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Magnesium 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:

Sodium (Na) 9 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 22 binding sites of Magnesium where determined in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron, PDB code: 7xyr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 22 in 7xyr

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Magnesium binding site 1 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg601

b:38.1
occ:1.00
 OE1 A:GLU25 2.7 26.9 1.0
NE A:ARG23 2.8 21.9 1.0
NH2 A:ARG23 3.2 23.7 1.0
OD1 A:ASP334 3.4 21.3 1.0
CZ A:ARG23 3.5 22.4 1.0
CD A:GLU25 3.6 26.3 1.0
MG A:MG621 3.6 34.0 1.0
CD A:ARG362 3.6 19.1 1.0
CB A:ASP334 3.6 21.4 1.0
CB A:GLU25 3.7 22.4 1.0
CG A:ASP334 3.8 22.0 1.0
NA A:NA625 3.8 28.8 1.0
NE A:ARG362 3.8 20.7 1.0
CD A:ARG23 3.9 19.8 1.0
CA A:ASP334 4.0 21.1 1.0
CG A:GLU25 4.1 23.4 1.0
CB A:ARG23 4.1 19.8 1.0
CA A:ARG23 4.1 20.5 1.0
N A:ASP334 4.1 20.4 1.0
O A:HOH888 4.1 27.3 1.0
N A:GLU25 4.3 19.3 1.0
C A:ARG23 4.4 22.3 1.0
OE2 A:GLU25 4.5 24.7 1.0
CA A:GLU25 4.5 19.9 1.0
CG A:ARG23 4.6 20.3 1.0
O A:ARG23 4.6 21.1 1.0
OD2 A:ASP334 4.7 21.3 1.0
NH1 A:ARG23 4.8 21.0 1.0
CG A:ARG362 4.9 18.4 1.0
CZ A:ARG362 4.9 22.9 1.0
O A:GLU25 4.9 17.0 1.0
C A:THR333 4.9 19.3 1.0

Magnesium binding site 2 out of 22 in 7xyr

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Magnesium binding site 2 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg602

b:32.5
occ:1.00
 OH A:TYR26 2.5 23.9 1.0
OE1 A:GLU195 2.8 20.6 1.0
CB A:GLU195 3.3 20.6 1.0
CZ A:TYR26 3.4 22.8 1.0
CB A:ARG33 3.4 33.6 1.0
CE1 A:TYR26 3.4 22.7 1.0
CB A:TRP36 3.6 24.1 1.0
CD A:GLU195 3.6 21.8 1.0
CZ3 A:TRP193 3.6 20.2 1.0
O A:ARG33 3.7 43.5 1.0
CG A:GLU195 4.0 21.2 1.0
N A:ARG33 4.0 24.7 1.0
C A:ARG33 4.0 35.3 1.0
CA A:ARG33 4.1 30.1 1.0
O A:THR35 4.2 27.7 1.0
CG A:ARG33 4.3 30.3 1.0
CG A:TRP36 4.3 23.5 1.0
NH1 A:ARG28 4.4 28.8 1.0
C A:THR35 4.4 27.4 1.0
CH2 A:TRP193 4.5 19.4 1.0
CE3 A:TRP193 4.5 19.1 1.0
CA A:TRP36 4.5 24.7 1.0
OE2 A:GLU195 4.5 19.3 1.0
CD A:ARG33 4.6 28.3 1.0
N A:TRP36 4.6 25.5 1.0
CA A:GLU195 4.6 20.2 1.0
CE2 A:TYR26 4.7 22.7 1.0
CD1 A:TRP36 4.8 23.3 1.0
CD1 A:TYR26 4.8 23.4 1.0
N A:THR35 4.8 26.0 1.0
N A:THR34 4.9 32.5 1.0

Magnesium binding site 3 out of 22 in 7xyr

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Magnesium binding site 3 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg603

