Atomistry » Sodium » PDB 7xu8-7z05 » 7xyr
Atomistry »
  Sodium »
    PDB 7xu8-7z05 »
      7xyr »

Sodium in PDB 7xyr: Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron

Enzymatic activity of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron

All present enzymatic activity of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron:
3.2.1.31;

Protein crystallography data

The structure of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron, PDB code: 7xyr was solved by X.Teng, C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.89 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 101.582, 122.249, 105.122, 90, 90, 90
R / Rfree (%) 19 / 23.2

Other elements in 7xyr:

The structure of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Magnesium (Mg) 22 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron (pdb code 7xyr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron, PDB code: 7xyr:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 1 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na622

b:28.7
occ:1.00
 O A:VAL433 3.0 15.9 1.0
O A:ASP451 3.0 19.6 1.0
CZ A:PHE449 3.3 15.9 1.0
CE2 A:PHE449 3.6 16.9 1.0
CB A:LEU436 3.7 17.4 1.0
CA A:VAL433 3.7 17.4 1.0
CD1 A:LEU417 3.7 15.8 1.0
CA A:ASP451 3.7 19.2 1.0
C A:VAL433 3.7 17.6 1.0
C A:ASP451 3.8 18.1 1.0
CG1 A:VAL433 3.8 19.3 1.0
CG A:PRO416 3.9 16.2 1.0
CB A:ASP451 4.0 19.8 1.0
N A:GLN437 4.2 17.9 1.0
CG A:LEU417 4.3 15.8 1.0
CB A:VAL433 4.3 17.7 1.0
CD1 A:LEU436 4.3 18.1 1.0
CE1 A:PHE449 4.5 16.3 1.0
O A:LEU432 4.5 15.2 1.0
C A:LEU436 4.5 17.7 1.0
CD A:PRO416 4.6 15.0 1.0
CA A:LEU436 4.6 17.2 1.0
CG A:LEU436 4.6 17.1 1.0
CB A:LEU417 4.7 15.4 1.0
CG2 A:VAL433 4.8 18.2 1.0
N A:VAL433 4.8 17.3 1.0
CA A:GLN437 4.9 17.3 1.0
CB A:GLN437 4.9 18.7 1.0
O A:ASN450 4.9 17.6 1.0
N A:LEU436 4.9 17.5 1.0
CD2 A:PHE449 5.0 16.9 1.0
N A:ASP451 5.0 18.0 1.0

Sodium binding site 2 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 2 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na623

b:21.9
occ:1.00
 O A:HOH806 2.7 17.4 1.0
O A:GLN356 2.7 15.6 1.0
N A:LYS170 2.9 16.7 1.0
NE1 A:TRP329 3.2 16.7 1.0
CZ2 A:TRP329 3.5 16.1 1.0
CB A:LYS170 3.6 17.3 1.0
CE2 A:TRP329 3.7 15.1 1.0
CE1 A:TYR323 3.7 16.5 1.0
C A:GLN356 3.8 15.3 1.0
CA A:GLY169 3.8 15.4 1.0
C A:GLY169 3.8 14.9 1.0
CA A:LYS170 3.8 17.0 1.0
CG A:LYS170 3.9 17.9 1.0
CB A:LYS357 4.2 15.4 1.0
OH A:TYR323 4.3 14.6 1.0
CB A:GLN356 4.3 15.5 1.0
CD1 A:TRP329 4.4 16.1 1.0
O A:CYS168 4.4 16.9 1.0
CZ A:TYR323 4.5 15.5 1.0
C A:LYS170 4.5 17.5 1.0
N A:GLN171 4.6 16.5 1.0
N A:LYS357 4.6 15.0 1.0
CG A:LYS357 4.6 14.9 1.0
CA A:GLN356 4.6 15.8 1.0
CD1 A:TYR323 4.6 15.7 1.0
CA A:LYS357 4.6 14.9 1.0
O A:GLN321 4.6 18.8 1.0
CH2 A:TRP329 4.8 15.6 1.0
O A:HIS355 4.8 14.9 1.0
N A:GLY169 4.9 14.1 1.0
O A:GLY169 5.0 15.3 1.0

