Sodium in PDB 2ya1: Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua

The structure of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua, PDB code: 2ya1 was solved by A.Lammerts Van Bueren, E.Ficko-Blean, B.Pluvinage, J.H.Hehemann, M.A.Higgins, L.Deng, A.D.Ogunniyi, U.H.Stroeher, N.E.Warry, R.D.Burke, M.Czjzek, J.C.Paton, 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)	20.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.137, 86.429, 193.225, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.5

The binding sites of Sodium atom in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua (pdb code 2ya1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua, PDB code: 2ya1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2153 b:7.2 occ:1.00 O A:HOH3515 3.1 17.6 1.0 ND1 A:HIS941 3.2 20.5 1.0 N A:LEU899 3.3 19.0 1.0 CA A:GLN944 3.5 20.8 1.0 CB A:GLN944 3.7 20.9 1.0 CB A:THR898 3.7 17.9 1.0 N A:GLN944 3.7 19.9 1.0 CB A:ALA892 3.8 22.5 1.0 CA A:THR898 3.9 18.6 1.0 CB A:LEU899 4.0 19.6 1.0 CG A:GLN944 4.1 20.5 1.0 C A:THR898 4.1 18.7 1.0 CG A:HIS941 4.1 21.4 1.0 CB A:HIS941 4.1 21.3 1.0 CE1 A:HIS941 4.2 18.6 1.0 CA A:LEU899 4.2 19.2 1.0 C A:GLY943 4.3 19.9 1.0 CG2 A:THR898 4.3 16.6 1.0 O A:GLY943 4.5 20.5 1.0 O A:HIS941 4.6 21.6 1.0 CB A:ARG948 4.7 18.8 1.0 O A:ARG948 4.8 19.9 1.0 OG1 A:THR898 4.8 18.5 1.0 OE1 A:GLN944 4.8 22.1 1.0 O A:SER942 4.8 18.8 1.0 CD A:GLN944 4.9 22.0 1.0 C A:GLN944 4.9 22.0 1.0 N A:PHE900 4.9 18.9 1.0

Sodium binding site 2 out of 5 in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2154 b:33.2 occ:1.00 O A:HOH3470 3.7 40.6 1.0 ND2 A:ASN878 3.8 33.5 1.0 NH1 A:ARG810 3.8 34.4 1.0 CB A:ASN878 3.9 33.7 1.0 O2 A:GLC2148 3.9 41.5 1.0 O A:HOH3450 3.9 45.6 1.0 O3 A:GLC2148 4.0 38.6 1.0 O A:HOH3466 4.2 27.4 1.0 CG A:ASN878 4.4 33.2 1.0 C2 A:GLC2148 4.7 39.7 1.0 O A:HOH3471 4.8 36.7 1.0 O A:ASN878 4.8 34.3 1.0 C3 A:GLC2148 4.9 38.8 1.0 CZ A:ARG810 5.0 35.9 1.0

Sodium binding site 3 out of 5 in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2155 b:35.2 occ:1.00 O A:HOH3344 3.4 38.2 1.0 NE A:ARG652 3.6 25.1 1.0 NH2 A:ARG652 3.9 23.0 1.0 CZ A:ARG652 4.2 23.9 1.0 O A:HOH3162 4.6 42.2 1.0 CD A:ARG652 4.6 28.6 1.0 CD1 A:PHE612 4.8 25.1 1.0 CB A:ALA605 4.8 34.9 1.0

Sodium binding site 4 out of 5 in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2156 b:49.5 occ:1.00 O A:HOH3325 2.9 46.9 1.0 NZ A:LYS583 3.6 44.6 1.0 NH1 A:ARG1035 3.6 41.4 1.0 CD A:LYS583 4.1 41.1 1.0 O A:HOH3622 4.2 38.8 1.0 CE A:LYS583 4.2 42.7 1.0 O A:HOH3620 4.4 44.7 1.0 CB A:ASP1032 4.6 37.1 1.0 CZ A:ARG1035 4.6 40.9 1.0 NH2 A:ARG1035 4.7 41.0 1.0

Sodium binding site 5 out of 5 in the Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Product Complex of A Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2157 b:54.8 occ:1.00 O A:HOH3175 2.2 32.6 1.0 OD1 A:ASP353 2.9 51.9 1.0 O A:HOH3083 2.9 46.1 1.0 O A:HOH3174 3.9 41.9 1.0 CG A:ASP353 4.0 52.0 1.0 CG2 A:THR346 4.0 40.4 1.0 OD1 A:ASN347 4.1 38.5 1.0 CA A:ASP353 4.2 49.6 1.0 O A:HOH3184 4.3 54.4 1.0 O A:HOH3185 4.4 52.2 1.0 NH2 A:ARG355 4.4 55.4 1.0 CB A:THR346 4.5 39.0 1.0 O A:HIS352 4.6 45.2 1.0 CB A:ASP353 4.6 50.1 1.0 N A:ASP353 4.7 47.7 1.0 O A:VAL351 4.8 42.8 1.0 C A:HIS352 4.9 45.7 1.0 CG A:ASN347 5.0 37.5 1.0 OD2 A:ASP353 5.0 54.2 1.0

A.Lammerts Van Bueren, E.Ficko-Blean, B.Pluvinage, J.Hehemann, M.A.Higgins, L.Deng, A.D.Ogunniyi, U.H.Stroeher, N.El Warry, R.D.Burke, M.Czjzek, J.C.Paton, D.J.Vocadlo, A.B.Boraston. The Conformation and Function of A Multimodular Glycogen-Degrading Pneumococcal Virulence Factor. Structure V. 19 640 2011.
ISSN: ISSN 0969-2126
PubMed: 21565699
DOI: 10.1016/J.STR.2011.03.001