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Magnesium in PDB 4az5: Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh

Enzymatic activity of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh

All present enzymatic activity of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh:
3.2.1.52;

Protein crystallography data

The structure of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4az5 was solved by B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.57 / 1.73
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.540, 110.050, 112.200, 90.00, 90.00, 90.00
R / Rfree (%) 15.644 / 18.629

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh (pdb code 4az5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4az5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4az5

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Magnesium binding site 1 out of 4 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1616

b:25.4
occ:1.00
 O A:HOH2147 2.0 18.8 1.0
O A:HOH2145 2.1 24.6 1.0
O A:HOH2146 2.2 21.9 1.0
O A:HOH2669 2.2 31.1 1.0
OD2 A:ASP259 2.2 14.0 0.5
O A:HOH2141 2.2 27.3 1.0
CG A:ASP259 3.3 14.7 0.5
OD1 A:ASP259 3.7 15.5 0.5
O A:HOH2233 4.0 21.7 1.0
ND2 A:ASN303 4.1 11.3 1.0
OD1 A:ASN303 4.2 14.2 1.0
O A:ASP259 4.2 13.4 0.5
O A:ASP259 4.2 13.7 0.5
O A:HOH2232 4.3 18.3 1.0
O A:HOH2272 4.4 21.4 1.0
O A:HOH2271 4.5 18.7 0.5
CB A:ASP259 4.6 13.9 0.5
CG A:ASN303 4.6 13.9 1.0
O A:HOH2237 4.6 22.9 1.0
CB A:ASP259 4.6 14.6 0.5
C A:ASP259 4.7 13.6 0.5
C A:ASP259 4.7 13.8 0.5

Magnesium binding site 2 out of 4 in 4az5

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Magnesium binding site 2 out of 4 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1617

b:3.6
occ:0.50
 ND1 A:HIS408 2.3 12.9 1.0
O A:HOH2418 2.4 5.9 1.0
CE1 A:HIS408 3.2 11.7 1.0
CG A:HIS408 3.4 12.6 1.0
CB A:HIS408 3.8 11.1 1.0
CA A:HIS408 3.9 11.4 1.0
CB A:ALA349 4.2 10.9 1.0
NE2 A:HIS408 4.4 14.5 1.0
CD2 A:HIS408 4.5 12.2 1.0
O A:SER407 4.6 12.0 1.0
CA A:ALA346 4.7 11.3 1.0
C A:HIS408 4.8 11.4 1.0
O A:HIS408 4.9 12.2 1.0
N A:HIS408 4.9 10.8 1.0
CB A:ALA346 5.0 12.2 1.0

Magnesium binding site 3 out of 4 in 4az5

Go back to Magnesium Binding Sites List in 4az5
Magnesium binding site 3 out of 4 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1622

b:28.2
occ:0.50
 O A:HOH2312 2.0 33.2 1.0
O A:HOH2411 2.2 34.8 1.0
O A:HOH2314 2.2 22.8 1.0
OG A:SER407 4.0 13.5 1.0
O A:HOH2412 4.3 28.3 1.0
CB A:SER407 4.4 12.4 1.0
NH1 A:ARG403 4.5 23.8 0.5
OD2 A:ASP342 4.6 20.1 1.0
OD1 A:ASP342 4.8 17.1 1.0

Magnesium binding site 4 out of 4 in 4az5

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Magnesium binding site 4 out of 4 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1623

b:34.1
occ:1.00
 O A:HOH2673 2.0 31.4 1.0
O A:HOH2671 2.0 35.1 1.0
O A:HOH2674 2.1 25.8 1.0
O A:HOH2672 2.3 39.0 1.0
O A:HOH2247 4.1 31.2 1.0
O A:HOH2420 4.6 25.2 1.0

Reference:

B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston. Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh. Org.Biomol.Chem. V. 11 7907 2013.
ISSN: ISSN 1477-0520
PubMed: 24132305
DOI: 10.1039/C3OB41579A
Page generated: Thu Aug 15 15:10:56 2024

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