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Magnesium in PDB 2yl5: Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis

Enzymatic activity of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis

All present enzymatic activity of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis:
3.2.1.52;

Protein crystallography data

The structure of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis, PDB code: 2yl5 was solved by B.Pluvinage, M.A.Higgins, D.W.Abbott, C.Robb, A.B.Dalia, L.Deng, J.N.Weiser, T.B.Parsons, A.J.Fairbanks, 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) 38.25 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.250, 115.860, 132.260, 90.00, 99.62, 90.00
R / Rfree (%) 23.706 / 29.282

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis (pdb code 2yl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis, PDB code: 2yl5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2yl5

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Magnesium binding site 1 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2042

b:6.3
occ:1.00
 O A:HOH3033 3.0 2.7 1.0
NZ A:LYS642 3.2 4.4 1.0
O A:HOH3559 3.4 35.2 1.0
N A:TYR959 3.4 8.2 1.0
ND2 A:ASN710 3.5 7.5 1.0
O A:HOH3571 3.6 30.9 1.0
CE A:LYS642 3.6 4.5 1.0
CA A:GLU958 3.9 8.1 1.0
CG A:GLU958 4.1 8.2 1.0
O A:HOH3126 4.1 17.2 1.0
C A:GLU958 4.2 8.1 1.0
O B:HOH3261 4.2 31.1 1.0
CB A:TYR959 4.3 8.2 1.0
O A:ALA957 4.4 7.9 1.0
CA A:TYR959 4.4 8.2 1.0
O A:HOH3020 4.4 10.1 1.0
O A:HOH3019 4.5 2.0 1.0
CB A:GLU958 4.5 8.1 1.0
CG A:ASN710 4.6 7.5 1.0
O A:TYR959 4.7 8.3 1.0
O A:HOH3021 4.8 7.3 1.0
N A:GLU958 4.9 8.0 1.0
OD1 A:ASN710 5.0 7.5 1.0

Magnesium binding site 2 out of 10 in 2yl5

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Magnesium binding site 2 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2043

b:2.0
occ:1.00
 O A:HOH3669 2.5 20.6 1.0
O A:HOH3670 2.7 18.5 1.0
N A:VAL765 3.3 7.7 1.0
CB A:LYS764 3.5 7.9 1.0
CA A:LYS764 3.8 7.9 1.0
CG2 A:VAL765 3.9 7.5 1.0
C A:LYS764 4.0 7.8 1.0
CB A:VAL765 4.1 7.5 1.0
CA A:VAL765 4.3 7.5 1.0
O A:HOH3407 4.4 26.1 1.0
CG A:LYS764 4.7 7.9 1.0
O A:HOH3404 4.7 14.1 1.0
O A:HOH3205 4.8 22.6 1.0
O A:VAL765 4.9 7.4 1.0

Magnesium binding site 3 out of 10 in 2yl5

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Magnesium binding site 3 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2044

b:4.3
occ:1.00
 O A:HOH3273 2.1 30.3 1.0
O A:HOH3264 2.8 25.9 1.0
O A:HOH3261 3.1 20.1 1.0
N A:GLY826 3.3 5.3 1.0
N A:TYR825 3.4 5.9 1.0
C A:GLN823 3.6 6.8 1.0
CB A:TYR825 3.6 5.7 1.0
CA A:GLN823 3.6 6.9 1.0
CA A:TYR825 3.8 5.7 1.0
N A:LEU824 3.9 6.5 1.0
O A:GLN823 3.9 6.8 1.0
C A:TYR825 4.0 5.5 1.0
O A:HOH3269 4.0 3.0 1.0
CB A:GLN823 4.3 7.0 1.0
CA A:GLY826 4.3 5.1 1.0
C A:LEU824 4.4 6.2 1.0
O A:LEU819 4.6 7.6 1.0
CA A:LEU824 4.6 6.3 1.0
O A:HOH3484 4.7 31.4 1.0
CG2 A:VAL861 4.7 7.7 1.0
CG A:TYR825 4.7 5.6 1.0
N A:GLN823 4.8 7.1 1.0
CG A:GLN823 4.8 7.0 1.0
CD2 A:TYR825 4.9 5.6 1.0
O A:LYS820 5.0 7.7 1.0