b:31.4
occ:1.00
 O A:ASN152 2.6 21.7 1.0
O A:PRO59 2.9 30.9 1.0
N A:GLY124 2.9 27.7 1.0
N A:ASP123 3.2 25.7 1.0
O A:TYR121 3.4 19.2 1.0
C A:TYR121 3.4 21.4 1.0
C A:ILE122 3.5 26.2 1.0
CB A:TYR121 3.6 23.3 1.0
C A:ASN152 3.6 22.8 1.0
CA A:ILE122 3.6 23.0 1.0
N A:ILE122 3.6 22.0 1.0
CA A:GLY124 3.7 24.5 1.0
N A:VAL154 3.8 21.0 1.0
C A:ASP123 3.9 28.5 1.0
CB A:VAL154 3.9 22.1 1.0
CA A:ASP123 3.9 26.8 1.0
CG2 A:VAL154 3.9 22.8 1.0
ND2 A:ASN152 4.0 24.2 1.0
C A:PRO59 4.1 30.4 1.0
CA A:TYR121 4.1 22.4 1.0
CB A:ASN152 4.2 26.6 1.0
C A:LEU153 4.3 20.2 1.0
O A:ILE122 4.3 24.9 1.0
N A:LEU153 4.3 21.6 1.0
CA A:LEU153 4.4 20.6 1.0
CG A:ASN152 4.4 26.1 1.0
CA A:VAL154 4.4 21.3 1.0
CA A:ASN152 4.5 27.1 1.0
C A:GLY124 4.6 23.8 1.0
CA A:PRO59 4.6 26.6 1.0
N A:ARG125 4.8 23.3 1.0
CG A:TYR121 4.9 22.9 1.0

Magnesium binding site 4 out of 22 in 7xyr

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Magnesium binding site 4 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg604

b:28.8
occ:1.00
 O A:GLY327 2.6 19.1 1.0
OG1 A:THR330 2.7 13.1 1.0
N A:CYS73 2.8 15.9 1.0
SG A:CYS73 3.3 15.7 1.0
CB A:THR330 3.3 14.5 1.0
CB A:CYS73 3.5 15.4 1.0
CA A:PHE72 3.6 16.7 1.0
C A:PHE72 3.7 16.2 1.0
CA A:CYS73 3.7 16.3 1.0
C A:GLY327 3.8 16.8 1.0
N A:THR330 3.9 15.5 1.0
O A:PRO71 4.0 18.5 1.0
CB A:TRP189 4.0 15.3 1.0
CA A:THR330 4.2 15.1 1.0
CB A:PHE72 4.3 16.2 1.0
CD1 A:PHE72 4.4 16.1 1.0
CG2 A:THR330 4.4 13.3 1.0
N A:TRP329 4.4 14.9 1.0
CA A:TRP189 4.5 15.0 1.0
CB A:SER76 4.5 19.3 1.0
CA A:GLY327 4.5 17.5 1.0
OG A:SER76 4.6 19.6 1.0
CG1 A:VAL185 4.6 16.7 1.0
O A:CYS73 4.7 16.9 1.0
N A:PHE72 4.7 16.5 1.0
C A:CYS73 4.7 16.4 1.0
CB A:ILE328 4.7 16.8 1.0
C A:PRO71 4.8 18.3 1.0
C A:TRP329 4.8 15.4 1.0
N A:ILE328 4.8 16.1 1.0
O A:TRP189 4.9 14.5 1.0
CG A:PHE72 4.9 15.9 1.0
O A:PHE72 4.9 16.1 1.0

Magnesium binding site 5 out of 22 in 7xyr

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Magnesium binding site 5 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg605

b:31.4
occ:1.00
 OH A:TYR92 2.5 16.5 1.0
O A:ILE188 2.7 15.3 1.0
O A:PHE72 2.9 16.1 1.0
CE2 A:TYR92 3.2 19.2 1.0
CZ A:TYR92 3.2 18.6 1.0
C A:PHE72 3.5 16.2 1.0
C A:ILE188 3.7 15.0 1.0
CB A:ILE188 3.7 14.2 1.0
CD1 A:ILE68 3.8 20.5 1.0
N A:ILE188 3.8 14.4 1.0
CA A:ILE188 4.0 14.7 1.0
CG2 A:VAL70 4.0 20.6 1.0
CA A:CYS73 4.0 16.3 1.0
N A:CYS73 4.0 15.9 1.0
N A:PHE72 4.1 16.5 1.0
CG1 A:ILE68 4.3 21.9 1.0
CA A:VAL70 4.4 19.8 1.0
C A:PRO71 4.4 18.3 1.0
CA A:PHE72 4.4 16.7 1.0
CD2 A:TYR92 4.5 18.6 1.0
CG2 A:ILE188 4.5 13.8 1.0
CD A:PRO74 4.5 17.0 1.0
CE1 A:TYR92 4.5 19.7 1.0
C A:CYS73 4.6 16.4 1.0
O A:THR69 4.7 19.4 1.0
CG1 A:ILE188 4.7 14.6 1.0
CA A:PRO71 4.7 17.9 1.0
CB A:VAL70 4.8 19.5 1.0
N A:PRO74 4.8 17.0 1.0
C A:GLY187 4.9 14.8 1.0
O A:PRO71 4.9 18.5 1.0
N A:TRP189 4.9 14.9 1.0
N A:VAL70 4.9 20.8 1.0
CG2 A:ILE68 5.0 25.5 1.0
O A:THR186 5.0 16.4 1.0

Magnesium binding site 6 out of 22 in 7xyr

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Magnesium binding site 6 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg606

b:25.7
occ:1.00
 O A:SER135 2.6 12.7 1.0
O A:GLY132 2.6 15.5 1.0
N A:VAL114 3.0 15.2 1.0
O A:VAL114 3.3 14.2 1.0
CA A:ALA113 3.4 13.3 1.0
NA A:NA627 3.4 22.4 1.0
N A:SER135 3.5 13.8 1.0
ND1 A:HIS130 3.5 15.2 1.0
CE1 A:HIS130 3.5 16.3 1.0
C A:GLY133 3.6 14.6 1.0
C A:SER135 3.6 14.1 1.0
C A:ALA113 3.7 13.6 1.0
C A:GLY132 3.7 15.1 1.0
N A:SER134 3.8 13.5 1.0
O A:GLY133 3.9 15.2 1.0
C A:VAL114 3.9 14.8 1.0
CA A:GLY133 3.9 14.0 1.0
CE1 A:PHE137 4.0 14.1 1.0
CA A:VAL114 4.0 15.0 1.0
CB A:ALA113 4.1 13.2 1.0
CD1 A:PHE137 4.1 14.6 1.0
CA A:SER135 4.1 14.2 1.0
N A:GLY133 4.3 15.0 1.0
C A:SER134 4.3 14.4 1.0
OG A:SER135 4.4 15.4 1.0
CB A:VAL114 4.5 15.7 1.0
CA A:SER134 4.5 14.0 1.0
N A:ALA113 4.5 13.2 1.0
CG A:HIS130 4.7 16.0 1.0
NE2 A:HIS130 4.7 15.7 1.0
O A:GLY112 4.8 13.0 1.0
N A:PRO136 4.8 13.4 1.0
O A:ALA113 4.9 12.4 1.0
CB A:SER135 4.9 15.3 1.0
CA A:GLY132 4.9 16.7 1.0

Magnesium binding site 7 out of 22 in 7xyr

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Magnesium binding site 7 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg607

b:30.4
occ:1.00
 OG1 A:THR549 2.9 17.2 1.0
O A:CYS547 3.0 21.9 1.0
O A:GLY497 3.2 24.0 1.0
SG A:CYS547 3.4 20.2 1.0
CE A:MET319 3.5 17.5 1.0
C A:CYS547 3.5 21.3 1.0
CB A:MET319 3.5 17.3 1.0
N A:THR549 3.6 17.1 1.0
C A:TYR548 3.6 17.0 1.0
CA A:GLU498 3.7 24.7 1.0
CB A:CYS547 3.7 21.0 1.0
O A:TYR548 3.8 17.1 1.0
CA A:THR549 3.9 17.6 1.0
CB A:THR549 4.0 17.0 1.0
CG A:GLU498 4.1 28.2 1.0
N A:TYR548 4.1 20.9 1.0
C A:GLY497 4.1 22.0 1.0
CB A:GLU498 4.2 26.4 1.0
CA A:CYS547 4.3 20.3 1.0
CA A:TYR548 4.3 19.3 1.0
N A:GLU498 4.3 22.5 1.0
CG A:MET319 4.4 16.4 1.0
SD A:MET319 4.4 17.1 1.0
N A:MET319 4.4 18.4 1.0
CA A:MET319 4.4 18.0 1.0
N A:PHE499 4.5 22.7 1.0
NH1 A:ARG353 4.6 18.7 1.0
C A:GLU498 4.6 23.2 1.0
OH A:TYR469 4.7 24.6 1.0
CG2 A:THR549 4.9 16.5 1.0
CD A:ARG353 5.0 18.3 1.0
O A:PHE499 5.0 24.9 1.0

