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Sodium in PDB 6d1p: Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3

Protein crystallography data

The structure of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3, PDB code: 6d1p was solved by W.G.Walton, S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.721, 68.209, 167.300, 90.00, 122.49, 90.00
R / Rfree (%) 17.6 / 22.2

Other elements in 6d1p:

The structure of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 also contains other interesting chemical elements:

Potassium (K) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 (pdb code 6d1p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3, PDB code: 6d1p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6d1p

Go back to Sodium Binding Sites List in 6d1p
Sodium binding site 1 out of 5 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:30.9
occ:1.00
 O A:ASP580 2.7 21.5 1.0
O A:HOH1287 2.8 22.6 1.0
CE A:LYS579 2.9 28.4 1.0
O A:ASP333 2.9 26.8 1.0
OD2 A:ASP333 3.0 26.4 1.0
CB A:PHE581 3.4 20.6 1.0
C A:ASP580 3.6 20.4 1.0
CG A:LYS579 3.6 24.3 1.0
C A:ASP333 3.6 26.5 1.0
CA A:PHE581 3.6 19.0 1.0
CD A:LYS579 3.8 25.4 1.0
CG A:ASP333 3.9 21.8 1.0
CB A:LYS579 3.9 21.5 1.0
CB A:ASP333 3.9 20.7 1.0
O A:LYS579 3.9 19.7 1.0
O A:HOH1045 4.0 23.8 1.0
N A:PHE581 4.0 19.9 1.0
NZ A:LYS579 4.1 31.2 1.0
CG A:ARG602 4.1 22.0 1.0
C A:LYS579 4.2 19.5 1.0
N A:HIS334 4.3 22.1 1.0
CA A:ASP333 4.4 23.1 1.0
CA A:HIS334 4.4 21.2 1.0
O A:ARG602 4.5 21.5 1.0
CA A:ARG602 4.6 20.6 1.0
N A:ASP580 4.7 21.9 1.0
CA A:LYS579 4.7 21.1 1.0
NE A:ARG602 4.8 19.1 1.0
O A:HOH1083 4.8 17.2 1.0
CA A:ASP580 4.8 19.9 1.0
CG A:PHE581 4.8 25.3 1.0
CB A:ARG602 4.9 20.5 1.0
CD A:ARG602 4.9 20.1 1.0
N A:ASP333 4.9 22.4 1.0

Sodium binding site 2 out of 5 in 6d1p

Go back to Sodium Binding Sites List in 6d1p
Sodium binding site 2 out of 5 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:25.7
occ:1.00
 OG1 A:THR174 2.6 22.4 1.0
O A:ASP434 2.7 23.4 1.0
OG B:SER44 2.8 21.9 1.0
O B:HOH1375 2.9 24.8 1.0
CB A:THR174 3.3 23.7 1.0
CB B:SER44 3.4 23.9 1.0
CG2 A:THR174 3.5 23.9 1.0
CD2 A:PHE435 3.7 24.8 1.0
CE2 A:PHE435 3.9 25.6 1.0
C A:ASP434 3.9 23.1 1.0
O B:HOH1319 4.0 28.6 1.0
CD1 B:TRP46 4.0 28.6 1.0
CB B:TRP46 4.0 21.4 1.0
O A:HOH1106 4.4 31.2 1.0
CG B:TRP46 4.4 28.8 1.0
O A:HOH1377 4.4 30.2 1.0
CG A:PHE435 4.5 28.8 1.0
CA A:PHE435 4.5 23.3 1.0
N A:PHE435 4.7 23.4 1.0
CA A:THR174 4.7 25.4 1.0
N B:GLU47 4.8 21.7 1.0
CZ A:PHE435 4.8 27.3 1.0
CA B:SER44 4.9 18.1 1.0
O B:HOH1300 4.9 32.4 1.0
CA A:ASP434 4.9 23.4 1.0
CB A:PHE435 5.0 21.5 1.0
CA B:TRP46 5.0 24.3 1.0