Magnesium binding site 4 out of 10 in 2yl5

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Magnesium binding site 4 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2045

b:27.3
occ:1.00
 O A:HOH3307 2.7 11.7 1.0
O A:HOH3310 3.0 34.4 1.0
O A:HOH3671 3.5 28.7 1.0
CD A:LYS840 3.6 3.9 1.0
CB A:ASP866 3.7 5.2 1.0
NE2 A:GLN845 3.7 2.9 1.0
CG A:LYS840 3.8 3.8 1.0
CD A:PRO846 4.0 2.9 1.0
O A:HOH3455 4.1 22.9 1.0
CG A:ASP866 4.2 5.2 1.0
CD A:GLN845 4.3 2.9 1.0
OE1 A:GLN845 4.4 2.9 1.0
O A:ASP866 4.4 5.0 1.0
O A:HOH3467 4.6 15.5 1.0
CG A:PRO846 4.6 2.8 1.0
OD2 A:ASP866 4.6 5.2 1.0
O C:HOH3373 4.6 12.6 1.0
OD1 A:ASP866 4.6 5.2 1.0
O A:HOH3362 4.6 20.0 1.0
O A:HOH3461 4.8 38.9 1.0
O A:HOH3290 4.8 12.4 1.0
CA A:ASP866 4.8 5.2 1.0
C A:ASP866 5.0 5.0 1.0
O A:HOH3311 5.0 6.3 1.0
CB A:LYS840 5.0 3.7 1.0

Magnesium binding site 5 out of 10 in 2yl5

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Magnesium binding site 5 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2046

b:9.7
occ:1.00
 O A:MET947 2.6 4.2 1.0
O A:ASN898 2.7 3.9 1.0
C A:THR897 3.4 3.8 1.0
O A:THR897 3.4 3.7 1.0
N A:SER949 3.5 4.3 1.0
CE1 A:TYR902 3.5 5.8 1.0
CD1 A:TYR902 3.5 5.8 1.0
CA A:LEU948 3.6 4.2 1.0
C A:ASN898 3.7 3.9 1.0
C A:MET947 3.7 4.2 1.0
CB A:TRP901 3.7 5.1 1.0
OG A:SER949 3.8 4.3 1.0
N A:ASN898 3.8 3.8 1.0
CG2 A:THR897 3.8 3.7 1.0
CE3 A:TRP901 3.8 4.7 1.0
CA A:THR897 3.9 3.7 1.0
C A:LEU948 4.0 4.2 1.0
CB A:SER949 4.0 4.3 1.0
N A:LEU948 4.1 4.2 1.0
C A:TRP901 4.2 5.4 1.0
CA A:ASN898 4.3 3.8 1.0
CA A:TRP901 4.3 5.1 1.0
CA A:SER949 4.4 4.3 1.0
N A:TYR902 4.5 5.7 1.0
N A:TRP901 4.5 4.9 1.0
CB A:THR897 4.5 3.7 1.0
CD2 A:TRP901 4.5 4.8 1.0
O A:TRP901 4.5 5.4 1.0
CG A:TRP901 4.5 4.9 1.0
N A:GLY899 4.6 4.0 1.0
CB A:LEU948 4.8 4.2 1.0
CZ A:TYR902 4.8 5.8 1.0
CZ3 A:TRP901 4.8 4.7 1.0
CG A:TYR902 4.8 6.0 1.0
CA A:GLY899 5.0 4.1 1.0
CA A:MET947 5.0 4.2 1.0

Magnesium binding site 6 out of 10 in 2yl5

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Magnesium binding site 6 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2041

b:35.9
occ:1.00
 O B:HOH3019 2.3 19.8 1.0
O B:HOH3021 2.4 22.9 1.0
O B:HOH3541 2.7 41.6 1.0
O B:HOH3540 3.5 39.9 1.0
CD2 B:TRP951 3.7 16.1 1.0
CG B:TRP951 3.9 16.2 1.0
CE3 B:TRP951 4.0 16.1 1.0
O2 B:EDO2043 4.0 27.0 1.0
CE2 B:TRP951 4.0 16.1 1.0
OD1 B:ASP953 4.0 17.5 1.0
NH1 B:ARG641 4.2 14.2 1.0
OD2 B:ASP953 4.2 17.5 1.0
CD1 B:TRP951 4.2 16.1 1.0
NE1 B:TRP951 4.3 16.1 1.0
CB B:TRP951 4.4 16.2 1.0
O1 B:EDO2043 4.4 27.0 1.0
CZ3 B:TRP951 4.5 16.1 1.0
NH2 B:ARG641 4.5 14.2 1.0
CZ2 B:TRP951 4.5 16.1 1.0
CG B:ASP953 4.5 17.5 1.0
CE2 B:TYR902 4.6 17.7 1.0
CH2 B:TRP951 4.7 16.1 1.0
C2 B:EDO2043 4.8 27.0 1.0
CZ B:ARG641 4.8 14.2 1.0
O B:HOH3055 4.9 15.0 1.0

Magnesium binding site 7 out of 10 in 2yl5

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Magnesium binding site 7 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2042

b:14.5
occ:1.00
 O B:HOH3034 3.1 18.4 1.0
O B:HOH3443 3.1 32.6 1.0
NZ B:LYS642 3.2 14.7 1.0
N B:TYR959 3.4 19.1 1.0
ND2 B:ASN710 3.5 20.3 1.0
CE B:LYS642 3.6 14.7 1.0
CA B:GLU958 3.8 19.0 1.0
C B:GLU958 4.1 19.0 1.0
CG B:GLU958 4.2 19.0 1.0
O B:ALA957 4.3 18.9 1.0
CB B:TYR959 4.3 19.1 1.0
CA B:TYR959 4.4 19.1 1.0
O B:HOH3023 4.5 15.9 1.0
CB B:GLU958 4.5 19.0 1.0
O B:HOH3022 4.6 18.0 1.0
CG B:ASN710 4.6 20.3 1.0
O B:TYR959 4.7 19.2 1.0
N B:GLU958 4.8 18.9 1.0
O B:HOH3024 4.9 20.9 1.0
C B:ALA957 4.9 18.8 1.0
OD1 B:ASN710 5.0 20.3 1.0

