Chlorine in PDB 1yj1: X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin, PDB code: 1yj1 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 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.872, 50.395, 92.941, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.8

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin (pdb code 1yj1). 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 [D-GLN35]Ubiquitin, PDB code: 1yj1:
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 [D-GLN35]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 [D-GLN35]Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl91 b:9.1 occ:1.00 CD A:CD90 2.5 12.0 1.0 O C:HOH1341 2.8 63.9 1.0 O A:HOH102 3.2 11.2 1.0 ND2 C:ASN25 3.3 3.6 1.0 N A:ASP21 3.5 4.9 1.0 O A:SER20 3.5 4.2 1.0 C A:SER20 3.5 4.3 1.0 CA A:ASP21 3.7 3.8 1.0 OD1 A:ASP21 3.9 7.9 1.0 CL B:CL93 4.0 9.8 1.0 O A:HOH95 4.0 16.7 1.0 CL A:CL92 4.0 10.3 1.0 CG A:ASP21 4.1 2.6 1.0 CB A:SER20 4.3 3.9 1.0 OE1 A:GLU18 4.3 7.5 1.0 CB A:GLU18 4.3 4.2 1.0 CG C:ASN25 4.3 2.3 1.0 CA A:SER20 4.4 4.4 1.0 O A:HOH97 4.5 24.7 1.0 OD1 C:ASN25 4.5 2.4 1.0 CB A:ASP21 4.5 4.4 1.0 O C:HOH94 4.6 25.6 1.0 O A:HOH303 4.6 13.0 1.0 CD A:CD101 4.7 8.7 1.0 OD2 A:ASP21 4.7 7.6 1.0 CD A:GLU18 4.7 6.9 1.0 N A:SER20 4.8 3.3 1.0 ND2 A:ASN25 4.8 4.0 1.0 OD1 C:ASP21 4.9 5.9 1.0 C A:ASP21 4.9 3.9 1.0

Chlorine binding site 2 out of 3 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl92 b:10.3 occ:1.00 CD A:CD90 2.5 12.0 1.0 O B:HOH203 3.1 12.9 1.0 ND2 A:ASN25 3.3 4.0 1.0 O B:SER20 3.5 7.6 1.0 C B:SER20 3.7 4.6 1.0 N B:ASP21 3.7 3.5 1.0 CA B:ASP21 3.8 4.5 1.0 O A:HOH95 3.8 16.7 1.0 OD1 B:ASP21 3.8 7.3 1.0 CL B:CL93 4.0 9.8 1.0 CL A:CL91 4.0 9.1 1.0 CG B:ASP21 4.2 7.0 1.0 O C:HOH96 4.2 11.8 1.0 OE1 B:GLU18 4.3 9.1 1.0 O B:HOH1257 4.3 6.8 0.5 CB B:SER20 4.4 4.8 1.0 CG A:ASN25 4.4 2.0 1.0 CB B:GLU18 4.5 5.3 1.0 CA B:SER20 4.5 4.5 1.0 CB B:ASP21 4.6 4.9 1.0 O A:HOH102 4.6 11.2 1.0 OD1 A:ASN25 4.7 2.8 1.0 CD B:CD201 4.7 9.6 1.0 OD1 A:ASP21 4.7 7.9 1.0 OD2 B:ASP21 4.7 7.4 1.0 ND2 B:ASN25 4.7 4.6 1.0 CD B:GLU18 4.8 9.3 1.0 C B:ASP21 4.9 4.2 1.0 N B:SER20 4.9 4.0 1.0

Chlorine binding site 3 out of 3 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl93 b:9.8 occ:1.00 CD A:CD90 2.5 12.0 1.0 O A:HOH303 3.2 13.0 1.0 ND2 B:ASN25 3.3 4.6 1.0 O C:HOH1341 3.5 63.9 1.0 N C:ASP21 3.6 3.5 1.0 O C:SER20 3.6 4.8 1.0 C C:SER20 3.7 3.1 1.0 O C:HOH94 3.7 25.6 1.0 CA C:ASP21 3.8 2.6 1.0 O C:HOH96 3.8 11.8 1.0 OD1 C:ASP21 3.9 5.9 1.0 CL A:CL91 4.0 9.1 1.0 CL A:CL92 4.0 10.3 1.0 CG C:ASP21 4.3 8.1 1.0 CG B:ASN25 4.3 3.1 1.0 CB C:SER20 4.4 3.6 1.0 OE2 C:GLU18 4.4 8.5 1.0 CB C:GLU18 4.4 2.9 1.0 CA C:SER20 4.5 3.8 1.0 OD1 B:ASN25 4.5 2.9 1.0 O B:HOH203 4.6 12.9 1.0 ND2 C:ASN25 4.6 3.6 1.0 CB C:ASP21 4.6 3.9 1.0 CD A:CD301 4.7 8.9 1.0 OD1 B:ASP21 4.8 7.3 1.0 CD C:GLU18 4.8 6.6 1.0 OD2 C:ASP21 4.8 7.5 1.0 N C:SER20 4.9 2.8 1.0 C C:ASP21 4.9 2.8 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