Chlorine in PDB 6tr4: Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4 was solved by C.D.Owen, H.Wu, E.Crost, A.Colvile, N.Juge, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.64 / 1.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.780, 74.060, 76.509, 82.47, 80.43, 70.41
R / Rfree (%)	14.1 / 16.1

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Calcium	(Ca)	6 atoms

The binding sites of Chlorine atom in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose (pdb code 6tr4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:9.8 occ:1.00 O A:HOH1117 3.1 8.6 1.0 O A:HOH960 3.2 10.2 1.0 N A:GLU55 3.4 7.6 1.0 CB A:GLU55 3.8 7.1 1.0 CG A:GLU55 3.9 7.2 1.0 O A:HOH1387 3.9 41.3 1.0 CA A:ILE54 4.1 8.7 1.0 CG1 A:ILE54 4.2 9.3 1.0 C A:ILE54 4.2 8.0 1.0 CA A:GLU55 4.3 7.2 1.0 O A:HOH773 4.7 22.1 1.0 CB A:ILE54 4.8 8.8 1.0 O A:GLU53 5.0 10.5 1.0

Chlorine binding site 2 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl610 b:18.2 occ:1.00 O A:HOH1300 2.8 38.7 1.0 O A:HOH1194 3.1 19.4 1.0 N A:ASP411 3.2 14.0 1.0 CA A:SER410 3.6 12.8 1.0 CZ A:ARG387 3.7 13.2 1.0 NH1 A:ARG387 3.7 13.3 1.0 CB A:SER410 3.8 13.1 1.0 CG A:ASP411 3.8 17.2 1.0 NH2 A:ARG387 3.9 13.9 1.0 C A:SER410 3.9 13.2 1.0 CG A:ARG387 4.0 12.6 1.0 OD1 A:ASP411 4.0 16.9 1.0 CB A:ASP411 4.1 16.2 1.0 OD2 A:ASP411 4.1 19.7 1.0 NE A:ARG387 4.2 12.8 1.0 OG A:SER410 4.2 13.2 1.0 CA A:ASP411 4.2 14.9 1.0 O A:HOH1135 4.2 35.9 1.0 CB A:ALA18 4.3 20.6 1.0 N A:GLY388 4.4 14.5 1.0 O A:HOH723 4.7 20.8 1.0 CD A:ARG387 4.7 12.5 1.0 CA A:GLY388 4.8 15.5 1.0 O A:HOH736 4.8 32.6 1.0 O A:HOH860 4.9 33.6 1.0 O A:HOH1316 4.9 36.4 1.0 N A:SER410 4.9 12.4 1.0

Chlorine binding site 3 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl707 b:15.4 occ:1.00 O B:HOH1271 3.1 16.4 1.0 N B:ASP411 3.2 12.2 1.0 O B:HOH1105 3.3 23.0 1.0 CA B:SER410 3.7 11.0 1.0 CZ B:ARG387 3.7 10.3 1.0 NH1 B:ARG387 3.7 10.2 1.0 CG B:ASP411 3.8 14.9 1.0 CB B:SER410 3.8 11.2 1.0 NH2 B:ARG387 3.9 10.5 1.0 C B:SER410 4.0 11.3 1.0 CG B:ARG387 4.0 10.0 1.0 OD1 B:ASP411 4.0 15.3 1.0 CB B:ASP411 4.1 14.2 1.0 OD2 B:ASP411 4.1 17.1 1.0 CB B:ALA18 4.1 13.8 1.0 NE B:ARG387 4.2 10.0 1.0 OG B:SER410 4.2 11.6 1.0 CA B:ASP411 4.3 13.0 1.0 N B:GLY388 4.3 11.0 1.0 O B:HOH1030 4.6 37.7 1.0 O B:HOH1073 4.7 27.8 1.0 CD B:ARG387 4.7 9.8 1.0 O B:HOH843 4.7 15.8 1.0 CA B:GLY388 4.7 11.4 1.0 O B:HOH1467 4.8 27.8 1.0 CA B:ALA18 4.8 14.1 1.0 N B:SER410 5.0 10.3 1.0

Chlorine binding site 4 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl708 b:9.9 occ:1.00 O B:HOH1141 3.1 11.2 1.0 O B:HOH1214 3.2 8.9 1.0 N B:GLU55 3.4 7.2 1.0 CB B:GLU55 3.8 6.7 1.0 CG B:GLU55 3.9 6.9 1.0 CA B:ILE54 4.1 8.4 1.0 C B:ILE54 4.2 7.8 1.0 CG1 B:ILE54 4.2 9.7 1.0 CA B:GLU55 4.3 6.9 1.0 CB B:ILE54 4.8 8.9 1.0 O B:HOH984 4.8 22.8 1.0 O B:GLU53 5.0 10.0 1.0

H.Wu, O.Rebello, E.H.Crost, C.D.Owen, S.Walpole, C.Bennati-Granier, D.Ndeh, S.Monaco, T.Hicks, A.Colvile, P.A.Urbanowicz, M.A.Walsh, J.Angulo, D.I.R.Spencer, N.Juge. Fucosidases From the Human Gut Symbiont Ruminococcus Gnavus. Cell.Mol.Life Sci. 2020.
ISSN: ESSN 1420-9071
PubMed: 32333083
DOI: 10.1007/S00018-020-03514-X