Magnesium binding site 8 out of 10 in 2yl5

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Magnesium binding site 8 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2041

b:3.0
occ:1.00
 O C:HOH3250 2.8 13.0 1.0
O C:HOH3249 3.3 35.9 1.0
N C:GLY826 3.4 5.6 1.0
N C:TYR825 3.4 5.9 1.0
C C:GLN823 3.6 6.4 1.0
CB C:TYR825 3.6 5.8 1.0
CA C:GLN823 3.6 6.5 1.0
N C:LEU824 3.9 6.2 1.0
CA C:TYR825 3.9 5.8 1.0
O C:HOH3256 3.9 2.4 1.0
O C:GLN823 4.0 6.4 1.0
O C:HOH3257 4.0 51.3 1.0
C C:TYR825 4.1 5.7 1.0
O C:HOH3325 4.2 35.0 1.0
CB C:GLN823 4.3 6.5 1.0
CA C:GLY826 4.3 5.5 1.0
C C:LEU824 4.4 6.0 1.0
O C:LEU819 4.5 7.1 1.0
CA C:LEU824 4.6 6.1 1.0
CG2 C:VAL861 4.7 6.9 1.0
N C:GLN823 4.8 6.6 1.0
CG C:TYR825 4.8 5.8 1.0
CG C:GLN823 4.8 6.5 1.0
O C:LYS820 4.9 7.0 1.0
CA C:LYS820 5.0 7.1 1.0

Magnesium binding site 9 out of 10 in 2yl5

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Magnesium binding site 9 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2042

b:6.2
occ:1.00
 O C:HOH3038 3.1 6.2 1.0
N C:TYR959 3.2 9.7 1.0
NZ C:LYS642 3.3 5.5 1.0
O C:HOH3515 3.6 32.2 1.0
CE C:LYS642 3.6 5.5 1.0
ND2 C:ASN710 3.6 8.7 1.0
CA C:GLU958 3.7 9.7 1.0
C C:GLU958 4.0 9.7 1.0
CG C:GLU958 4.1 9.8 1.0
CB C:TYR959 4.2 9.6 1.0
CA C:TYR959 4.2 9.6 1.0
O C:ALA957 4.3 9.6 1.0
O C:HOH3125 4.3 20.6 1.0
CB C:GLU958 4.4 9.7 1.0
O C:HOH3024 4.5 13.2 1.0
O C:TYR959 4.6 9.6 1.0
O C:HOH3023 4.6 3.2 1.0
N C:GLU958 4.7 9.7 1.0
CG C:ASN710 4.8 8.7 1.0
O C:HOH3025 4.8 6.0 1.0
C C:TYR959 4.9 9.6 1.0
C C:ALA957 4.9 9.6 1.0

Magnesium binding site 10 out of 10 in 2yl5

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Magnesium binding site 10 out of 10 in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2043

b:20.9
occ:1.00
 O C:HOH3259 2.4 12.6 1.0
O C:HOH3268 2.4 24.9 1.0
O C:GLN862 2.9 6.3 1.0
O C:HOH3333 3.1 15.0 1.0
ND2 C:ASN833 3.5 3.0 1.0
N C:GLN862 3.7 6.6 1.0
C C:GLN862 3.8 6.3 1.0
O C:HOH3267 3.9 8.6 1.0
CB C:ALA829 4.0 4.4 1.0
CG1 C:VAL861 4.0 6.9 1.0
CA C:GLN862 4.1 6.5 1.0
CB C:GLN862 4.3 6.5 1.0
C C:VAL861 4.6 6.8 1.0
N C:GLU830 4.7 4.2 1.0
C C:ALA829 4.8 4.3 1.0
O C:GLY826 4.8 5.4 1.0
CG C:ASN833 4.8 3.0 1.0
O C:HOH3269 4.8 11.5 1.0
CA C:VAL861 5.0 6.9 1.0

Reference:

B.Pluvinage, M.A.Higgins, D.W.Abbott, C.Robb, A.B.Dalia, L.Deng, J.N.Weiser, T.B.Parsons, A.J.Fairbanks, D.J.Vocadlo, A.B.Boraston. Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis. Structure V. 19 1603 2011.
ISSN: ISSN 0969-2126
PubMed: 22078560
DOI: 10.1016/J.STR.2011.08.011
Page generated: Wed Aug 14 07:34:53 2024

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