Magnesium binding site 8 out of 22 in 7xyr

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Magnesium binding site 8 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg608

b:42.4
occ:1.00
 OE1 A:GLU498 2.6 29.6 1.0
NH2 A:ARG353 2.9 18.8 1.0
NH1 A:ARG353 3.1 18.7 1.0
OG1 A:THR453 3.2 17.3 1.0
CZ A:ARG353 3.4 18.4 1.0
CD A:GLU498 3.4 32.2 1.0
CE1 A:HIS355 3.4 17.5 1.0
CB A:THR453 3.5 19.6 1.0
N A:GLY454 3.5 19.6 1.0
O A:HOH714 3.6 22.1 1.0
CA A:GLY454 3.6 24.1 1.0
CG2 A:THR418 3.8 19.0 1.0
CG A:GLU498 3.8 28.2 1.0
C A:THR453 3.9 20.5 1.0
OG1 A:THR418 4.0 18.5 1.0
NE2 A:HIS355 4.1 17.3 1.0
ND1 A:HIS355 4.3 17.2 1.0
CA A:THR453 4.3 19.2 1.0
OE2 A:GLU498 4.4 33.2 1.0
O A:THR453 4.5 17.0 1.0
CB A:THR418 4.5 17.9 1.0
CG2 A:THR453 4.6 19.2 1.0
NE A:ARG353 4.7 17.4 1.0
CE A:MET319 4.7 17.5 1.0
O A:HOH845 5.0 22.5 1.0

Magnesium binding site 9 out of 22 in 7xyr

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Magnesium binding site 9 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg609

b:23.9
occ:1.00
 OG A:SER134 2.9 15.4 1.0
N A:PHE358 3.0 14.5 1.0
CB A:SER134 3.3 15.0 1.0
CG A:LYS357 3.4 14.9 1.0
CH2 A:TRP329 3.4 15.6 1.0
CA A:LYS357 3.4 14.9 1.0
CZ3 A:TRP329 3.5 16.1 1.0
C A:LYS357 3.7 15.6 1.0
CG A:PRO379 3.8 14.8 1.0
CZ2 A:TRP329 3.8 16.1 1.0
CB A:LYS357 3.9 15.4 1.0
CB A:PRO379 4.0 14.6 1.0
O A:PHE358 4.0 15.6 1.0
CZ2 A:TRP189 4.0 16.1 1.0
CA A:PHE358 4.1 15.5 1.0
CE3 A:TRP329 4.1 15.9 1.0
CH2 A:TRP189 4.2 16.0 1.0
CB A:PHE358 4.2 13.7 1.0
CE2 A:TRP329 4.3 15.1 1.0
CD A:PRO379 4.3 14.2 1.0
CA A:SER134 4.4 14.0 1.0
CD2 A:TRP329 4.4 15.5 1.0
C A:PHE358 4.5 15.5 1.0
N A:LYS357 4.6 15.0 1.0
CD A:LYS357 4.7 14.9 1.0
CG A:PHE358 4.7 13.8 1.0
CD2 A:PHE358 4.8 14.9 1.0
O A:GLN356 4.8 15.6 1.0
O A:SER134 4.9 15.6 1.0
O A:LYS357 5.0 12.9 1.0

Magnesium binding site 10 out of 22 in 7xyr

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Magnesium binding site 10 out of 22 in the Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:30.8
occ:1.00
 O A:HOH830 2.9 36.4 1.0
CG A:PRO332 3.2 22.6 1.0
N A:ASP326 3.2 19.4 1.0
CB A:ASP326 3.3 22.5 1.0
CD A:PRO325 3.7 19.9 1.0
CA A:ASP326 3.8 20.1 1.0
N A:PRO325 3.8 20.5 1.0
CG A:PRO325 3.8 20.4 1.0
CG A:ASP326 3.8 25.8 1.0
CB A:TYR324 3.8 17.0 1.0
OD2 A:ASP326 3.9 30.3 1.0
CD A:PRO332 4.0 21.4 1.0
N A:GLY327 4.1 17.7 1.0
C A:TYR324 4.1 18.9 1.0
C A:PRO325 4.2 18.5 1.0
CA A:PRO325 4.3 20.1 1.0
CB A:PRO332 4.4 20.7 1.0
CB A:PRO325 4.4 19.5 1.0
CA A:TYR324 4.4 16.4 1.0
C A:ASP326 4.4 19.6 1.0
OD1 A:ASP326 4.6 24.7 1.0
CD2 A:TYR324 4.7 19.6 1.0
CG A:TYR324 4.7 18.5 1.0
O A:TYR324 4.8 18.9 1.0
O A:HOH1059 4.9 37.6 1.0

Reference:

X.Teng, C.Wang. Cystal Structure of Beta-Glucuronidase From Bacteroides Thetaiotaomicron To Be Published.
Page generated: Thu Oct 3 13:24:52 2024

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