Iodine in PDB 2yll: 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;

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

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:

Calcium

(Ca)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 68;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 68 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 68 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 Iodine with other atoms in the I 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:I1620 b:19.8 occ:0.76 O A:HOH2012 2.9 34.1 1.0 O A:HOH2499 3.4 15.1 1.0 CB A:GLU543 3.7 11.8 1.0 O A:HOH2497 3.8 27.1 1.0 N A:GLU543 3.8 10.7 1.0 C A:ASN541 3.9 9.5 1.0 CA A:ASN541 3.9 9.4 1.0 CG A:GLU543 4.0 14.3 1.0 N A:ALA542 4.0 9.5 1.0 CD1 A:TYR544 4.0 12.1 1.0 CE1 A:TYR544 4.1 12.4 1.0 CD A:GLU543 4.2 18.8 1.0 O A:ASN541 4.3 8.8 1.0 CA A:GLU543 4.3 11.2 1.0 O A:HOH2310 4.5 35.7 1.0 O A:ALA540 4.5 9.7 1.0 OE1 A:GLU543 4.6 22.0 1.0 OE2 A:GLU543 4.7 22.3 1.0 O A:HOH2308 4.8 40.8 1.0 CB A:ASN541 4.8 9.2 1.0 C A:ALA542 4.8 10.3 1.0 N A:TYR544 4.9 10.4 1.0 N A:ASN541 5.0 9.4 1.0 CA A:ALA542 5.0 10.1 1.0

Iodine binding site 2 out of 68 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 Iodine with other atoms in the I 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:I1621 b:27.0 occ:0.59 NZ A:LYS210 3.5 20.6 1.0 CB A:HIS213 4.0 13.1 1.0 O A:ASP209 4.0 11.4 1.0 CD A:LYS210 4.1 16.9 1.0 C A:ASP209 4.1 10.8 1.0 CG A:HIS213 4.2 17.0 1.0 CB A:ASP209 4.2 11.3 1.0 CE A:LYS210 4.2 19.4 1.0 N A:LYS210 4.4 10.6 1.0 O A:HOH2043 4.4 15.8 1.0 CA A:LYS210 4.5 10.3 1.0 O A:HOH2045 4.5 26.7 1.0 CD2 A:HIS213 4.6 19.9 1.0 CG A:LYS210 4.6 13.5 1.0 ND1 A:HIS213 4.6 19.1 1.0 CA A:ASP209 4.8 11.0 1.0

Iodine binding site 3 out of 68 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 Iodine with other atoms in the I 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:I1622 b:25.1 occ:0.43 N A:GLU503 3.5 15.5 1.0 O A:HOH2475 3.7 23.2 1.0 CA A:GLU503 3.8 17.1 1.0 CA A:LYS501 4.0 10.8 1.0 CG A:LYS501 4.1 9.8 1.0 N A:THR502 4.1 12.1 1.0 C A:LYS501 4.2 11.4 1.0 CB A:LYS501 4.7 11.0 1.0 C A:THR502 4.7 14.1 1.0 C A:GLU503 4.8 17.4 1.0 N A:GLY504 4.9 17.5 1.0 CG A:GLU503 4.9 20.7 1.0 CB A:GLU503 4.9 17.4 1.0 O A:LYS501 5.0 10.9 1.0 CA A:THR502 5.0 13.2 1.0

Iodine binding site 4 out of 68 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 Iodine with other atoms in the I 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:I1623 b:22.0 occ:0.41 O A:HOH2161 3.2 35.1 1.0 OG A:SER522 3.3 11.6 1.0 O A:HOH2127 3.7 29.5 1.0 CB A:SER522 3.7 10.9 1.0 CD A:PRO521 3.7 8.9 1.0 N A:SER522 3.8 9.7 1.0 N A:PRO521 4.1 9.2 1.0 CG2 A:THR520 4.1 11.4 1.0 CG A:PRO521 4.2 9.1 1.0 CA A:SER522 4.4 10.8 1.0 C A:THR520 4.5 9.4 1.0 CD1 A:TYR261 4.5 10.6 1.0 CE1 A:TYR261 4.5 11.3 1.0 CA A:THR520 4.6 10.2 1.0 O A:HOH2151 4.7 39.7 1.0 C A:PRO521 4.7 9.0 1.0 O A:HOH2114 4.8 33.0 1.0 O A:HOH2485 4.8 33.9 1.0 CA A:PRO521 4.9 8.9 1.0 CB A:THR520 5.0 10.9 1.0

Iodine binding site 5 out of 68 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 Iodine with other atoms in the I 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:I1624 b:28.4 occ:0.41 OE1 A:GLU456 2.4 28.9 1.0 CD A:GLU456 3.4 25.4 1.0 O A:HOH2417 3.5 29.2 1.0 NZ A:LYS452 3.6 24.2 1.0 CA A:LEU453 4.0 10.9 1.0 OE2 A:GLU456 4.1 28.7 1.0 CD1 A:LEU453 4.2 14.3 1.0 N A:LEU453 4.3 10.8 1.0 CG A:LYS452 4.3 14.3 1.0 CB A:LEU453 4.4 10.5 1.0 CG A:GLU456 4.5 18.9 1.0 CD A:LYS452 4.6 17.6 1.0 CB A:GLU456 4.6 14.4 1.0 OE2 A:GLU503 4.6 26.1 1.0 C A:LYS452 4.6 11.1 1.0 CE A:LYS452 4.7 20.8 1.0 O A:LYS452 4.7 11.5 1.0 CG A:LEU453 4.9 11.8 1.0

