Sodium in PDB 5dyn: B. Fragilis Cysteine Protease

The structure of B. Fragilis Cysteine Protease, PDB code: 5dyn was solved by V.M.Choi, J.Herrou, A.L.Hecht, J.R.Turner, S.Crosson, J.Bubeck Wardenburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.43 / 2.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.320, 48.900, 60.880, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.3

The structure of B. Fragilis Cysteine Protease also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the B. Fragilis Cysteine Protease (pdb code 5dyn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the B. Fragilis Cysteine Protease, PDB code: 5dyn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:34.0 occ:1.00 O A:GLN104 2.3 41.8 1.0 OE1 A:GLN42 2.4 38.5 1.0 OD1 B:ASP152 2.5 38.6 1.0 OD2 B:ASP152 2.6 40.5 1.0 OD2 A:ASP75 2.6 33.8 1.0 CG B:ASP152 2.9 34.6 1.0 CD A:GLN42 3.1 38.9 1.0 OE1 A:GLU103 3.4 54.3 1.0 NE2 A:GLN42 3.4 43.2 1.0 C A:GLN104 3.4 34.0 1.0 CG A:ASP75 3.5 39.8 1.0 OD1 A:ASP75 3.7 44.1 1.0 NA A:NA402 4.0 47.5 1.0 N A:GLN104 4.1 45.8 1.0 N A:ASN105 4.2 38.3 1.0 CA A:ASN105 4.2 35.4 1.0 CG A:GLN42 4.3 33.1 1.0 CB A:GLN42 4.3 33.1 1.0 N A:SER106 4.3 34.5 1.0 OG A:SER106 4.4 31.2 1.0 CA A:GLN104 4.4 42.6 1.0 CB B:ASP152 4.4 28.5 1.0 CD A:GLU103 4.5 62.7 1.0 C A:ASN105 4.8 37.8 1.0 O B:HOH508 4.9 43.5 1.0 CB A:ASP75 4.9 33.5 1.0 OE2 A:GLU103 4.9 66.1 1.0

Sodium binding site 2 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:47.5 occ:1.00 OD1 A:ASP75 2.4 44.1 1.0 OE1 A:GLN42 2.4 38.5 1.0 O A:ASP76 2.5 38.9 1.0 OE2 A:GLU103 2.7 66.1 1.0 O A:SER78 2.8 49.2 1.0 OE1 A:GLU103 3.2 54.3 1.0 CD A:GLU103 3.3 62.7 1.0 C A:ASP76 3.5 35.5 1.0 CD A:GLN42 3.5 38.9 1.0 CG A:ASP75 3.5 39.8 1.0 C A:SER78 3.7 48.7 1.0 N A:SER78 3.9 44.3 1.0 NA A:NA401 4.0 34.0 1.0 N A:ASP76 4.0 32.0 1.0 OD2 A:ASP75 4.0 33.8 1.0 CG A:GLN42 4.0 33.1 1.0 C A:ASP75 4.0 36.9 1.0 C A:TYR77 4.2 43.0 1.0 N A:TYR77 4.3 38.4 1.0 CA A:TYR77 4.3 40.5 1.0 CB A:GLN42 4.3 33.1 1.0 O A:ASP75 4.3 38.2 1.0 CA A:ASP76 4.3 39.9 1.0 CA A:SER78 4.3 49.7 1.0 CA A:ASP75 4.5 35.2 1.0 NE2 A:GLN42 4.5 43.2 1.0 CB A:ASP75 4.6 33.5 1.0 N A:ALA79 4.6 47.2 1.0 CD A:PRO80 4.6 39.2 1.0 CG A:GLU103 4.8 50.8 1.0 O A:TYR77 4.8 51.0 1.0 CA A:ALA79 4.9 47.3 1.0 CG A:PRO80 4.9 35.4 1.0 N A:PRO80 4.9 39.3 1.0 OD1 A:ASP76 5.0 37.8 1.0 C A:ALA79 5.0 43.6 1.0

Sodium binding site 3 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:41.1 occ:1.00 O B:PRO208 2.3 35.4 1.0 OD1 A:ASP52 2.4 37.4 1.0 OE1 A:GLU55 2.5 39.4 1.0 O A:HOH504 2.6 35.1 1.0 O B:ALA210 2.6 38.4 1.0 OE2 A:GLU55 3.0 35.1 1.0 CD A:GLU55 3.0 40.5 1.0 CG A:ASP52 3.4 41.4 1.0 C B:PRO208 3.5 33.3 1.0 C B:ALA210 3.6 42.2 1.0 OD2 A:ASP52 4.0 39.4 1.0 C B:GLY209 4.2 34.8 1.0 N B:ALA210 4.3 34.0 1.0 O B:GLY209 4.3 37.3 1.0 CD2 B:TYR212 4.3 32.7 1.0 CA B:PRO208 4.3 34.3 1.0 CA A:ASP52 4.4 36.3 1.0 N B:PRO211 4.4 43.5 1.0 CB B:PRO208 4.5 29.8 1.0 CG A:GLU55 4.5 39.5 1.0 CB A:ASP52 4.5 35.2 1.0 N B:GLY209 4.5 35.2 1.0 CA B:PRO211 4.5 36.3 1.0 CA B:ALA210 4.6 39.1 1.0 CA B:GLY209 4.6 33.1 1.0 N B:TYR212 4.7 36.1 1.0 CE2 B:TYR212 4.8 37.6 1.0 N A:ASP52 4.8 38.5 1.0 CB A:GLU55 5.0 42.4 1.0