Sodium binding site 3 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 3 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na624

b:25.3
occ:1.00
 NA A:NA629 2.7 26.3 1.0
OE1 A:GLU377 2.7 16.1 1.0
N A:GLN356 2.8 16.8 1.0
NE2 A:GLN356 3.1 13.3 1.0
ND1 A:HIS355 3.2 17.2 1.0
O A:SER378 3.3 15.0 1.0
OG1 A:THR418 3.4 18.5 1.0
CB A:GLU377 3.4 15.6 1.0
CA A:GLN356 3.4 15.8 1.0
CE1 A:HIS355 3.5 17.5 1.0
CG A:GLN356 3.6 15.1 1.0
CD A:GLN356 3.6 15.4 1.0
NA A:NA630 3.6 28.5 1.0
CD A:GLU377 3.8 17.3 1.0
C A:HIS355 3.8 15.5 1.0
CA A:HIS355 3.8 15.6 1.0
CG A:HIS355 3.9 16.3 1.0
CB A:GLN356 4.1 15.5 1.0
N A:SER378 4.1 13.9 1.0
CG A:GLU377 4.1 15.9 1.0
NE2 A:HIS355 4.4 17.3 1.0
C A:SER378 4.4 14.5 1.0
CB A:HIS355 4.4 16.2 1.0
CD2 A:HIS355 4.5 16.4 1.0
CB A:THR418 4.6 17.9 1.0
OE1 A:GLN356 4.6 14.5 1.0
CA A:GLU377 4.6 14.6 1.0
O A:LEU354 4.6 15.1 1.0
OD1 A:ASN380 4.7 14.2 1.0
C A:GLN356 4.7 15.3 1.0
C A:GLU377 4.8 14.0 1.0
OE2 A:GLU377 4.9 18.0 1.0
O A:ALA415 4.9 14.4 1.0
CA A:SER378 4.9 13.1 1.0
O A:HIS355 4.9 14.9 1.0
N A:LYS357 5.0 15.0 1.0
NH2 A:ARG353 5.0 18.8 1.0

Sodium binding site 4 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 4 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na625

b:28.8
occ:1.00
 MG A:MG621 2.7 34.0 1.0
O A:HOH1007 2.7 21.0 1.0
O A:HOH740 2.8 21.9 1.0
NH2 A:ARG23 3.3 23.7 1.0
OG1 A:THR191 3.5 15.3 1.0
CD A:ARG362 3.8 19.1 1.0
MG A:MG601 3.8 38.1 1.0
OE2 A:GLU360 4.0 24.9 1.0
CB A:PRO27 4.1 21.2 1.0
CA A:PRO27 4.1 20.3 1.0
CZ A:ARG23 4.1 22.4 1.0
CG A:ARG362 4.2 18.4 1.0
CB A:THR191 4.2 15.2 1.0
NE A:ARG23 4.6 21.9 1.0
O A:GLU25 4.6 17.0 1.0
O A:HOH786 4.7 25.1 1.0
CB A:ARG362 4.8 17.4 1.0
O A:HOH868 4.8 27.5 1.0
N A:PRO27 4.9 20.5 1.0
O A:PRO27 4.9 18.5 1.0
NH1 A:ARG23 5.0 21.0 1.0

Sodium binding site 5 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 5 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na626

