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Sodium in PDB 6d7j: The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site

Protein crystallography data

The structure of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site, PDB code: 6d7j 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) 48.34 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.920, 171.968, 125.322, 90.00, 107.84, 90.00
R / Rfree (%) 16.5 / 20

Other elements in 6d7j:

The structure of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site also contains other interesting chemical elements:

Potassium (K) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site (pdb code 6d7j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site, PDB code: 6d7j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6d7j

Go back to Sodium Binding Sites List in 6d7j
Sodium binding site 1 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na915

b:16.7
occ:1.00
 O A:HOH1113 2.4 15.5 1.0
O A:MET176 2.4 20.8 1.0
O A:ASP173 2.4 16.2 1.0
O A:PRO178 2.5 16.6 1.0
O A:HOH1271 2.5 17.2 1.0
C A:ASP173 3.4 18.8 1.0
C A:PRO178 3.5 18.4 1.0
C A:MET176 3.5 20.7 1.0
O A:HOH1231 3.7 16.6 0.7
CA A:SER179 3.8 16.5 1.0
OD2 A:ASP180 4.0 20.6 1.0
N A:SER179 4.1 18.1 1.0
N A:ASP173 4.1 18.2 1.0
O A:HOH1059 4.2 15.0 1.0
N A:ASP180 4.2 18.0 1.0
CA A:MET176 4.3 20.0 1.0
N A:MET176 4.3 18.2 1.0
N A:LEU174 4.3 20.6 1.0
CA A:ASP173 4.3 17.4 1.0
C A:SER179 4.3 21.1 1.0
CB A:MET176 4.3 21.5 1.0
CA A:LEU174 4.3 21.9 1.0
N A:ILE177 4.5 19.9 1.0
O A:HOH1051 4.6 20.4 0.9
CE A:MET176 4.6 17.2 1.0
C A:LEU174 4.6 20.7 1.0
CA A:ILE177 4.7 20.7 1.0
CD1 A:ILE186 4.7 18.6 1.0
CB A:ASP173 4.7 16.6 1.0
CA A:PRO178 4.7 14.2 1.0
N A:PRO178 4.8 18.5 1.0
C A:ILE177 4.9 17.6 1.0
CG A:ASP180 4.9 19.8 1.0
O A:LEU174 4.9 20.1 1.0
CB A:SER179 5.0 18.0 1.0

Sodium binding site 2 out of 4 in 6d7j

Go back to Sodium Binding Sites List in 6d7j
Sodium binding site 2 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na918

b:16.1
occ:1.00
 O B:HOH1057 2.3 17.8 1.0
O B:HOH1248 2.4 15.1 1.0
O B:PRO178 2.4 19.9 1.0
O B:MET176 2.5 19.9 1.0
O B:ASP173 2.5 18.8 1.0
C B:PRO178 3.5 19.7 1.0
C B:ASP173 3.5 16.6 1.0
C B:MET176 3.6 17.9 1.0
CA B:SER179 3.7 17.6 1.0
O B:HOH1242 3.8 18.1 1.0
N B:ASP180 4.0 17.2 1.0
OD2 B:ASP180 4.0 20.6 1.0
N B:SER179 4.0 18.1 1.0
O A:HOH1168 4.1 16.1 0.9
N B:ASP173 4.1 18.3 1.0
C B:SER179 4.2 17.4 1.0
CA B:ASP173 4.4 17.9 1.0
CA B:LEU174 4.4 17.8 1.0
N B:LEU174 4.4 14.5 1.0
CA B:MET176 4.4 15.7 1.0
N B:MET176 4.4 17.2 1.0
CB B:MET176 4.5 17.0 1.0
CD1 B:ILE186 4.5 18.6 1.0
N B:ILE177 4.6 18.8 1.0
O B:HOH1053 4.6 19.8 0.9
CE B:MET176 4.6 18.2 1.0
C B:LEU174 4.7 20.6 1.0
CA B:ILE177 4.7 18.6 1.0
CA B:PRO178 4.8 18.2 1.0
O B:HOH1264 4.8 15.9 0.8
CG B:ASP180 4.8 20.8 1.0
CB B:ASP173 4.8 17.1 1.0
C B:ILE177 4.8 17.9 1.0
N B:PRO178 4.9 16.7 1.0
CB B:SER179 4.9 16.3 1.0
O B:LEU174 4.9 21.6 1.0

Sodium binding site 3 out of 4 in 6d7j

Go back to Sodium Binding Sites List in 6d7j
Sodium binding site 3 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na919

b:14.6
occ:1.00
 O C:HOH1099 2.2 16.2 1.0
O C:MET176 2.4 20.5 1.0
O C:PRO178 2.5 19.4 1.0
O C:ASP173 2.5 17.8 1.0
O C:HOH1267 2.5 18.5 1.0
C C:ASP173 3.5 19.2 1.0
C C:PRO178 3.5 22.0 1.0
C C:MET176 3.6 20.5 1.0
CA C:SER179 3.8 17.7 1.0
O C:HOH1290 3.8 17.9 0.9
OD2 C:ASP180 3.9 21.0 1.0
N C:ASP180 4.0 16.9 1.0
N C:SER179 4.1 19.0 1.0
N C:ASP173 4.1 21.5 1.0
C C:SER179 4.2 20.5 1.0
CA C:ASP173 4.3 20.2 1.0
N C:LEU174 4.3 22.1 1.0
CA C:MET176 4.4 19.6 1.0
N C:MET176 4.4 18.5 1.0
CA C:LEU174 4.4 20.0 1.0
CB C:MET176 4.5 21.0 1.0
O C:HOH1021 4.5 22.1 0.8
O D:HOH1022 4.5 19.0 0.9
N C:ILE177 4.6 19.7 1.0
CD1 C:ILE186 4.6 17.9 1.0
CA C:ILE177 4.7 20.3 1.0
CE C:MET176 4.7 16.8 1.0
CG C:ASP180 4.7 21.5 1.0
CA C:PRO178 4.7 23.7 1.0
C C:LEU174 4.8 20.5 1.0
CB C:ASP173 4.8 19.6 1.0
N C:PRO178 4.9 19.3 1.0
C C:ILE177 4.9 23.8 1.0
O C:HOH1186 4.9 13.7 0.9
CB C:SER179 5.0 17.4 1.0

Sodium binding site 4 out of 4 in 6d7j

Go back to Sodium Binding Sites List in 6d7j
Sodium binding site 4 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na911

b:18.9
occ:1.00
 O D:HOH1050 2.2 26.1 1.0
O D:MET176 2.4 21.8 1.0
O D:PRO178 2.4 20.5 1.0
O D:ASP173 2.5 18.2 1.0
O D:HOH1229 2.7 22.6 1.0
C D:MET176 3.5 21.7 1.0
C D:ASP173 3.5 22.2 1.0
C D:PRO178 3.5 19.5 1.0
O D:HOH1064 3.6 20.0 0.8
CA D:SER179 3.8 20.9 1.0
O D:HOH1118 4.1 20.0 1.0
OD2 D:ASP180 4.1 26.6 1.0
N D:SER179 4.1 22.6 1.0
N D:ASP180 4.1 20.8 1.0
N D:ASP173 4.2 18.9 1.0
CA D:MET176 4.2 22.2 1.0
N D:MET176 4.3 22.4 1.0
C D:SER179 4.3 23.8 1.0
CB D:MET176 4.3 22.7 1.0
N D:LEU174 4.3 22.3 1.0
CA D:ASP173 4.4 19.4 1.0
CA D:LEU174 4.4 22.2 1.0
N D:ILE177 4.4 23.3 1.0
O D:HOH1083 4.5 25.9 0.9
CA D:ILE177 4.6 23.5 1.0
CD1 D:ILE186 4.6 25.1 1.0
CE D:MET176 4.6 24.2 1.0
C D:LEU174 4.7 22.9 1.0
CA D:PRO178 4.7 20.7 1.0
C D:ILE177 4.7 22.2 1.0
N D:PRO178 4.8 23.7 1.0
CB D:ASP173 4.8 21.7 1.0
O D:HOH1191 4.9 20.7 0.8
CG D:ASP180 4.9 25.8 1.0
O D:LEU174 4.9 22.1 1.0

Reference:

M.S.Little, M.R.Redinbo. Structural Basis For Parabacteroides Merdae Beta-Glucuronidase (Gus) Glycosaminoglycan Metabolism and Recognition of Alginate To Be Published.
Page generated: Tue Dec 15 12:07:36 2020

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