Sodium binding site 4 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:45.2 occ:1.00 O B:TRP252 2.5 35.4 1.0 N B:GLY255 2.9 33.8 1.0 O B:TYR237 3.0 41.6 1.0 CA B:THR253 3.0 40.7 1.0 C B:THR253 3.0 44.1 1.0 C B:TRP252 3.2 38.4 1.0 N B:GLY254 3.3 35.1 1.0 N B:THR253 3.4 39.0 1.0 O B:ARG240 3.4 39.5 1.0 CA B:TYR241 3.5 34.4 1.0 O B:THR253 3.5 41.6 1.0 CA B:GLY255 3.5 38.4 1.0 C B:ARG240 3.5 38.9 1.0 N B:TYR241 3.5 34.1 1.0 CD1 B:TRP252 3.8 33.4 1.0 C B:TYR237 3.9 39.5 1.0 C B:GLY254 4.0 37.4 1.0 CB B:TYR241 4.1 38.5 1.0 CA B:GLY254 4.2 39.5 1.0 CA B:TYR237 4.2 43.1 1.0 CB B:ARG240 4.3 44.2 1.0 CD1 B:TYR237 4.3 38.8 1.0 CB B:TYR237 4.3 40.2 1.0 CB B:THR253 4.4 37.6 1.0 CA B:ARG240 4.4 41.8 1.0 CA B:TRP252 4.5 38.2 1.0 C B:GLY255 4.5 40.5 1.0 CD1 B:TYR241 4.5 39.6 1.0 CG B:TRP252 4.5 38.8 1.0 CB B:TRP252 4.6 34.3 1.0 C B:TYR241 4.7 37.7 1.0 O B:GLY255 4.7 37.3 1.0 NE1 B:TRP252 4.8 41.2 1.0 N B:ASP242 4.8 41.6 1.0 CG B:TYR237 4.8 35.8 1.0 CG B:TYR241 4.8 39.1 1.0 N B:ARG240 4.9 37.1 1.0 CG2 B:THR253 5.0 39.3 1.0

Sodium binding site 5 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:40.1 occ:1.00 NE1 B:TRP379 2.6 30.0 1.0 OG1 B:THR360 2.7 32.5 1.0 OH B:TYR374 2.8 29.5 1.0 NE1 B:TRP385 3.0 35.3 1.0 CD1 B:TRP379 3.3 25.3 1.0 CD1 B:TRP385 3.6 35.2 1.0 CE2 B:TRP379 3.8 29.0 1.0 OE2 B:GLU186 3.9 27.2 1.0 CZ B:TYR374 4.0 29.9 1.0 CB B:THR360 4.0 33.8 1.0 CE2 B:TRP385 4.2 36.8 1.0 O B:TYR361 4.2 32.2 1.0 CG1 B:VAL185 4.4 28.9 1.0 CZ2 B:TRP379 4.4 29.0 1.0 CE2 B:TYR374 4.5 25.8 1.0 N B:TYR361 4.6 30.6 1.0 CG B:TRP379 4.6 29.7 1.0 CZ2 B:TRP385 4.8 35.5 1.0 CD1 B:LEU307 4.8 27.6 1.0 CD B:GLU186 4.8 30.7 1.0 OG B:SER383 4.8 37.4 1.0 CB B:SER383 4.8 35.4 1.0 CD2 B:TRP379 4.9 33.5 1.0 CA B:THR360 4.9 26.5 1.0 CG B:TRP385 4.9 35.5 1.0 CG2 B:THR360 5.0 26.7 1.0

