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Magnesium in PDB 4jkl: Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212

Enzymatic activity of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212

All present enzymatic activity of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212:
3.2.1.31;

Protein crystallography data

The structure of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212, PDB code: 4jkl was solved by B.D.Wallace, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.31 / 2.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.001, 198.759, 75.573, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212 (pdb code 4jkl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212, PDB code: 4jkl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jkl

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Magnesium binding site 1 out of 4 in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:25.0
occ:1.00
 OD1 A:ASP535 3.2 19.9 1.0
NE2 A:HIS592 3.4 25.2 1.0
O A:HOH762 3.6 16.0 1.0
CE A:LYS594 3.7 15.5 1.0
CG A:ASP535 3.8 19.9 1.0
CD2 A:HIS592 4.1 18.7 1.0
CB A:ASP535 4.2 16.7 1.0
CA A:ASP535 4.3 23.1 1.0
CE1 A:HIS592 4.4 21.7 1.0
CD1 A:ILE588 4.4 15.7 1.0
OD2 A:ASP535 4.5 18.5 1.0
CD A:LYS594 4.5 26.7 1.0
NZ A:LYS594 4.7 14.6 1.0
CG1 A:ILE588 4.9 10.5 1.0
O A:ASP535 4.9 19.4 1.0

Magnesium binding site 2 out of 4 in 4jkl

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Magnesium binding site 2 out of 4 in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:25.4
occ:1.00
 O A:HOH1093 3.6 27.1 1.0
CG B:ASN306 3.8 9.6 1.0
ND2 A:ASN301 3.9 6.8 1.0
O B:HOH756 3.9 11.0 1.0
OD1 B:ASN306 3.9 7.8 1.0
ND2 B:ASN306 4.0 8.8 1.0
O B:LEU305 4.2 8.1 1.0
CG A:ASN306 4.2 9.4 1.0
ND2 B:ASN301 4.3 6.5 1.0
ND2 A:ASN306 4.3 8.4 1.0
O A:HOH989 4.3 21.3 1.0
O A:LEU305 4.3 10.3 1.0
OD1 A:ASN306 4.4 9.4 1.0
CA B:ASN306 4.4 9.0 1.0
CB B:ASN306 4.4 7.8 1.0
CG A:ASN301 4.6 10.4 1.0
OD1 A:ASN301 4.7 17.3 1.0
CB A:ASN306 4.7 9.9 1.0
O A:HOH845 4.8 8.7 1.0
CA A:ASN306 4.8 8.2 1.0
CG B:ASN301 5.0 10.8 1.0

Magnesium binding site 3 out of 4 in 4jkl

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Magnesium binding site 3 out of 4 in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:14.3
occ:1.00
 O A:HOH1106 1.9 13.8 1.0
O A:HOH1051 2.3 16.3 1.0
N A:TYR465 2.8 10.1 1.0
O A:ARG463 3.2 6.5 1.0
C A:ARG463 3.4 11.5 1.0
CB A:TYR465 3.5 15.1 1.0
CA A:TYR465 3.6 14.2 1.0
N A:TYR464 3.6 12.6 1.0
C A:TYR464 3.6 15.4 1.0
O A:TYR465 3.6 9.5 1.0
CA A:TYR464 3.7 9.7 1.0
CB A:ARG463 3.8 11.4 1.0
CD2 A:TYR465 3.9 13.4 1.0
C A:TYR465 4.1 16.9 1.0
CD1 A:ILE481 4.1 9.5 1.0
CG A:TYR465 4.2 12.0 1.0
CG1 A:ILE481 4.2 11.8 1.0
CA A:ARG463 4.3 12.5 1.0
CZ A:PHE526 4.3 9.9 1.0
CB A:ILE481 4.4 12.5 1.0
CE1 A:PHE526 4.7 10.5 1.0
OG A:SER530 4.8 11.0 1.0
O A:TYR464 4.8 14.6 1.0
CB A:TYR502 4.8 8.0 1.0

Magnesium binding site 4 out of 4 in 4jkl

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Magnesium binding site 4 out of 4 in the Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Streptococcus Agalactiae Beta-Glucuronidase in Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:15.9
occ:1.00
 N B:TYR465 3.2 15.9 1.0
O B:ARG463 3.3 11.5 1.0
C B:ARG463 3.6 13.3 1.0
O B:TYR465 3.8 13.3 1.0
CB B:TYR465 3.8 13.9 1.0
N B:TYR464 3.8 16.1 1.0
CB B:ARG463 3.9 16.8 1.0
CA B:TYR465 3.9 13.7 1.0
CA B:TYR464 4.0 11.1 1.0
C B:TYR464 4.0 18.1 1.0
CD1 B:ILE481 4.0 7.0 1.0
CG1 B:ILE481 4.1 10.0 1.0
CD2 B:TYR465 4.2 13.4 1.0
C B:TYR465 4.3 15.3 1.0
CZ B:PHE526 4.3 16.2 1.0
CB B:ILE481 4.4 11.7 1.0
CA B:ARG463 4.4 18.6 1.0
OG B:SER530 4.4 17.2 1.0
CG B:TYR465 4.5 14.1 1.0
CB B:TYR502 4.6 12.1 1.0
CE1 B:PHE526 4.6 8.5 1.0
CG2 B:ILE481 5.0 10.6 1.0

Reference:

B.D.Wallace, A.B.Roberts, M.Dollinger, E.Figueroa, M.R.Redinbo. Structure and Inhibition of the Beta-Glucuronidases From Clostridium Perfringens and Streptococcus Agalactiae To Be Published.
Page generated: Mon Aug 11 17:15:31 2025

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