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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Fri Jul 28 02:47:33 2023

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