Sodium in PDB 6dxu: Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)

The structure of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus), PDB code: 6dxu was solved by M.S.Little, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.63 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.371, 163.393, 120.607, 90.00, 103.35, 90.00
R / Rfree (%)	15.4 / 18.4

The binding sites of Sodium atom in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) (pdb code 6dxu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus), PDB code: 6dxu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:22.0 occ:1.00 O D:VAL84 2.6 22.3 1.0 O D:ASP78 2.7 21.9 1.0 O D:ASP81 2.8 20.6 1.0 O D:HOH1334 3.0 21.4 1.0 O D:ALA79 3.2 20.7 1.0 CE2 D:TYR608 3.5 20.2 1.0 CD2 D:TYR608 3.5 19.9 1.0 C D:ALA79 3.6 18.7 1.0 C D:VAL84 3.8 21.1 1.0 CZ D:TYR608 3.8 19.3 1.0 C D:ASP78 3.8 19.7 1.0 CG D:TYR608 3.8 17.5 1.0 C D:ASP81 3.9 20.4 1.0 N D:ASP81 4.0 19.9 1.0 O D:HOH1123 4.1 18.0 1.0 N D:TYR86 4.1 18.1 1.0 CE1 D:TYR608 4.2 18.1 1.0 CD1 D:TYR608 4.2 17.7 1.0 N D:VAL80 4.2 17.2 1.0 CA D:ALA79 4.2 21.7 1.0 C D:VAL80 4.2 18.6 1.0 CG2 D:VAL84 4.3 26.2 1.0 CA D:ASP81 4.4 20.9 1.0 CA D:VAL80 4.4 19.4 1.0 N D:ALA79 4.5 18.2 1.0 OH D:TYR608 4.5 18.4 1.0 C D:ASN85 4.5 20.0 1.0 N D:VAL84 4.6 21.0 1.0 CA D:ASN85 4.6 18.9 1.0 CB D:TYR608 4.6 16.0 1.0 N D:ASN85 4.7 17.6 1.0 CA D:VAL84 4.7 21.3 1.0 CB D:ASP81 4.7 20.5 1.0 CA D:TYR86 4.7 19.5 1.0 CB D:TYR86 4.8 19.0 1.0 O D:VAL80 4.8 20.1 1.0 CA D:ASP78 4.9 19.2 1.0 N D:PRO82 4.9 20.3 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na903 b:20.5 occ:1.00 O D:MET176 2.3 18.6 1.0 O D:ASP173 2.4 14.9 1.0 O D:HOH1160 2.5 18.9 1.0 O D:PRO178 2.5 16.7 1.0 O D:HOH1428 2.5 17.7 1.0 C D:ASP173 3.5 17.9 1.0 C D:MET176 3.5 19.2 1.0 C D:PRO178 3.5 19.5 1.0 O D:HOH1372 3.7 23.6 1.0 CA D:SER179 3.8 18.0 1.0 N D:SER179 4.1 19.8 1.0 N D:ASP180 4.2 18.5 1.0 N D:ASP173 4.2 18.6 1.0 OD2 D:ASP180 4.2 20.7 1.0 CA D:MET176 4.3 17.8 1.0 N D:MET176 4.3 17.2 1.0 O C:HOH1033 4.3 22.2 1.0 N D:LEU174 4.3 16.2 1.0 CA D:ASP173 4.3 18.6 1.0 CA D:LEU174 4.3 17.9 1.0 C D:SER179 4.4 17.9 1.0 CB D:MET176 4.4 19.3 1.0 N D:ILE177 4.5 16.3 1.0 O D:HOH1016 4.5 27.7 1.0 CA D:ILE177 4.6 13.2 1.0 CE D:MET176 4.6 23.2 1.0 C D:LEU174 4.6 19.9 1.0 CA D:PRO178 4.7 14.5 1.0 CD1 D:ILE186 4.7 17.9 1.0 C D:ILE177 4.7 17.3 1.0 CB D:ASP173 4.8 18.3 1.0 N D:PRO178 4.8 16.3 1.0 O D:LEU174 4.8 18.6 1.0 O D:HOH1348 4.9 22.5 1.0 CG D:ASP180 5.0 18.0 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:20.9 occ:1.00 O A:VAL84 2.5 20.5 1.0 O A:ASP81 2.7 20.5 1.0 O A:ASP78 2.7 22.1 1.0 O A:HOH1404 2.9 22.1 1.0 O A:ALA79 3.1 21.1 1.0 CE2 A:TYR608 3.4 21.6 1.0 CD2 A:TYR608 3.4 18.4 1.0 C A:ALA79 3.6 21.7 1.0 C A:VAL84 3.8 22.4 1.0 CZ A:TYR608 3.8 22.9 1.0 CG A:TYR608 3.8 18.5 1.0 C A:ASP81 3.8 19.4 1.0 C A:ASP78 3.9 18.7 1.0 N A:ASP81 4.0 19.7 1.0 CE1 A:TYR608 4.1 18.8 1.0 N A:TYR86 4.1 18.3 1.0 CD1 A:TYR608 4.1 17.1 1.0 O A:HOH1169 4.2 18.8 1.0 N A:VAL80 4.2 17.5 1.0 CA A:ALA79 4.2 20.8 1.0 C A:VAL80 4.2 21.4 1.0 CG2 A:VAL84 4.3 25.1 1.0 CA A:ASP81 4.4 19.5 1.0 CA A:VAL80 4.4 18.5 1.0 OH A:TYR608 4.4 19.0 1.0 C A:ASN85 4.5 21.8 1.0 N A:VAL84 4.5 22.4 1.0 N A:ALA79 4.6 17.2 1.0 CB A:TYR608 4.6 15.8 1.0 CA A:ASN85 4.6 18.8 1.0 N A:ASN85 4.6 20.8 1.0 CA A:VAL84 4.7 22.1 1.0 CA A:TYR86 4.7 16.9 1.0 CB A:ASP81 4.8 22.4 1.0 CB A:TYR86 4.8 15.7 1.0 O A:VAL80 4.8 21.8 1.0 N A:PRO82 4.9 21.6 1.0 CA A:ASP78 5.0 20.3 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:20.3 occ:1.00 O A:MET176 2.4 18.5 1.0 O A:ASP173 2.4 17.6 1.0 O A:HOH1449 2.5 17.1 1.0 O A:PRO178 2.5 18.0 1.0 O A:HOH1154 2.5 19.4 1.0 C A:ASP173 3.5 19.2 1.0 C A:MET176 3.5 17.7 1.0 C A:PRO178 3.5 17.8 1.0 O A:HOH1426 3.7 22.5 1.0 CA A:SER179 3.8 18.3 1.0 N A:SER179 4.1 17.7 1.0 N A:ASP180 4.1 18.1 1.0 N A:ASP173 4.2 18.3 1.0 OD2 A:ASP180 4.2 18.9 1.0 N A:MET176 4.2 17.1 1.0 CA A:MET176 4.3 18.9 1.0 O A:HOH1015 4.3 27.4 1.0 O B:HOH1061 4.3 21.0 1.0 C A:SER179 4.3 18.8 1.0 CB A:MET176 4.3 20.3 1.0 CA A:ASP173 4.3 18.8 1.0 N A:LEU174 4.3 18.5 1.0 CA A:LEU174 4.4 20.3 1.0 N A:ILE177 4.5 17.2 1.0 CA A:ILE177 4.6 17.6 1.0 C A:LEU174 4.6 22.0 1.0 CE A:MET176 4.7 22.3 1.0 CA A:PRO178 4.7 16.4 1.0 C A:ILE177 4.7 20.0 1.0 O A:LEU174 4.7 20.9 1.0 CB A:ASP173 4.7 18.6 1.0 N A:PRO178 4.7 19.6 1.0 CD1 A:ILE186 4.8 19.5 1.0 O A:HOH1316 4.9 21.9 1.0 CG A:ASP180 4.9 19.3 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:24.1 occ:1.00 O B:VAL84 2.6 25.2 1.0 O B:ASP81 2.7 22.7 1.0 O B:HOH1324 2.7 24.1 1.0 O B:ASP78 2.8 23.1 1.0 O B:ALA79 3.1 22.7 1.0 CD2 B:TYR608 3.3 21.6 1.0 CE2 B:TYR608 3.3 21.9 1.0 C B:ALA79 3.6 23.6 1.0 CZ B:TYR608 3.7 19.9 1.0 CG B:TYR608 3.7 19.6 1.0 C B:VAL84 3.8 23.9 1.0 C B:ASP81 3.8 23.5 1.0 C B:ASP78 3.9 22.1 1.0 N B:ASP81 4.0 22.8 1.0 CD1 B:TYR608 4.0 19.0 1.0 CE1 B:TYR608 4.0 18.8 1.0 O B:HOH1125 4.1 20.7 1.0 CA B:ALA79 4.2 21.7 1.0 N B:VAL80 4.2 21.3 1.0 N B:TYR86 4.2 19.9 1.0 C B:VAL80 4.3 26.8 1.0 OH B:TYR608 4.4 23.2 1.0 CA B:ASP81 4.4 21.2 1.0 CG2 B:VAL84 4.5 24.3 1.0 CA B:VAL80 4.5 21.5 1.0 CB B:TYR608 4.5 18.3 1.0 N B:ALA79 4.5 22.7 1.0 N B:VAL84 4.6 23.6 1.0 C B:ASN85 4.6 23.2 1.0 CA B:ASN85 4.7 26.6 1.0 N B:ASN85 4.7 22.4 1.0 CB B:ASP81 4.7 25.1 1.0 CA B:VAL84 4.8 22.7 1.0 CA B:TYR86 4.8 19.2 1.0 CB B:TYR86 4.9 21.0 1.0 O B:VAL80 4.9 23.2 1.0 N B:PRO82 4.9 22.2 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:21.4 occ:1.00 O B:ASP173 2.4 17.9 1.0 O B:HOH1170 2.4 17.4 1.0 O B:MET176 2.4 21.2 1.0 O B:HOH1486 2.4 18.0 1.0 O B:PRO178 2.4 18.1 1.0 C B:ASP173 3.5 19.4 1.0 C B:PRO178 3.5 22.0 1.0 C B:MET176 3.5 16.9 1.0 O B:HOH1280 3.6 24.2 1.0 CA B:SER179 3.8 20.1 1.0 N B:SER179 4.1 20.3 1.0 N B:ASP173 4.1 18.3 1.0 N B:ASP180 4.2 17.2 1.0 OD2 B:ASP180 4.2 18.8 1.0 O A:HOH1055 4.3 22.7 1.0 N B:MET176 4.3 17.4 1.0 CA B:MET176 4.3 16.3 1.0 N B:LEU174 4.3 19.3 1.0 CA B:ASP173 4.3 19.1 1.0 C B:SER179 4.3 17.2 1.0 CA B:LEU174 4.3 21.6 1.0 CB B:MET176 4.4 19.6 1.0 N B:ILE177 4.5 16.3 1.0 O B:HOH1022 4.5 28.8 1.0 CE B:MET176 4.5 22.9 1.0 CA B:ILE177 4.6 16.4 1.0 C B:LEU174 4.6 23.1 1.0 CD1 B:ILE186 4.7 20.1 1.0 CA B:PRO178 4.7 19.9 1.0 CB B:ASP173 4.7 17.3 1.0 C B:ILE177 4.8 19.8 1.0 N B:PRO178 4.8 20.4 1.0 O B:LEU174 4.8 18.1 1.0 O B:HOH1376 4.9 22.2 1.0 CG B:ASP180 5.0 18.3 1.0 CB B:SER179 5.0 21.6 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:22.1 occ:1.00 O C:VAL84 2.5 22.9 1.0 