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Potassium 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:

Sodium (Na) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3, PDB code: 6d1p:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6d1p

Go back to Potassium Binding Sites List in 6d1p
Potassium binding site 1 out of 4 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K908

b:20.6
occ:1.00
 O A:VAL83 2.8 21.6 1.0
O A:ASP77 2.8 21.9 1.0
O A:ASP80 2.8 26.7 1.0
O A:HOH1152 2.9 12.5 1.0
O A:ALA78 2.9 18.1 1.0
CD2 A:TYR593 3.3 20.8 1.0
CE2 A:TYR593 3.3 23.9 1.0
C A:ALA78 3.5 17.2 1.0
CG A:TYR593 3.6 20.9 1.0
CZ A:TYR593 3.7 20.0 1.0
C A:ASP80 3.9 21.9 1.0
N A:ASP80 3.9 21.1 1.0
CD1 A:TYR593 4.0 18.5 1.0
C A:VAL83 4.0 28.8 1.0
O A:HOH1058 4.0 15.5 1.0
C A:ASP77 4.0 22.2 1.0
CE1 A:TYR593 4.0 19.6 1.0
N A:VAL79 4.1 15.8 1.0
N A:TYR85 4.1 21.4 1.0
C A:VAL79 4.2 22.4 1.0
CA A:ALA78 4.2 16.8 1.0
CA A:VAL79 4.3 17.6 1.0
CA A:ASP80 4.4 20.5 1.0
CB A:TYR593 4.4 19.3 1.0
OH A:TYR593 4.5 23.0 1.0
CG2 A:VAL83 4.5 22.8 1.0
C A:ASN84 4.6 22.0 1.0
CB A:ASP80 4.6 24.6 1.0
CB A:TYR85 4.6 19.8 1.0
N A:ALA78 4.6 19.3 1.0
CA A:TYR85 4.7 23.4 1.0
CA A:ASN84 4.7 22.4 1.0
N A:VAL83 4.7 22.3 1.0
N A:ASN84 4.8 26.1 1.0
CA A:VAL83 4.9 22.4 1.0
O A:VAL79 4.9 22.7 1.0
N A:PRO81 5.0 23.7 1.0

Potassium binding site 2 out of 4 in 6d1p

Go back to Potassium Binding Sites List in 6d1p
Potassium binding site 2 out of 4 in the Apo Structure of Bacteroides Uniformis Beta-Glucuronidase 3


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K909

b:21.4
occ:1.00
 O A:MET176 2.5 21.4 1.0
O A:PRO178 2.6 19.6 1.0
O A:HOH1024 2.6 22.9 1.0
O A:ASP173 2.7 25.1 1.0
O A:HOH1031 3.2 23.0 1.0
C A:PRO178 3.6 20.2 1.0
C A:MET176 3.6 22.0 1.0
C A:ASP173 3.7 24.9 1.0
OD2 A:ASP180 3.8 21.2 1.0
CA A:SER179 3.8 18.2 1.0
O A:HOH1248 3.9 24.8 1.0
N A:ASP180 3.9 18.9 1.0
CD2 A:LEU186 4.0 17.3 1.0
N A:SER179 4.1 22.7 1.0
C A:SER179 4.2 20.9 1.0
O B:HOH1161 4.3 16.4 1.0
N A:ASP173 4.3 22.9 1.0
CB A:MET176 4.3 22.5 1.0
CA A:MET176 4.3 24.4 1.0
CA A:THR174 4.4 25.4 1.0
N A:MET176 4.4 21.0 1.0
N A:THR174 4.5 24.3 1.0
CA A:ASP173 4.6 21.5 1.0
CG A:ASP180 4.6 20.1 1.0
CE A:MET176 4.6 16.9 1.0
N A:ILE177 4.6 21.2 1.0
CA A:ILE177 4.7 20.2 1.0
C A:THR174 4.7 22.5 1.0
C A:ILE177 4.8 22.4 1.0
CA A:PRO178 4.8 21.8 1.0
N A:PRO178 4.8 23.7 1.0
CA A:ASP180 5.0 17.1 1.0
O A:HOH1065 5.0 22.1 1.0
O A:THR174 5.0 23.1 1.0

