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Sodium in PDB 2ya2: Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor.

Protein crystallography data

The structure of Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor., PDB code: 2ya2 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 / 2.37
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.779, 75.803, 88.089, 90.00, 97.72, 90.00
R / Rfree (%) 20.8 / 26

Other elements in 2ya2:

The structure of Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor. also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor. (pdb code 2ya2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor., PDB code: 2ya2:

Sodium binding site 1 out of 1 in 2ya2

Go back to Sodium Binding Sites List in 2ya2
Sodium binding site 1 out of 1 in the Catalytic Module of the Multi-Modular Glycogen-Degrading Pneumococcal Virulence Factor Spua in Complex with An Inhibitor.


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 in Complex with An Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1692

b:13.0
occ:1.00
O A:HOH2157 3.1 38.6 1.0
O A:HOH2135 3.1 22.2 1.0
O A:HOH2154 3.2 22.2 1.0
N A:LEU442 3.4 20.7 1.0
CB A:ASP441 3.7 21.0 1.0
CD1 A:ILE447 3.8 25.9 1.0
CB A:LEU442 3.8 19.7 1.0
CB A:GLU397 3.8 30.8 1.0
OD1 A:ASP441 4.1 23.0 1.0
CA A:LEU442 4.2 19.8 1.0
CA A:ASP441 4.3 20.8 1.0
CD2 A:LEU442 4.3 19.7 1.0
CG A:ASP441 4.3 22.4 1.0
C A:ASP441 4.3 20.5 1.0
CG1 A:ILE447 4.4 24.8 1.0
O A:HOH2134 4.5 29.7 1.0
CG A:LEU442 4.5 20.1 1.0
CG A:GLU397 4.6 31.7 1.0
O A:LEU442 4.8 19.7 1.0
CE1 A:HIS516 4.9 24.5 1.0
CB A:HIS533 5.0 20.3 1.0
CA A:GLU397 5.0 30.1 1.0
CB A:ILE447 5.0 24.6 1.0

Reference:

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
Page generated: Tue Dec 15 06:00:26 2020

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