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Calcium in PDB 2yll: 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: 2yll 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) 78.39 / 1.85
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.520, 109.420, 112.360, 90.00, 90.00, 90.00
R / Rfree (%) 16.123 / 20.033

Other elements in 2yll:

The structure of Inhibition of the Pneumococcal Virulence Factor Strh and Molecular Insights Into N-Glycan Recognition and Hydrolysis also contains other interesting chemical elements:

Iodine (I) 68 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 2yll

Go back to Calcium Binding Sites List in 2yll
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca1615

b:19.5
occ:0.77
 O A:HOH2302 2.3 26.5 1.0
O A:HOH2026 2.3 25.9 1.0
O A:HOH2299 2.4 34.0 1.0
OE2 A:GLU361 2.4 12.4 1.0
OE1 A:GLU361 2.4 9.1 1.0
O A:HOH2484 2.4 37.3 1.0
O A:HOH2301 2.5 28.4 1.0
CD A:GLU361 2.8 11.1 1.0
O A:HOH2300 2.9 22.4 1.0
O A:HOH2213 4.1 36.5 1.0
CG A:GLU361 4.3 10.4 1.0
O1 A:EDO1618 4.4 16.3 1.0
O A:HOH2303 4.5 24.7 1.0
CE1 A:HIS297 4.5 11.8 1.0
NE2 A:HIS297 4.5 10.8 1.0
O2 A:EDO1618 4.6 14.3 1.0
C2 A:EDO1618 4.7 15.6 1.0
O2 A:EDO1619 4.8 20.4 1.0
O A:HOH2456 4.9 26.5 1.0
NH2 A:ARG196 4.9 9.6 1.0

Calcium binding site 2 out of 2 in 2yll

Go back to Calcium Binding Sites List in 2yll
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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:Ca1616

b:15.3
occ:0.52
 OD1 A:ASP477 2.4 12.1 1.0
OD2 A:ASP485 2.4 9.2 1.0
O A:HOH2449 2.5 30.2 1.0
O A:HOH2448 2.6 37.4 1.0
O A:HOH2594 2.6 34.0 1.0
CG A:ASP477 3.5 12.1 1.0
CG A:ASP485 3.5 11.0 1.0
OD1 A:ASP485 4.0 11.6 1.0
N A:ASP477 4.0 10.2 1.0
CB A:ASP477 4.1 10.3 1.0
O A:HOH2274 4.2 33.3 1.0
CB A:ALA476 4.3 11.0 1.0
OD2 A:ASP477 4.4 11.7 1.0
CB A:ASP485 4.6 8.2 1.0
O A:HOH2450 4.7 23.8 1.0
CA A:ASP477 4.7 10.3 1.0
CA A:ALA476 4.8 10.8 1.0
C A:ALA476 4.9 10.5 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: Tue Jul 8 09:42:07 2025

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