Chlorine in PDB 6pdk: The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System

The structure of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System, PDB code: 6pdk was solved by B.Y.Matsuyama, C.S.Farah, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.87 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	67.532, 67.532, 149.386, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 24.9

The structure of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System also contains other interesting chemical elements:

Bromine

(Br)

11 atoms

The binding sites of Chlorine atom in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System (pdb code 6pdk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System, PDB code: 6pdk:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:25.7 occ:1.00 O A:GLN252 3.5 34.5 1.0 CA A:GLY255 3.6 33.8 1.0 N A:GLY255 3.8 32.9 1.0 O A:GLY253 4.2 38.0 1.0 CB A:ARG251 4.2 29.8 1.0 CD A:ARG251 4.3 27.1 1.0 C A:GLY253 4.5 39.7 1.0 C A:GLN252 4.6 34.0 1.0 C A:GLY255 4.8 30.7 1.0 C A:ASP254 4.9 41.0 1.0 CA A:GLY253 4.9 39.7 1.0 CG A:ARG251 4.9 28.4 1.0

Chlorine binding site 2 out of 4 in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:55.3 occ:1.00 N A:ASP104 3.3 35.0 1.0 CA A:VAL103 3.7 34.0 1.0 C A:VAL103 4.0 34.2 1.0 CG1 A:VAL103 4.0 40.2 1.0 CB A:ASP104 4.1 36.5 1.0 NH2 A:ARG113 4.2 54.7 1.0 CG A:ASP104 4.2 43.7 1.0 O A:PRO102 4.3 36.4 1.0 CA A:ASP104 4.3 34.9 1.0 CB A:VAL103 4.3 35.4 1.0 OD2 A:ASP104 4.6 54.1 1.0 OD1 A:ASP104 4.6 47.8 1.0 CG2 A:VAL103 4.7 34.6 1.0 N A:VAL103 4.8 27.6 1.0 C A:PRO102 5.0 34.6 1.0 O A:ASP104 5.0 35.5 1.0

Chlorine binding site 3 out of 4 in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:49.7 occ:1.00 O A:HOH589 2.9 43.1 1.0 OE2 A:GLU129 3.1 28.0 0.6 CG A:GLU129 3.2 36.1 0.6 OE2 A:GLU129 3.3 40.6 0.5 N A:GLY108 3.6 32.2 1.0 CD A:GLU129 3.6 33.2 0.6 CD A:GLU129 3.7 38.8 0.5 CB A:GLU129 4.1 37.8 0.5 CB A:TYR166 4.1 32.3 1.0 OE1 A:GLU129 4.2 41.2 0.5 CA A:LEU107 4.3 29.6 1.0 CG A:GLU129 4.3 37.5 0.5 O A:LYS106 4.3 30.4 1.0 CA A:GLY108 4.4 40.6 1.0 CB A:GLU129 4.4 36.9 0.6 CD2 A:TYR166 4.4 41.3 1.0 C A:LEU107 4.4 30.7 1.0 N A:GLY130 4.5 36.6 1.0 CA A:GLU129 4.6 32.9 0.5 CA A:GLU129 4.6 32.9 0.6 CG A:TYR166 4.7 37.2 1.0 OE1 A:GLU129 4.9 30.8 0.6 C A:LYS106 4.9 28.9 1.0 N A:LEU107 5.0 30.3 1.0

Chlorine binding site 4 out of 4 in the The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of SMLT3025, An Immunity Protein of the Stenotrophomonas Maltophilia Type IV Secretion System within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:53.7 occ:1.00 O A:HOH543 3.1 41.7 1.0 OG1 A:THR213 4.1 39.1 1.0 CG2 A:THR213 4.2 31.7 1.0 O A:HOH529 4.4 41.4 1.0 CB A:THR213 4.8 29.9 1.0

E.Bayer-Santos, W.Cenens, B.Y.Matsuyama, G.U.Oka, G.Di Sessa, I.D.V.Mininel, T.L.Alves, C.S.Farah. The Opportunistic Pathogen Stenotrophomonas Maltophilia Utilizes A Type IV Secretion System For Interbacterial Killing. Plos Pathog. V. 15 07651 2019.
ISSN: ESSN 1553-7374
PubMed: 31513674
DOI: 10.1371/JOURNAL.PPAT.1007651