b:25.5
occ:1.00
 O A:HOH1085 2.6 25.5 1.0
O A:PHE137 2.8 15.4 1.0
ND1 A:HIS110 2.9 18.0 1.0
O A:HOH1043 3.1 17.4 1.0
O A:HOH1044 3.3 29.3 1.0
C A:PHE137 3.4 16.8 1.0
CB A:HIS110 3.6 16.4 1.0
CG A:HIS110 3.7 17.2 1.0
N A:PHE137 3.8 14.4 1.0
O A:PHE111 3.8 16.7 1.0
CB A:PRO136 3.9 14.2 1.0
CA A:HIS110 3.9 15.6 1.0
CE1 A:HIS110 4.0 18.1 1.0
N A:PHE111 4.0 16.6 1.0
CB A:VAL138 4.1 20.3 1.0
CA A:PHE137 4.1 14.7 1.0
N A:VAL138 4.2 16.9 1.0
CA A:VAL138 4.3 18.3 1.0
O A:HOH810 4.4 35.4 1.0
C A:HIS110 4.4 16.1 1.0
C A:PRO136 4.4 14.7 1.0
C A:PHE111 4.5 16.4 1.0
CA A:PRO136 4.6 13.9 1.0
O A:HOH1012 4.6 31.3 1.0
O A:HOH1132 4.8 22.5 1.0
O A:HOH753 4.8 24.4 1.0
CG2 A:VAL138 4.9 21.1 1.0
CD2 A:HIS110 4.9 17.3 1.0
CA A:PHE111 4.9 15.5 1.0
CG A:PRO136 5.0 13.5 1.0

Sodium binding site 6 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 6 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na627

b:22.4
occ:1.00
 O A:VAL114 2.9 14.2 1.0
ND1 A:HIS130 2.9 15.2 1.0
O A:TYR116 2.9 18.2 1.0
O A:GLY132 3.0 15.5 1.0
O A:HIS130 3.0 19.0 1.0
MG A:MG606 3.4 25.7 1.0
C A:HIS130 3.7 20.7 1.0
C A:TYR116 3.7 18.2 1.0
CG A:HIS130 3.7 16.0 1.0
CB A:HIS130 3.7 17.6 1.0
N A:ALA118 3.7 20.9 1.0
CB A:ALA118 3.8 18.8 1.0
C A:GLY132 3.9 15.1 1.0
CE1 A:PHE137 3.9 14.1 1.0
CE1 A:HIS130 3.9 16.3 1.0
C A:VAL114 4.0 14.8 1.0
N A:GLY132 4.1 17.4 1.0
CB A:VAL114 4.1 15.7 1.0
CA A:LEU117 4.2 21.6 1.0
CA A:HIS130 4.3 19.8 1.0
N A:LEU117 4.3 19.1 1.0
C A:LEU117 4.3 23.1 1.0
CA A:ALA118 4.4 19.8 1.0
N A:ASN131 4.4 20.0 1.0
CA A:VAL114 4.5 15.0 1.0
C A:ASN131 4.5 19.4 1.0
CD1 A:PHE137 4.5 14.6 1.0
N A:VAL114 4.5 15.2 1.0
CZ A:PHE137 4.5 15.7 1.0
CA A:GLY132 4.6 16.7 1.0
CA A:GLY133 4.7 14.0 1.0
N A:GLY133 4.7 15.0 1.0
CA A:ASN131 4.7 21.4 1.0
CA A:TYR116 4.7 16.6 1.0
CG1 A:VAL114 4.8 17.6 1.0
CD2 A:HIS130 4.9 16.6 1.0

Sodium binding site 7 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 7 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na628

b:26.5
occ:1.00
 O A:GLU377 2.7 14.5 1.0
O A:HOH858 2.9 16.9 1.0
N A:GLU377 3.2 14.7 1.0
C A:GLY376 3.2 15.0 1.0
CZ3 A:TRP398 3.4 17.0 1.0
CA A:GLY376 3.4 14.4 1.0
CZ3 A:TRP414 3.6 15.7 1.0
C A:GLU377 3.7 14.0 1.0
CH2 A:TRP398 3.8 18.1 1.0
O A:GLY376 3.8 16.8 1.0
CG2 A:ILE401 3.8 16.0 1.0
CD1 A:PHE358 3.9 14.2 1.0
CE3 A:TRP414 3.9 15.9 1.0
CE1 A:PHE358 3.9 15.1 1.0
CA A:GLU377 4.0 14.6 1.0
O A:HOH765 4.1 15.1 1.0
O A:HOH921 4.3 19.3 1.0
CE3 A:TRP398 4.3 16.1 1.0
CH2 A:TRP414 4.8 16.1 1.0
N A:GLY376 4.9 15.3 1.0
N A:SER378 4.9 13.9 1.0
CB A:ILE401 4.9 15.0 1.0
CZ2 A:TRP398 5.0 18.5 1.0

