Chlorine in PDB 2vm9: Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom

The structure of Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom, PDB code: 2vm9 was solved by K.S.Aragao, M.Satre, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	81.833, 81.833, 257.823, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 17.8

The structure of Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Chlorine atom in the Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom (pdb code 2vm9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom, PDB code: 2vm9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl509 b:17.2 occ:1.00 O A:HOH2052 3.0 31.4 1.0 N A:GLY239 3.1 6.6 1.0 O A:HOH2116 3.1 22.1 0.5 CA A:GLY181 3.7 6.7 1.0 CA A:GLY239 3.7 6.2 1.0 CB A:TRP238 3.8 6.1 1.0 N A:SER182 3.9 7.4 1.0 C A:GLY181 3.9 7.6 1.0 O A:HOH2327 4.0 40.8 1.0 C A:TRP238 4.1 6.4 1.0 O A:HOH2285 4.2 16.0 1.0 CD1 A:TRP238 4.2 7.0 1.0 CA A:TRP238 4.3 6.2 1.0 CG A:TRP238 4.4 6.5 1.0 N A:GLY181 4.7 6.5 1.0 O A:GLY239 4.7 7.5 1.0 O A:GLY181 4.7 7.1 1.0 C A:GLY239 4.7 6.5 1.0 CA A:SER182 4.8 8.7 1.0 O A:HOH2348 4.9 24.5 0.5

Chlorine binding site 2 out of 3 in the Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl510 b:19.4 occ:1.00 O A:HOH2039 2.9 34.0 1.0 O A:HOH2097 3.0 16.2 1.0 N A:LYS59 3.1 6.7 1.0 O A:HOH2110 3.3 35.8 1.0 CE A:LYS59 3.5 17.7 1.0 CB A:ASP58 3.5 7.3 1.0 CB A:LYS59 3.6 8.0 1.0 CG A:LYS59 3.8 9.1 1.0 ND2 A:ASN60 3.9 11.3 1.0 CA A:LYS59 3.9 7.4 1.0 C A:ASP58 4.0 6.7 1.0 CA A:ASP58 4.0 6.8 1.0 CD A:LYS59 4.3 13.5 1.0 CG A:ASP58 4.3 8.4 1.0 CG A:ASN60 4.6 10.4 1.0 C A:LYS59 4.6 7.4 1.0 OD2 A:ASP58 4.6 9.5 1.0 NZ A:LYS59 4.7 24.1 1.0 N A:ASN60 4.8 7.1 1.0 OD1 A:ASN60 4.8 13.1 1.0 O A:HOH2102 4.9 22.4 1.0 O A:HOH2223 4.9 6.7 1.0

Chlorine binding site 3 out of 3 in the Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Native Structure of the Recombinant Discoidin II of Dictyostelium Discoideum at 1.75 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl511 b:22.6 occ:1.00 N A:ASP85 3.1 6.3 1.0 ND1 A:HIS84 3.2 18.2 1.0 NH2 A:ARG117 3.6 9.7 1.0 CA A:HIS84 3.6 7.8 1.0 CG A:ASP85 3.7 10.1 1.0 CB A:ASP85 3.8 7.6 1.0 CB A:HIS84 3.8 8.7 1.0 C A:HIS84 3.9 6.9 1.0 OD2 A:ASP85 3.9 10.6 1.0 CG A:HIS84 4.0 12.6 1.0 OD1 A:ASP85 4.1 8.7 1.0 O A:HOH2143 4.1 13.9 1.0 CA A:ASP85 4.1 6.3 1.0 CE1 A:HIS84 4.3 21.1 1.0 CZ A:ARG117 4.6 7.2 1.0 O A:HOH2146 4.6 30.9 1.0 O A:ASP83 4.9 8.1 1.0 NE A:ARG117 4.9 8.0 1.0 N A:HIS84 4.9 7.4 1.0

K.S.Aragao, M.Satre, A.Imberty, A.Varrot. Structure Determination of Discoidin II From Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain. Proteins V. 73 43 2008.
ISSN: ISSN 0887-3585
PubMed: 18384150
DOI: 10.1002/PROT.22038