450 3.4 0.9 1.0 NH2 B:ARG798 3.6 83.1 1.0 CZ B:ARG450 3.7 92.4 1.0 CG B:LYS769 4.6 0.1 1.0 CZ B:ARG798 4.6 82.4 1.0 NH1 B:ARG798 4.8 91.7 1.0 NZ B:LYS769 4.9 0.2 1.0 NE B:ARG450 5.0 62.6 1.0

Chlorine binding site 5 out of 5 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1-R486E within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl903 b:87.8 occ:1.00 NE2 B:GLN487 3.5 68.5 1.0 N B:SER490 4.1 77.4 1.0 CB B:SER490 4.2 82.4 1.0 CA B:TRP489 4.3 78.1 1.0 C B:TRP489 4.3 75.0 1.0 O B:GLN487 4.5 63.5 1.0 N B:TRP489 4.5 74.1 1.0 O B:VAL488 4.5 80.3 1.0 CD B:GLN487 4.6 75.8 1.0 C B:VAL488 4.6 75.2 1.0 CG B:GLN487 4.7 66.8 1.0 CA B:SER490 4.8 73.5 1.0

M.Wegrecki, O.Rodriguez-Galan, J.De La Cruz, J.Bravo. The Structure of ERB1-YTM1 Complex Reveals the Functional Importance of A High-Affinity Binding Between Two Beta-Propellers During the Assembly of Large Ribosomal Subunits in Eukaryotes. Nucleic Acids Res. V. 43 11017 2015.
ISSN: ESSN 1362-4962
PubMed: 26476442
DOI: 10.1093/NAR/GKV1043