Sodium in PDB 3h09: The Structure of Haemophilus Influenzae IGA1 Protease

All present enzymatic activity of The Structure of Haemophilus Influenzae IGA1 Protease:
3.4.21.72;

The structure of The Structure of Haemophilus Influenzae IGA1 Protease, PDB code: 3h09 was solved by T.A.Johnson, J.Qiu, A.G.Plaut, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.18 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.385, 131.872, 111.813, 90.00, 113.11, 90.00
R / Rfree (%)	16.1 / 19

The binding sites of Sodium atom in the The Structure of Haemophilus Influenzae IGA1 Protease (pdb code 3h09). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of Haemophilus Influenzae IGA1 Protease, PDB code: 3h09:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2300 b:20.6 occ:1.00 O A:THR338 2.2 4.1 1.0 O A:HOH1047 2.3 18.2 1.0 O A:HOH1873 2.3 19.2 1.0 O A:HOH1631 2.4 12.8 1.0 O A:ASP335 2.5 4.3 1.0 O A:HOH1366 2.5 15.0 1.0 O A:HOH1763 3.4 34.6 1.0 C A:THR338 3.5 3.7 1.0 C A:ASP335 3.7 4.7 1.0 OD1 A:ASP335 4.1 11.8 1.0 CG2 A:THR338 4.1 8.9 1.0 O A:LYS336 4.1 5.1 1.0 N A:THR338 4.2 4.0 1.0 CG A:ASP335 4.3 9.6 1.0 C A:LYS336 4.3 4.8 1.0 OD2 A:ASP335 4.3 12.8 1.0 CA A:THR338 4.3 5.3 1.0 O A:HOH1532 4.4 17.9 1.0 N A:ALA339 4.4 3.0 1.0 C A:ALA339 4.5 4.4 1.0 CA A:LYS336 4.5 4.7 1.0 O A:ALA339 4.5 5.6 1.0 N A:LYS336 4.5 3.9 1.0 CA A:ALA339 4.5 3.7 1.0 CA A:ASP335 4.6 5.8 1.0 CB A:THR338 4.8 6.2 1.0 O A:HOH1673 4.8 25.7 1.0 O A:HOH1546 4.9 22.0 1.0 N A:ASP337 4.9 4.1 1.0 N A:GLY340 5.0 4.2 1.0

Sodium binding site 2 out of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2100 b:28.7 occ:1.00 O B:HOH1569 2.3 16.8 1.0 O B:THR338 2.3 5.6 1.0 O B:HOH1192 2.3 21.2 1.0 O B:ASP335 2.3 6.2 1.0 O B:HOH1496 2.4 18.7 1.0 O B:HOH1441 2.5 12.8 1.0 O B:HOH1764 3.5 23.7 1.0 C B:ASP335 3.5 6.5 1.0 C B:THR338 3.6 5.1 1.0 CG2 B:THR338 4.0 6.4 1.0 O B:LYS336 4.0 6.0 1.0 OD1 B:ASP335 4.1 14.2 1.0 CG B:ASP335 4.2 11.2 1.0 OD2 B:ASP335 4.2 14.6 1.0 O B:HOH1167 4.2 17.5 1.0 C B:LYS336 4.2 4.9 1.0 N B:THR338 4.2 4.0 1.0 CA B:LYS336 4.4 5.6 1.0 N B:LYS336 4.4 5.2 1.0 CA B:THR338 4.4 5.1 1.0 O B:HOH1765 4.5 27.1 1.0 CA B:ASP335 4.5 7.4 1.0 N B:ALA339 4.5 3.9 1.0 O B:ALA339 4.6 5.7 1.0 C B:ALA339 4.6 4.6 1.0 CA B:ALA339 4.6 4.8 1.0 O B:HOH1469 4.7 26.1 1.0 CB B:THR338 4.8 5.8 1.0 N B:ASP337 4.9 4.3 1.0 CB B:ASP335 5.0 7.8 1.0

Sodium binding site 3 out of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2200 b:30.5 occ:1.00 O B:HOH1535 2.3 22.8 1.0 O B:HOH1725 2.3 16.0 1.0 O B:VAL491 2.3 7.3 1.0 O B:HOH1751 2.4 13.6 1.0 O B:HOH1228 2.5 24.9 1.0 O B:HOH1203 2.7 21.0 1.0 C B:VAL491 3.5 6.9 1.0 O B:HOH1577 4.0 26.8 1.0 O B:LYS512 4.1 9.7 1.0 O B:HOH1077 4.1 29.6 1.0 N B:VAL491 4.2 8.3 1.0 CA B:VAL491 4.4 7.8 1.0 O B:HOH1738 4.4 18.6 1.0 OE2 B:GLU467 4.4 17.7 1.0 CB B:LYS492 4.4 4.8 1.0 N B:LYS492 4.5 5.7 1.0 CG1 B:VAL491 4.5 9.3 1.0 CA B:LYS492 4.6 5.1 1.0

Sodium binding site 4 out of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2300 b:25.1 occ:1.00 O B:HOH1045 2.3 21.5 1.0 O B:HOH1810 2.3 22.4 1.0 O B:HOH1397 2.4 13.2 1.0 OG1 B:THR52 2.5 9.2 1.0 O B:THR52 2.5 6.1 1.0 C B:THR52 3.3 6.1 1.0 O B:HOH1519 3.4 34.1 1.0 N B:THR52 3.6 6.2 1.0 CB B:THR52 3.6 6.9 1.0 CA B:THR52 3.7 6.6 1.0 O B:HOH1416 4.1 35.8 1.0 O B:HOH1217 4.2 26.5 1.0 ND2 B:ASN53 4.2 4.0 1.0 N B:ASN53 4.4 4.8 1.0 CB B:ASN53 4.5 5.3 1.0 CG2 B:THR52 4.8 7.4 1.0 CG B:ASN53 4.8 3.8 1.0 CA B:ASN53 4.9 4.3 1.0 C B:ALA51 4.9 5.5 1.0 O B:ASN53 5.0 4.2 1.0

T.A.Johnson, J.Qiu, A.G.Plaut, T.Holyoak. Active-Site Gating Regulates Substrate Selectivity in A Chymotrypsin-Like Serine Protease the Structure of Haemophilus Influenzae Immunoglobulin A1 Protease. J.Mol.Biol. V. 389 559 2009.
ISSN: ISSN 0022-2836
PubMed: 19393662
DOI: 10.1016/J.JMB.2009.04.041