Chlorine in PDB 1yiw: X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin

The structure of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin, PDB code: 1yiw was solved by D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.776, 50.476, 92.649, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.7

The structure of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin also contains other interesting chemical elements:

Cadmium

(Cd)

17 atoms

The binding sites of Chlorine atom in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin (pdb code 1yiw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin, PDB code: 1yiw:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl92 b:14.6 occ:1.00 CD A:CD90 2.5 17.2 1.0 O B:HOH203 3.2 11.9 1.0 ND2 A:ASN25 3.3 6.6 1.0 O A:HOH95 3.3 26.7 1.0 O B:HOH96 3.4 22.2 1.0 O B:SER20 3.6 10.3 1.0 N B:ASP21 3.7 6.1 1.0 C B:SER20 3.7 7.5 1.0 CA B:ASP21 3.8 7.5 1.0 OD1 B:ASP21 3.9 8.4 1.0 CL C:CL91 4.0 13.0 1.0 CL B:CL93 4.0 15.1 1.0 CG B:ASP21 4.2 9.6 1.0 OE1 B:GLU18 4.2 12.6 1.0 CB B:SER20 4.4 7.4 1.0 CG A:ASN25 4.4 6.7 1.0 CB B:GLU18 4.4 7.7 1.0 CA B:SER20 4.5 7.0 1.0 O A:HOH102 4.6 15.2 1.0 CB B:ASP21 4.6 6.6 1.0 OD1 A:ASN25 4.6 5.2 1.0 OD1 A:ASP21 4.7 6.0 1.0 CD B:GLU18 4.7 9.8 1.0 ND2 B:ASN25 4.7 6.8 1.0 CD B:CD201 4.7 14.1 1.0 OD2 B:ASP21 4.8 11.8 1.0 N B:SER20 4.9 7.4 1.0 CG B:GLU18 4.9 7.3 1.0 C B:ASP21 5.0 7.1 1.0

Chlorine binding site 2 out of 3 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl93 b:15.1 occ:1.00 CD A:CD90 2.5 17.2 1.0 ND2 B:ASN25 3.2 6.8 1.0 O C:HOH94 3.2 25.0 1.0 O C:HOH303 3.2 17.3 1.0 N C:ASP21 3.5 7.2 1.0 C C:SER20 3.6 7.2 1.0 O C:SER20 3.6 8.1 1.0 CA C:ASP21 3.8 7.3 1.0 O B:HOH96 3.8 22.2 1.0 OD1 C:ASP21 3.9 6.5 1.0 CL C:CL91 4.0 13.0 1.0 CL A:CL92 4.0 14.6 1.0 OE2 C:GLU18 4.1 11.0 1.0 CG C:ASP21 4.2 10.3 1.0 CB C:SER20 4.3 9.6 1.0 CG B:ASN25 4.3 5.5 1.0 CB C:GLU18 4.3 8.7 1.0 CA C:SER20 4.4 7.2 1.0 O B:HOH203 4.5 11.9 1.0 OD1 B:ASN25 4.5 5.5 1.0 CB C:ASP21 4.6 7.4 1.0 ND2 C:ASN25 4.6 6.0 1.0 CD C:GLU18 4.7 9.2 1.0 CD A:CD301 4.7 13.4 1.0 N C:SER20 4.8 6.0 1.0 OD2 C:ASP21 4.8 10.1 1.0 O A:HOH95 4.8 26.7 1.0 OD1 B:ASP21 4.9 8.4 1.0 C C:ASP21 4.9 7.4 1.0 CG C:GLU18 5.0 9.0 1.0

Chlorine binding site 3 out of 3 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl91 b:13.0 occ:1.00 CD A:CD90 2.5 17.2 1.0 ND2 C:ASN25 3.2 6.0 1.0 O A:HOH102 3.3 15.2 1.0 O A:HOH95 3.3 26.7 1.0 O A:SER20 3.5 8.6 1.0 N A:ASP21 3.6 8.1 1.0 C A:SER20 3.6 7.6 1.0 O C:HOH94 3.6 25.0 1.0 CA A:ASP21 3.7 6.7 1.0 OD1 A:ASP21 3.8 6.0 1.0 CL A:CL92 4.0 14.6 1.0 CL B:CL93 4.0 15.1 1.0 CG A:ASP21 4.1 8.2 1.0 OE1 A:GLU18 4.2 9.5 1.0 CG C:ASN25 4.3 7.4 1.0 CB A:SER20 4.3 6.8 1.0 CB A:GLU18 4.3 9.1 1.0 CA A:SER20 4.4 6.1 1.0 O A:HOH97 4.4 36.6 1.0 OD1 C:ASN25 4.5 6.1 1.0 CB A:ASP21 4.5 8.2 1.0 OD2 A:ASP21 4.7 8.6 1.0 O C:HOH303 4.7 17.3 1.0 CD A:GLU18 4.7 10.3 1.0 CD A:CD101 4.7 12.6 1.0 O B:HOH96 4.7 22.2 1.0 ND2 A:ASN25 4.8 6.6 1.0 N A:SER20 4.8 6.2 1.0 OD1 C:ASP21 4.8 6.5 1.0 C A:ASP21 4.9 6.5 1.0 CG A:GLU18 5.0 9.4 1.0

D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent. X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin Angew.Chem.Int.Ed.Engl. V. 44 3852 2005.
ISSN: ISSN 1433-7851
PubMed: 15834850
DOI: 10.1002/ANIE.200463040