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Manganese in PDB 2yl8: 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: 2yl8 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) 35.60 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.570, 109.290, 112.930, 90.00, 90.00, 90.00
R / Rfree (%) 16.444 / 20.522

Manganese Binding Sites:

The binding sites of Manganese atom in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis (pdb code 2yl8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis, PDB code: 2yl8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 2yl8

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Manganese binding site 1 out of 9 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 Manganese with other atoms in the Mn 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:Mn1615

b:21.4
occ:1.00
 O A:HOH2260 2.1 18.0 1.0
O A:HOH2258 2.2 23.9 1.0
OD2 A:ASP329 2.2 15.7 1.0
O A:HOH2257 2.2 17.8 1.0
O A:HOH2359 2.3 14.9 1.0
O A:HOH2259 2.3 29.0 1.0
CG A:ASP329 3.2 14.0 1.0
OD1 A:ASP329 3.6 16.1 1.0
O A:HOH2191 4.0 32.0 1.0
N A:VAL388 4.0 13.7 1.0
O1 A:EDO1628 4.1 19.3 1.0
O A:HOH2251 4.2 16.6 1.0
C1 A:EDO1628 4.3 15.2 1.0
CA A:PRO387 4.4 14.8 1.0
O A:HOH2360 4.4 31.5 1.0
O A:VAL388 4.5 13.8 1.0
CB A:ASP329 4.5 11.5 1.0
O A:HOH2190 4.6 33.4 1.0
C A:PRO387 4.6 14.6 1.0
CB A:PRO387 4.8 15.1 1.0
CA A:VAL388 4.9 14.4 1.0
CB A:VAL388 4.9 14.4 1.0

Manganese binding site 2 out of 9 in 2yl8

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Manganese binding site 2 out of 9 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 Manganese with other atoms in the Mn 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:Mn1616

b:26.0
occ:1.00
 O A:HOH2466 2.1 31.5 1.0
OD2 A:ASP485 2.2 11.0 1.0
O A:HOH2455 2.2 19.6 1.0
OD1 A:ASP477 2.3 16.1 1.0
CG A:ASP485 3.3 13.0 1.0
CG A:ASP477 3.3 14.1 1.0
O A:HOH2639 3.4 31.1 1.0
N A:ASP477 3.8 12.6 1.0
OD1 A:ASP485 3.9 15.9 1.0
CB A:ASP477 3.9 13.7 1.0
OD2 A:ASP477 4.2 15.2 1.0
CB A:ASP485 4.3 9.2 1.0
CB A:ALA476 4.4 14.4 1.0
CA A:ASP477 4.5 12.9 1.0
O A:HOH2456 4.5 30.1 1.0
CA A:ALA476 4.7 13.5 1.0
C A:ALA476 4.8 13.0 1.0

Manganese binding site 3 out of 9 in 2yl8

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Manganese binding site 3 out of 9 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 Manganese with other atoms in the Mn 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:Mn1617

b:37.9
occ:1.00
 OD1 A:ASN422 2.1 12.6 1.0
O A:HOH2393 2.2 46.7 1.0
O A:HOH2394 2.4 29.9 1.0
O A:HOH2640 2.6 42.3 1.0
OD2 A:ASP447 3.1 31.2 1.0
CG A:ASN422 3.1 13.8 1.0
O A:HOH2392 3.2 39.1 1.0
ND2 A:ASN422 3.6 13.8 1.0
CG A:ASP447 3.7 23.0 1.0
CB A:ASP447 3.7 17.1 1.0
O A:HOH2419 4.3 41.4 1.0
CB A:ASN422 4.4 12.4 1.0
OD1 A:ASP447 4.7 29.2 1.0
O A:HOH2395 4.7 26.3 1.0
O A:HOH2332 4.7 11.3 0.5
CA A:ASN422 4.7 12.0 1.0
O A:ASN422 4.8 12.5 1.0

Manganese binding site 4 out of 9 in 2yl8

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Manganese binding site 4 out of 9 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 Manganese with other atoms in the Mn 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:Mn1618

b:15.1
occ:1.00
 O A:HOH2127 2.1 15.3 1.0
OD2 A:ASP259 2.1 16.0 1.0
O A:HOH2641 2.2 17.3 1.0
O A:HOH2124 2.2 15.4 1.0
O A:HOH2126 2.2 16.6 1.0
O A:HOH2128 2.3 12.2 1.0
CG A:ASP259 3.2 14.3 1.0
OD1 A:ASP259 3.6 17.0 1.0
O A:HOH2205 4.1 16.1 1.0
ND2 A:ASN303 4.1 9.8 1.0
OD1 A:ASN303 4.3 12.7 1.0
O A:ASP259 4.3 11.7 1.0
O A:HOH2171 4.3 15.0 1.0
O A:HOH2204 4.4 13.2 1.0
O A:HOH2217 4.4 23.3 1.0
CB A:ASP259 4.5 12.1 1.0
O A:HOH2001 4.6 37.4 1.0
CG A:ASN303 4.6 10.7 1.0
C A:ASP259 4.7 11.1 1.0
O A:HOH2211 4.8 15.8 1.0