Sodium binding site 3 out of 5 in 6d1p

Go back to Sodium Binding Sites List in 6d1p
Sodium binding site 3 out of 5 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na901

b:38.4
occ:1.00
 O A:HOH1409 2.4 31.5 1.0
CG2 B:THR174 2.6 35.7 1.0
OG A:SER44 2.7 31.6 1.0
O B:ASP434 2.9 34.0 1.0
CB B:THR174 3.2 32.9 1.0
CB A:SER44 3.3 30.6 1.0
OG1 B:THR174 3.3 37.6 1.0
CD2 B:PHE435 3.8 30.1 1.0
O A:HOH1354 4.0 34.2 1.0
CE2 B:PHE435 4.0 28.7 1.0
CB A:TRP46 4.0 36.9 1.0
CD1 A:TRP46 4.1 38.3 1.0
C B:ASP434 4.1 36.0 1.0
CG A:TRP46 4.4 37.8 1.0
CG B:PHE435 4.6 30.2 1.0
CA B:PHE435 4.6 35.1 1.0
CA B:THR174 4.7 25.6 1.0
O A:HOH1353 4.7 35.3 1.0
CA A:SER44 4.8 29.3 1.0
N B:PHE435 4.9 37.6 1.0
N A:GLU47 4.9 30.6 1.0
CZ B:PHE435 5.0 34.1 1.0

Sodium binding site 4 out of 5 in 6d1p

Go back to Sodium Binding Sites List in 6d1p
Sodium binding site 4 out of 5 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:36.8
occ:1.00
 OD1 B:ASP333 2.7 25.3 1.0
O B:ASP580 2.8 22.8 1.0
O B:HOH1193 2.9 22.6 1.0
CE B:LYS579 3.0 29.5 1.0
CB B:PHE581 3.1 22.0 1.0
O B:ASP333 3.2 27.7 1.0
CA B:PHE581 3.4 23.3 1.0
CG B:ASP333 3.5 24.9 1.0
C B:ASP580 3.6 22.9 1.0
C B:ASP333 3.6 26.7 1.0
CB B:ASP333 3.6 23.2 1.0
CG B:LYS579 3.8 23.1 1.0
O B:LYS579 3.9 22.8 1.0
N B:PHE581 3.9 18.7 1.0
CD B:LYS579 4.0 23.8 1.0
NZ B:LYS579 4.0 30.2 1.0
CG B:ARG602 4.1 24.5 1.0
CB B:LYS579 4.1 20.1 1.0
O B:HOH1044 4.1 25.9 1.0
CA B:ASP333 4.2 24.0 1.0
N B:HIS334 4.2 24.4 1.0
C B:LYS579 4.3 22.4 1.0
CD B:ARG602 4.4 23.8 1.0
CA B:HIS334 4.5 24.2 1.0
CG B:PHE581 4.5 21.2 1.0
OD2 B:ASP333 4.7 21.6 1.0
O B:HOH1098 4.8 22.3 1.0
O B:ARG602 4.8 25.1 1.0
C B:PHE581 4.8 21.9 1.0
N B:ASP333 4.8 22.3 1.0
CA B:LYS579 4.8 24.6 1.0
N B:ASP580 4.8 25.7 1.0
CA B:ARG602 4.9 23.2 1.0
CA B:ASP580 4.9 21.9 1.0
O B:HIS331 4.9 21.7 1.0
CB B:HIS331 4.9 21.6 1.0
CB B:ARG602 5.0 22.4 1.0

Sodium binding site 5 out of 5 in 6d1p

Go back to Sodium Binding Sites List in 6d1p
Sodium binding site 5 out of 5 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na903

b:47.4
occ:1.00
 O B:HOH1231 2.2 31.6 1.0
O B:HOH1260 2.3 35.8 1.0
OG B:SER398 2.4 32.5 1.0
O B:GLU175 2.9 27.3 1.0
CB B:GLU175 3.5 26.0 1.0
C B:GLU175 3.5 29.3 1.0
CB B:SER398 3.6 29.0 1.0
N B:TYR399 3.9 29.7 1.0
C B:SER398 4.0 30.7 1.0
CA B:GLU175 4.2 28.4 1.0
O B:HOH1060 4.2 33.4 1.0
N B:MET176 4.3 26.4 1.0
CA B:SER398 4.4 34.8 1.0
O B:SER398 4.5 30.0 1.0
OD2 B:ASP173 4.5 31.6 1.0
CA B:TYR399 4.5 32.0 1.0
CA B:MET176 4.6 25.6 1.0
CG B:GLU175 4.7 28.2 1.0
O B:HOH1301 4.7 31.6 1.0
CB B:MET176 4.9 25.1 1.0

Reference:

S.J.Pellock, W.G.Walton, K.A.Biernat, D.Torres-Rivera, B.C.Creekmore, Y.Xu, J.Liu, A.Tripathy, L.J.Stewart, M.R.Redinbo. Three Structurally and Functionally Distinct Beta-Glucuronidases From the Human Gut Microbebacteroides Uniformis. J. Biol. Chem. V. 293 18559 2018.
ISSN: ESSN 1083-351X
PubMed: 30301767
DOI: 10.1074/JBC.RA118.005414
Page generated: Tue Oct 8 06:52:18 2024

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