Atomistry » Magnesium » PDB 2ybb-2yni » 2yl5
Atomistry »
  Magnesium »
    PDB 2ybb-2yni »
      2yl5 »

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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Go back to Magnesium Binding Sites List in 2yl5
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy