Sodium in PDB 2ya0: Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua

The structure of Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua, PDB code: 2ya0 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 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.574, 75.196, 87.038, 90.00, 97.31, 90.00
R / Rfree (%)	17.2 / 22.7

The structure of Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua (pdb code 2ya0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua, PDB code: 2ya0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Catalytic Module of the 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 Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1701 b:17.9 occ:1.00 O A:HOH2675 3.0 35.5 1.0 O A:HOH2545 3.1 26.9 1.0 O A:HOH2601 3.2 22.8 1.0 N A:LEU442 3.3 21.1 1.0 O A:HOH2598 3.4 19.1 1.0 CD1 A:ILE447 3.7 20.8 1.0 CB A:ASN441 3.7 19.6 1.0 CG A:LEU442 3.8 21.3 1.0 CB A:LEU442 3.8 19.2 1.0 CB A:GLU397 3.9 25.4 1.0 CG A:GLU397 4.0 24.7 1.0 CA A:ASN441 4.1 20.5 1.0 CA A:LEU442 4.2 20.4 1.0 C A:ASN441 4.2 21.9 1.0 CD1 A:LEU442 4.3 18.5 1.0 OD1 A:ASN441 4.4 23.2 1.0 O A:HOH2594 4.4 23.3 1.0 CG A:ASN441 4.4 22.1 1.0 CG1 A:ILE447 4.6 22.2 1.0 CB A:HIS533 4.7 21.4 1.0 O A:LEU442 4.8 18.5 1.0 CE1 A:HIS516 4.9 22.6 1.0 CA A:GLU397 4.9 25.3 1.0 CB A:ILE447 5.0 22.2 1.0

Sodium binding site 2 out of 2 in the Catalytic Module of the 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 Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1702 b:12.9 occ:1.00 ND1 A:HIS486 3.2 17.6 1.0 O A:HOH2625 3.2 19.3 1.0 N A:LEU444 3.3 20.3 1.0 CA A:GLN489 3.5 18.1 1.0 CB A:GLN489 3.6 18.9 1.0 CB A:THR443 3.6 20.9 1.0 N A:GLN489 3.6 18.3 1.0 CB A:ALA437 3.8 18.2 1.0 CA A:THR443 3.8 19.8 1.0 CB A:HIS486 4.0 19.5 1.0 CG A:HIS486 4.0 19.8 1.0 CB A:LEU444 4.0 20.9 1.0 C A:THR443 4.0 20.4 1.0 CE1 A:HIS486 4.2 22.0 1.0 CG A:GLN489 4.2 19.5 1.0 C A:GLY488 4.2 19.0 1.0 CA A:LEU444 4.2 20.3 1.0 CG2 A:THR443 4.3 19.8 1.0 O A:HIS486 4.6 17.6 1.0 O A:GLY488 4.6 18.4 1.0 OG1 A:THR443 4.7 19.9 1.0 O A:SER487 4.8 17.9 1.0 CB A:ARG493 4.8 19.2 1.0 O A:ARG493 4.8 21.3 1.0 OE1 A:GLN489 4.8 18.1 1.0 C A:GLN489 4.9 19.9 1.0 N A:PHE445 5.0 21.1 1.0 CD A:GLN489 5.0 18.7 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