Iodine binding site 6 out of 68 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 Iodine with other atoms in the I 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:I1625 b:23.6 occ:0.38 O A:HOH2165 2.9 26.9 1.0 O A:HOH2172 3.3 18.3 1.0 O A:HOH2167 3.4 40.3 1.0 O A:SER272 3.8 9.5 1.0 C A:SER272 4.0 9.7 1.0 CA A:GLN273 4.1 9.3 1.0 N A:GLN273 4.1 9.7 1.0 CB A:ASP276 4.2 11.3 1.0 CB A:SER272 4.2 11.3 1.0 O A:HOH2183 4.2 35.5 1.0 CG A:GLN273 4.3 8.7 1.0 O A:HOH2169 4.4 40.8 1.0 O A:HOH2176 4.4 21.3 1.0 CG A:ASP276 4.6 14.4 1.0 OD2 A:ASP276 4.7 17.6 1.0 O A:HOH2182 4.7 28.9 1.0 CA A:SER272 4.7 10.5 1.0 CB A:GLN273 4.8 9.6 1.0 O A:HOH2181 4.8 13.3 1.0

Iodine binding site 7 out of 68 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 Iodine with other atoms in the I 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:I1626 b:29.7 occ:0.45 O A:HOH2221 3.3 27.8 1.0 CD A:LYS321 3.8 27.3 1.0 ND2 A:ASN314 3.8 14.2 1.0 CG A:LYS321 3.9 24.5 1.0 CA A:ALA323 4.1 14.6 1.0 O A:SER322 4.1 17.1 1.0 NZ A:LYS306 4.4 19.4 1.0 CB A:ALA323 4.5 15.2 1.0 CG A:ASN314 4.5 14.8 1.0 N A:ALA323 4.5 15.3 1.0 C A:SER322 4.5 16.6 1.0 CB A:LYS321 4.6 22.0 1.0 OD1 A:ASN314 5.0 17.3 1.0

Iodine binding site 8 out of 68 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 Iodine with other atoms in the I 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:I1627 b:36.5 occ:0.45 ND2 A:ASN609 3.0 23.0 1.0 O A:HOH2330 3.6 25.9 1.0 CG2 A:THR606 4.0 13.6 1.0 CG A:ASN609 4.1 20.0 1.0 CG A:GLU605 4.1 21.8 1.0 CA A:THR606 4.1 13.6 1.0 CB A:ASN609 4.2 16.2 1.0 OE1 A:GLU605 4.4 30.4 1.0 CD A:GLU605 4.4 28.4 1.0 N A:THR606 4.5 14.1 1.0 O A:GLU605 4.5 14.6 1.0 NZ A:LYS602 4.5 26.6 1.0 CB A:THR606 4.6 13.3 1.0 O A:HOH2582 4.6 52.8 1.0 C A:GLU605 4.6 15.0 1.0 CB A:ALA573 4.9 11.7 1.0 O A:HOH2542 5.0 14.0 1.0

Iodine binding site 9 out of 68 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 Iodine with other atoms in the I 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:I1628 b:22.0 occ:0.31 O A:HOH2368 3.0 25.2 1.0 OD1 A:ASP400 3.0 11.8 0.4 OD1 A:ASP400 3.9 16.1 0.6 O A:ASN399 3.9 9.8 1.0 CD A:ARG403 4.0 19.2 1.0 O A:HOH2369 4.0 13.2 1.0 NE A:ARG403 4.1 24.0 1.0 C A:ASN399 4.1 9.6 1.0 CA A:ASP400 4.1 10.0 0.6 CA A:ASP400 4.1 9.7 0.4 N A:ASP400 4.1 9.9 1.0 CG A:ASP400 4.2 10.9 0.4 CB A:ARG403 4.3 10.8 1.0 O A:HOH2236 4.4 26.8 1.0 CB A:ASN399 4.5 9.9 1.0 O A:HOH2370 4.5 36.8 1.0 CB A:ASP400 4.6 10.8 0.6 CG A:ASP400 4.6 12.3 0.6 CG A:ARG403 4.7 13.2 1.0 CB A:ASP400 4.8 10.2 0.4 CA A:ASN399 4.9 9.4 1.0

Iodine binding site 10 out of 68 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 Iodine with other atoms in the I 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 A:I1629 b:31.8 occ:0.39 I A:IOD1656 3.2 29.2 0.1 N A:ASN312 3.6 13.7 1.0 CD A:LYS306 3.6 15.6 1.0 ND2 A:ASN312 3.9 17.2 1.0 CA A:ASN312 4.0 14.4 1.0 CG A:LYS306 4.0 11.2 1.0 CD A:PRO313 4.3 13.9 1.0 C A:GLN311 4.7 13.8 1.0 CG A:ASN312 4.7 16.5 1.0 NZ A:LYS321 4.8 32.0 1.0 CA A:GLN311 4.9 13.9 1.0 CE A:LYS306 5.0 16.2 1.0 CB A:ASN312 5.0 15.0 1.0

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