Potassium binding site 3 out of 4 in 6d1p

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K906

b:23.5
occ:1.00
 O B:VAL83 2.8 20.8 1.0
O B:ASP77 2.8 20.8 1.0
O B:ASP80 2.8 24.6 1.0
O B:HOH1255 2.9 15.1 1.0
O B:ALA78 2.9 21.4 1.0
CD2 B:TYR593 3.3 23.7 1.0
CE2 B:TYR593 3.4 22.5 1.0
C B:ALA78 3.6 21.6 1.0
CG B:TYR593 3.6 21.9 1.0
CZ B:TYR593 3.7 23.6 1.0
O B:HOH1154 3.8 23.2 1.0
C B:ASP80 3.8 22.5 1.0
N B:ASP80 3.9 21.4 1.0
C B:ASP77 3.9 20.6 1.0
CD1 B:TYR593 4.0 21.0 1.0
C B:VAL83 4.0 26.3 1.0
CE1 B:TYR593 4.0 21.6 1.0
N B:TYR85 4.1 21.6 1.0
N B:VAL79 4.2 17.5 1.0
CA B:ALA78 4.2 18.9 1.0
C B:VAL79 4.3 23.1 1.0
CA B:ASP80 4.3 20.3 1.0
CB B:TYR593 4.4 22.1 1.0
CA B:VAL79 4.4 20.4 1.0
CG2 B:VAL83 4.5 22.7 1.0
OH B:TYR593 4.5 25.9 1.0
CB B:ASP80 4.5 24.0 1.0
N B:ALA78 4.6 23.4 1.0
C B:ASN84 4.7 23.3 1.0
CA B:ASN84 4.7 21.8 1.0
CB B:TYR85 4.7 23.6 1.0
N B:VAL83 4.7 23.9 1.0
CA B:TYR85 4.7 19.6 1.0
N B:ASN84 4.8 23.9 1.0
CA B:VAL83 4.9 26.4 1.0
N B:PRO81 4.9 25.0 1.0

Potassium binding site 4 out of 4 in 6d1p

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


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K907

b:27.8
occ:1.00
 O B:PRO178 2.5 27.4 1.0
O B:MET176 2.6 23.8 1.0
O B:ASP173 2.6 25.6 1.0
O B:HOH1178 2.9 21.9 1.0
O B:HOH1314 3.1 24.3 1.0
C B:PRO178 3.6 27.5 1.0
C B:ASP173 3.7 26.4 1.0
C B:MET176 3.7 27.4 1.0
CA B:SER179 3.9 26.7 1.0
OD2 B:ASP180 3.9 26.3 1.0
N B:ASP180 3.9 22.8 1.0
O B:HOH1223 3.9 29.1 1.0
O B:HOH1051 4.0 24.3 1.0
CD2 B:LEU186 4.1 20.7 1.0
N B:SER179 4.2 28.5 1.0
C B:SER179 4.2 27.6 1.0
N B:ASP173 4.4 25.1 1.0
CE B:MET176 4.4 21.9 1.0
CA B:MET176 4.4 25.6 1.0
CB B:MET176 4.5 25.1 1.0
N B:THR174 4.5 25.9 1.0
CA B:THR174 4.5 25.6 1.0
N B:MET176 4.5 26.4 1.0
CG B:ASP180 4.5 25.7 1.0
CA B:ASP173 4.6 25.4 1.0
N B:ILE177 4.6 25.9 1.0
C B:THR174 4.7 31.5 1.0
CA B:ILE177 4.7 25.7 1.0
O B:THR174 4.7 33.9 1.0
CA B:PRO178 4.8 26.1 1.0
N B:PRO178 4.8 26.9 1.0
C B:ILE177 4.8 25.6 1.0
O B:HOH1036 4.8 27.2 1.0
CA B:ASP180 5.0 26.2 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: Mon Aug 12 15:42:36 2024

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