O C:ASP78 2.7 22.8 1.0 O C:ASP81 2.8 21.7 1.0 O C:HOH1473 2.8 21.7 1.0 O C:ALA79 3.1 23.7 1.0 CE2 C:TYR608 3.4 19.4 1.0 CD2 C:TYR608 3.4 24.3 1.0 C C:ALA79 3.6 21.3 1.0 CZ C:TYR608 3.7 20.9 1.0 C C:VAL84 3.8 25.8 1.0 CG C:TYR608 3.8 19.9 1.0 C C:ASP81 3.9 20.4 1.0 C C:ASP78 3.9 20.7 1.0 N C:ASP81 4.0 22.8 1.0 CE1 C:TYR608 4.1 21.6 1.0 CD1 C:TYR608 4.1 19.4 1.0 O C:HOH1212 4.1 23.1 1.0 N C:TYR86 4.2 21.8 1.0 CA C:ALA79 4.2 22.6 1.0 N C:VAL80 4.2 18.9 1.0 C C:VAL80 4.2 23.6 1.0 CG2 C:VAL84 4.3 24.0 1.0 OH C:TYR608 4.4 22.4 1.0 CA C:ASP81 4.4 23.0 1.0 CA C:VAL80 4.4 20.4 1.0 N C:ALA79 4.5 18.4 1.0 C C:ASN85 4.6 18.5 1.0 N C:VAL84 4.6 23.1 1.0 CB C:TYR608 4.6 19.5 1.0 CA C:ASN85 4.6 20.1 1.0 N C:ASN85 4.6 20.9 1.0 CA C:VAL84 4.7 24.9 1.0 CB C:ASP81 4.8 21.1 1.0 CA C:TYR86 4.8 19.2 1.0 CB C:TYR86 4.8 18.5 1.0 O C:VAL80 4.8 25.3 1.0 N C:PRO82 4.9 21.6 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na904 b:21.2 occ:1.00 O C:ASP173 2.4 18.2 1.0 O C:HOH1202 2.4 19.8 1.0 O C:MET176 2.4 18.2 1.0 O C:HOH1462 2.4 17.6 1.0 O C:PRO178 2.5 18.4 1.0 C C:ASP173 3.4 18.7 1.0 C C:PRO178 3.5 19.9 1.0 C C:MET176 3.6 20.0 1.0 O C:HOH1275 3.6 23.5 1.0 CA C:SER179 3.8 19.2 1.0 N C:SER179 4.1 19.0 1.0 N C:ASP173 4.1 19.5 1.0 N C:ASP180 4.2 18.9 1.0 OD2 C:ASP180 4.2 20.1 1.0 N C:MET176 4.3 18.9 1.0 N C:LEU174 4.3 18.6 1.0 CA C:MET176 4.3 19.1 1.0 O D:HOH1106 4.3 22.3 1.0 CA C:ASP173 4.3 17.8 1.0 CA C:LEU174 4.3 19.8 1.0 C C:SER179 4.3 18.0 1.0 O C:HOH1040 4.4 24.0 1.0 CB C:MET176 4.4 20.9 1.0 N C:ILE177 4.6 17.8 1.0 C C:LEU174 4.6 19.1 1.0 CE C:MET176 4.6 21.0 1.0 CA C:ILE177 4.6 18.0 1.0 CB C:ASP173 4.7 19.1 1.0 CD1 C:ILE186 4.7 20.1 1.0 O C:LEU174 4.8 17.9 1.0 CA C:PRO178 4.8 15.6 1.0 C C:ILE177 4.8 16.7 1.0 N C:PRO178 4.9 15.7 1.0 O C:HOH1361 4.9 20.9 1.0 CG C:ASP180 5.0 19.8 1.0 CB C:SER179 5.0 20.2 1.0

M.S.Little, S.M.Ervin, W.G.Walton, A.Tripathy, Y.Xu, J.Liu, M.R.Redinbo. Active Site Flexibility Revealed in Crystal Structures of Parabacteroides Merdae Beta-Glucuronidase From the Human Gut Microbiome. Protein Sci. V. 27 2010 2018.
ISSN: ESSN 1469-896X
PubMed: 30230652
DOI: 10.1002/PRO.3507