Chlorine in PDB 5k4b: Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1

The structure of Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1, PDB code: 5k4b was solved by P.J.Kranzusch, A.S.Y.Lee, J.A.Doudna, J.H.D.Cate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.832, 62.909, 192.112, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.3

The binding sites of Chlorine atom in the Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1 (pdb code 5k4b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1, PDB code: 5k4b:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:54.8 occ:1.00 O A:HOH1100 3.1 28.0 1.0 O A:HOH981 3.2 40.8 1.0 ND2 A:ASN510 3.2 34.1 1.0 CB A:ASN510 3.8 22.5 1.0 CA A:ILE507 3.8 16.3 1.0 CG A:ASN510 4.0 33.4 1.0 NE2 A:GLN511 4.2 25.3 1.0 CG2 A:ILE507 4.2 20.7 1.0 O A:ILE507 4.2 15.9 1.0 CG1 A:ILE507 4.3 18.6 1.0 CB A:ILE507 4.3 17.0 1.0 OE1 A:GLU183 4.5 25.4 1.0 C A:ILE507 4.6 14.8 1.0 O A:ASP506 4.6 16.8 1.0 N A:ILE507 4.7 15.0 1.0 O A:HOH1090 4.8 35.1 1.0

Chlorine binding site 2 out of 3 in the Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:17.8 occ:1.00 O A:HOH973 2.8 28.9 1.0 O A:HOH853 3.0 20.3 1.0 O A:HOH1069 3.2 13.9 1.0 N A:THR301 3.3 11.2 1.0 CB A:LYS441 3.5 9.0 1.0 CG A:LYS441 3.6 9.3 1.0 OG1 A:THR301 3.6 12.8 1.0 CA A:LYS441 3.7 9.0 1.0 CA A:LEU300 3.7 12.9 1.0 CD A:LYS441 3.9 10.3 1.0 CD2 A:LEU300 3.9 13.2 1.0 CE A:LYS444 3.9 12.6 1.0 C A:LEU300 4.0 16.0 1.0 NZ A:LYS444 4.0 19.0 1.0 CG2 A:THR301 4.2 12.7 1.0 CB A:LEU300 4.2 13.7 1.0 CB A:THR301 4.3 12.5 1.0 CA A:THR301 4.3 13.5 1.0 N A:LYS441 4.4 10.5 1.0 O A:LEU299 4.5 15.2 1.0 O A:THR301 4.7 12.3 1.0 O A:HOH929 4.7 22.8 1.0 CG A:LEU300 4.8 11.7 1.0 O A:HOH1124 4.8 27.8 1.0 N A:LEU300 4.8 13.8 1.0 C A:LYS441 4.9 7.8 1.0 O A:HOH1021 4.9 25.0 1.0 C A:THR301 5.0 11.5 1.0

Chlorine binding site 3 out of 3 in the Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Eukaryotic Translation Initiation Factor 3 Subunit D (EIF3D) Cap Binding Domain From Nasonia Vitripennis, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:22.5 occ:1.00 O B:HOH833 3.2 19.1 1.0 CG B:GLN229 3.6 20.9 1.0 CD1 B:ILE231 3.7 34.0 1.0 CB B:GLN229 3.8 18.7 1.0 CG B:GLN337 4.2 18.4 1.0 CG1 B:ILE231 4.3 35.6 1.0 CD B:GLN337 4.6 20.9 1.0 CD B:GLN229 4.8 19.7 1.0 CB B:GLN337 4.8 14.9 1.0 CA B:GLN337 4.9 14.9 1.0

A.S.Lee, P.J.Kranzusch, J.A.Doudna, J.H.Cate. EIF3D Is An Mrna Cap-Binding Protein That Is Required For Specialized Translation Initiation. Nature V. 536 96 2016.
ISSN: ESSN 1476-4687
PubMed: 27462815
DOI: 10.1038/NATURE18954