Sodium binding site 8 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 8 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na629

b:26.3
occ:1.00
 NA A:NA624 2.7 25.3 1.0
OD1 A:ASN380 2.9 14.2 1.0
O A:SER378 2.9 15.0 1.0
NA A:NA630 3.1 28.5 1.0
O A:PRO416 3.2 17.1 1.0
N A:SER378 3.3 13.9 1.0
C A:PRO416 3.3 15.6 1.0
NE2 A:GLN356 3.4 13.3 1.0
N A:THR418 3.5 16.5 1.0
N A:LEU417 3.5 14.7 1.0
OG1 A:THR418 3.5 18.5 1.0
O A:ALA415 3.6 14.4 1.0
CA A:LEU417 3.7 15.6 1.0
C A:LEU417 3.7 16.6 1.0
OG A:SER378 3.7 13.5 1.0
C A:SER378 3.8 14.5 1.0
CB A:GLU377 3.8 15.6 1.0
CA A:SER378 4.0 13.1 1.0
CG A:ASN380 4.0 15.2 1.0
CA A:PRO416 4.2 15.1 1.0
OE1 A:GLU377 4.2 16.1 1.0
C A:GLU377 4.3 14.0 1.0
CB A:THR418 4.3 17.9 1.0
CB A:SER378 4.4 13.3 1.0
CA A:GLU377 4.4 14.6 1.0
CD A:GLN356 4.5 15.4 1.0
CA A:THR418 4.5 18.0 1.0
O A:LEU417 4.6 16.3 1.0
C A:ALA415 4.6 14.5 1.0
N A:ASN380 4.7 14.2 1.0
CB A:ASN380 4.7 15.7 1.0
N A:PRO416 4.9 14.6 1.0
CG A:GLU377 4.9 15.9 1.0
CD A:GLU377 5.0 17.3 1.0

Sodium binding site 9 out of 9 in 7xyr

Go back to Sodium Binding Sites List in 7xyr
Sodium binding site 9 out of 9 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na630

b:28.5
occ:1.00
 OG1 A:THR453 2.7 17.3 1.0
O A:ALA415 2.8 14.4 1.0
OE1 A:GLU377 3.0 16.1 1.0
OG1 A:THR418 3.1 18.5 1.0
NA A:NA629 3.1 26.3 1.0
O A:LEU417 3.4 16.3 1.0
C A:LEU417 3.4 16.6 1.0
MG A:MG613 3.5 25.9 1.0
CG2 A:THR453 3.5 19.2 1.0
CD A:GLU377 3.6 17.3 1.0
NA A:NA624 3.6 25.3 1.0
N A:THR418 3.7 16.5 1.0
CB A:THR453 3.7 19.6 1.0
C A:ALA415 3.7 14.5 1.0
NH2 A:ARG353 3.8 18.8 1.0
N A:LEU417 3.8 14.7 1.0
CB A:ALA415 4.0 15.7 1.0
CB A:GLU377 4.0 15.6 1.0
CG A:GLU377 4.1 15.9 1.0
CA A:THR418 4.1 18.0 1.0
CA A:LEU417 4.1 15.6 1.0
CB A:THR418 4.2 17.9 1.0
OE2 A:GLU377 4.4 18.0 1.0
C A:PRO416 4.4 15.6 1.0
CA A:ALA415 4.5 15.4 1.0
N A:PRO416 4.6 14.6 1.0
N A:THR453 4.7 18.4 1.0
CA A:THR453 4.8 19.2 1.0
CA A:PRO416 4.9 15.1 1.0
ND1 A:HIS355 4.9 17.2 1.0
CE1 A:HIS355 4.9 17.5 1.0
CZ A:ARG353 5.0 18.4 1.0

Reference:

X.Teng, C.Wang. Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron To Be Published.
Page generated: Mon Aug 18 12:38:14 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy