Atomistry » Sodium » PDB 6d50-6dmi » 6d7j
Atomistry »
  Sodium »
    PDB 6d50-6dmi »
      6d7j »

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 Oct 8 07:41:38 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy