Chlorine in PDB 5d3d: Crystal Structure of Staphylococcal Superantigen-Like Protein 3

The structure of Crystal Structure of Staphylococcal Superantigen-Like Protein 3, PDB code: 5d3d was solved by L.J.Feitsma, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.20 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.000, 79.220, 96.380, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.4

The structure of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3 (pdb code 5d3d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3, PDB code: 5d3d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:52.3 occ:1.00 N A:ASN292 3.4 32.8 1.0 OD1 A:ASN292 3.6 33.8 1.0 CB A:ASN317 3.6 35.8 1.0 CB A:ASN292 3.6 36.8 1.0 CG A:ASN292 3.7 35.6 1.0 ND2 A:ASN317 3.8 41.6 1.0 CG A:ASN317 3.9 40.0 1.0 N A:LYS291 3.9 29.7 1.0 CB A:MET290 4.0 28.9 1.0 O A:HOH616 4.1 51.9 1.0 CA A:ASN292 4.2 35.8 1.0 C A:LYS291 4.3 32.7 1.0 O A:ASN317 4.3 32.2 1.0 CA A:LYS291 4.4 32.0 1.0 ND2 A:ASN292 4.4 37.9 1.0 CB A:LYS291 4.4 33.5 1.0 O A:HOH558 4.5 38.7 1.0 CE A:MET290 4.5 30.1 1.0 C A:MET290 4.5 29.1 1.0 OD1 A:ASN317 4.6 41.6 1.0 CA A:MET290 4.8 28.0 1.0 CA A:ASN317 4.8 33.9 1.0 CG A:MET290 4.9 28.6 1.0 C A:ASN317 4.9 31.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:56.6 occ:1.00 NE2 A:GLN270 3.1 39.0 1.0 CD1 A:ILE235 3.2 37.6 1.0 CG A:GLN270 3.3 36.7 1.0 CD2 A:HIS275 3.6 34.0 1.0 CD A:GLN270 3.7 39.1 1.0 NE2 A:HIS275 3.8 35.0 1.0 CD2 A:LEU233 3.9 29.3 1.0 CD2 A:LEU271 4.0 27.1 1.0 CD A:LYS274 4.1 44.9 1.0 CB A:GLN270 4.1 32.5 1.0 O A:GLN270 4.2 29.8 1.0 C A:GLN270 4.2 30.2 1.0 CB A:LYS274 4.4 36.9 1.0 CG1 A:ILE235 4.4 34.3 1.0 N A:LEU271 4.5 28.0 1.0 CA A:LEU271 4.7 27.4 1.0 CG A:LEU271 4.8 26.2 1.0 OG A:SER249 4.8 22.2 0.5 CA A:GLN270 4.8 29.7 1.0 CG A:LYS274 4.9 41.5 1.0 CG A:HIS275 4.9 34.0 1.0 CG A:LEU233 4.9 26.8 1.0 OE1 A:GLN270 4.9 44.8 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:76.6 occ:1.00 O A:HOH567 3.0 42.2 1.0 NZ A:LYS185 3.4 49.5 1.0 O A:VAL312 4.0 29.9 1.0 CB A:ASP311 4.1 28.7 1.0 OD1 A:ASP311 4.1 32.1 1.0 CG A:ASP311 4.2 30.1 1.0 OH A:TYR296 4.4 37.8 1.0 CE A:LYS185 4.5 47.0 1.0 N A:VAL312 4.6 29.0 1.0 CE1 A:TYR296 4.6 33.0 1.0 CD A:LYS185 4.7 44.1 1.0 OD2 A:ASP311 4.7 33.0 1.0 CA A:ASP311 4.7 28.1 1.0 CZ A:TYR296 4.9 33.2 1.0 CG2 A:ILE313 4.9 27.8 1.0 C A:VAL312 4.9 30.2 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:66.2 occ:1.00 CB B:ASN317 3.2 40.1 1.0 N B:ASN292 3.3 37.6 1.0 OD1 B:ASN292 3.5 35.0 1.0 CB B:ASN292 3.5 38.0 1.0 CG B:ASN292 3.5 35.8 1.0 CG B:ASN317 3.7 44.5 1.0 O B:ASN317 3.8 35.4 1.0 N B:LYS291 3.9 35.9 1.0 ND2 B:ASN317 3.9 45.6 1.0 CB B:MET290 4.0 33.9 1.0 CA B:ASN292 4.0 38.9 1.0 C B:LYS291 4.1 38.9 1.0 ND2 B:ASN292 4.2 36.5 1.0 CA B:LYS291 4.3 38.9 1.0 CB B:LYS291 4.3 40.5 1.0 CA B:ASN317 4.3 38.3 1.0 CE B:MET290 4.4 32.0 1.0 OD1 B:ASN317 4.4 47.3 1.0 C B:ASN317 4.5 36.4 1.0 C B:MET290 4.5 35.5 1.0 CA B:MET290 4.7 34.6 1.0 O B:HOH563 4.7 42.3 1.0 CG B:MET290 4.9 32.7 1.0

K.J.Koymans, L.J.Feitsma, T.H.Brondijk, P.C.Aerts, E.Lukkien, P.Lossl, K.P.Van Kessel, C.J.De Haas, J.A.Van Strijp, E.G.Huizinga. Structural Basis For Inhibition of TLR2 By Staphylococcal Superantigen-Like Protein 3 (SSL3). Proc.Natl.Acad.Sci.Usa V. 112 11018 2015.
ISSN: ESSN 1091-6490
PubMed: 26283364
DOI: 10.1073/PNAS.1502026112