Manganese binding site 5 out of 9 in 2yl8

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Manganese binding site 5 out of 9 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 Manganese with other atoms in the Mn 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:Mn1619

b:44.1
occ:1.00
 OD2 A:ASP247 2.3 13.8 0.5
O A:HOH2642 2.3 26.0 1.0
O A:HOH2089 2.4 28.4 1.0
CG A:ASP247 3.2 11.8 0.5
OD1 A:ASP247 3.3 11.5 0.5
O A:HOH2094 3.9 26.6 1.0
NH2 A:ARG251 4.2 32.7 1.0
OD1 A:ASP248 4.4 11.6 1.0
CB A:ASP247 4.6 11.4 0.5
CB A:ASP247 4.7 12.2 0.5
OD2 A:ASP248 5.0 10.6 1.0

Manganese binding site 6 out of 9 in 2yl8

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Manganese binding site 6 out of 9 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 Manganese with other atoms in the Mn 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
A:Mn1620

b:41.9
occ:0.50
 OD2 A:ASP585 2.2 25.1 1.0
CG A:ASP585 3.0 23.6 1.0
OD1 A:ASP585 3.1 28.1 1.0
ND2 A:ASN587 3.8 24.8 0.5
CB A:ASN587 4.4 21.4 0.5
CB A:ASP585 4.4 20.3 1.0
CG A:ASN587 4.6 23.2 0.5
ND2 A:ASN181 4.7 25.6 1.0
OD1 A:ASN181 4.8 30.6 1.0
O A:HOH2602 5.0 23.9 0.5

Manganese binding site 7 out of 9 in 2yl8

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Manganese binding site 7 out of 9 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 Manganese with other atoms in the Mn 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
A:Mn1621

b:37.3
occ:1.00
 OE1 A:GLU553 2.1 27.0 1.0
OE1 A:GLU550 2.2 30.7 1.0
CD A:GLU553 3.1 27.2 1.0
O A:HOH2548 3.1 29.1 0.5
MN A:MN1623 3.2 50.5 1.0
CD A:GLU550 3.3 28.6 1.0
MN A:MN1622 3.3 47.3 1.0
O A:HOH2545 3.4 13.4 1.0
OE2 A:GLU553 3.4 29.5 1.0
O A:HOH2643 3.4 21.5 1.0
OE2 A:GLU550 3.6 30.8 1.0
O A:HOH2548 3.7 22.8 0.5
CG A:GLU553 4.3 19.4 1.0
CB A:GLU553 4.6 14.7 1.0
CG A:GLU550 4.6 22.4 1.0
O A:HOH2051 5.0 31.8 1.0

Manganese binding site 8 out of 9 in 2yl8

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Manganese binding site 8 out of 9 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 Manganese with other atoms in the Mn 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
A:Mn1622

b:47.3
occ:1.00
 O A:HOH2051 2.3 31.8 1.0
OE2 A:GLU550 2.3 30.8 1.0
O A:HOH2544 3.0 32.0 1.0
CD A:GLU550 3.2 28.6 1.0
MN A:MN1621 3.3 37.3 1.0
OE1 A:GLU550 3.4 30.7 1.0
O A:HOH2545 3.4 13.4 1.0
O A:HOH2643 3.5 21.5 1.0
CG A:GLU550 4.5 22.4 1.0
CE A:LYS212 4.6 20.6 1.0
OE1 A:GLU553 4.7 27.0 1.0
NZ A:LYS212 4.8 22.8 1.0
O A:HOH2182 4.9 45.9 1.0

Manganese binding site 9 out of 9 in 2yl8

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Manganese binding site 9 out of 9 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 Manganese with other atoms in the Mn 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
A:Mn1623

b:50.5
occ:1.00
 O A:HOH2645 2.4 39.7 1.0
O A:HOH2548 2.9 22.8 0.5
MN A:MN1621 3.2 37.3 1.0
OE1 A:GLU550 3.7 30.7 1.0
O A:HOH2548 4.0 29.1 0.5
OE1 A:GLU553 4.2 27.0 1.0
CD A:GLU553 4.4 27.2 1.0
O A:HOH2643 4.5 21.5 1.0
OE1 A:GLN554 4.7 18.5 1.0
OE2 A:GLU553 4.7 29.5 1.0
CD A:GLU550 4.8 28.6 1.0
O A:GLU550 4.9 14.4 1.0
CG A:GLU553 5.0 19.4 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: Sat Oct 5 15:32:12 2024

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