Sodium binding site 6 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:53.6 occ:1.00 OD1 B:ASN268 2.5 38.3 0.5 O B:ALA327 2.6 44.7 1.0 OE1 B:GLU265 2.9 44.2 1.0 CB B:ASN268 3.3 38.6 0.6 CG B:ASN268 3.3 37.5 0.5 CB B:ASN268 3.4 38.7 0.5 O B:GLU265 3.4 35.4 1.0 C B:ALA327 3.5 43.2 1.0 CA B:ALA327 3.7 42.7 1.0 CB B:GLU265 3.7 34.1 1.0 CD B:GLU265 3.7 47.2 1.0 CB B:LYS330 3.8 44.6 1.0 CD B:LYS330 3.8 52.4 1.0 CB B:ALA327 3.9 33.8 1.0 ND2 B:ASN268 4.1 29.0 0.6 N B:LEU269 4.1 38.1 1.0 CG B:GLU265 4.2 35.7 1.0 CG B:ASN268 4.3 39.4 0.6 C B:GLU265 4.3 35.8 1.0 CA B:GLU265 4.3 37.4 1.0 C B:ASN268 4.3 37.1 1.0 CG2 B:VAL331 4.3 37.9 1.0 CA B:ASN268 4.4 37.2 0.6 CG B:LYS330 4.4 45.4 1.0 CA B:ASN268 4.4 37.1 0.5 ND2 B:ASN268 4.6 36.0 0.5 OE2 B:GLU265 4.6 49.8 1.0 CA B:LEU269 4.7 37.1 1.0 N B:PHE328 4.7 36.1 1.0 CA B:LYS330 4.8 45.0 1.0 CB B:LEU269 4.9 38.1 1.0 O B:ASN268 4.9 36.9 1.0 C B:LYS330 4.9 41.9 1.0

Sodium binding site 7 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:36.9 occ:1.00 O B:GLY291 2.5 38.7 1.0 OD1 B:ASP354 2.7 42.0 1.0 ND2 B:ASN352 2.8 33.5 1.0 N B:MET293 3.1 34.2 1.0 CB B:ASN352 3.5 36.1 1.0 CG B:ASP354 3.5 37.1 1.0 CB B:MET293 3.6 31.8 1.0 CG B:ARG309 3.6 35.9 1.0 CG B:ASN352 3.6 34.9 1.0 C B:GLY291 3.6 39.8 1.0 OD2 B:ASP354 3.7 38.1 1.0 CA B:MET293 3.7 29.2 1.0 CD B:ARG309 3.8 37.4 1.0 C B:VAL292 3.9 31.0 1.0 CA B:VAL292 4.0 35.7 1.0 CB B:ARG309 4.2 35.8 1.0 N B:VAL292 4.2 38.9 1.0 CA B:GLY291 4.7 37.6 1.0 OD1 B:ASN352 4.8 31.4 1.0 N B:ALA355 4.8 38.2 1.0 CG B:MET293 4.9 28.2 1.0 CB B:ASP354 4.9 37.5 1.0 CA B:ASN352 4.9 39.6 1.0 O B:VAL292 5.0 29.4 1.0

Sodium binding site 8 out of 8 in the B. Fragilis Cysteine Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of B. Fragilis Cysteine Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:40.1 occ:1.00 O B:PRO202 2.6 28.8 1.0 O B:PHE181 2.7 30.7 1.0 OG B:SER359 2.7 29.7 1.0 C B:PHE181 3.3 30.5 1.0 CB B:SER359 3.4 31.8 1.0 CD1 B:TYR304 3.4 35.0 1.0 C B:PRO202 3.5 36.4 1.0 CA B:PHE181 3.5 29.0 1.0 CG B:TYR304 3.5 36.0 1.0 CA B:PRO202 3.7 32.4 1.0 CB B:PHE181 3.7 29.6 1.0 CB B:TYR304 3.7 35.5 1.0 CE1 B:TYR304 4.0 30.6 1.0 CB B:ALA184 4.1 27.9 1.0 CD2 B:TYR304 4.1 34.3 1.0 O B:GLU183 4.2 30.3 1.0 C B:GLU183 4.3 34.4 1.0 CD1 B:PHE181 4.3 28.9 1.0 N B:MET182 4.3 28.8 1.0 CB B:PRO202 4.4 32.0 1.0 O B:HOH516 4.4 27.2 1.0 N B:ALA184 4.5 31.3 1.0 N B:GLU183 4.5 26.6 1.0 CA B:ALA184 4.5 30.4 1.0 CG B:PHE181 4.5 30.1 1.0 CZ B:TYR304 4.5 32.4 1.0 O B:SER201 4.5 34.4 1.0 CE2 B:TYR304 4.6 34.0 1.0 N B:THR203 4.7 27.6 1.0 CA B:SER359 4.8 30.4 1.0 N B:PHE181 4.8 33.2 1.0 N B:PRO202 4.9 31.8 1.0 C B:MET182 4.9 35.8 1.0 CA B:GLU183 5.0 31.4 1.0

V.M.Choi, J.Herrou, A.L.Hecht, W.P.Teoh, J.R.Turner, S.Crosson, J.Bubeck Wardenburg. Activation of Bacteroides Fragilis Toxin By A Novel Bacterial Protease Contributes to Anaerobic Sepsis in Mice. Nat. Med. V. 22 563 2016.
ISSN: ISSN 1546-170X
PubMed: 27089515
DOI: 10.1038/NM.4077