Sodium in PDB 2yfa: X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate

The structure of X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate, PDB code: 2yfa was solved by E.Pineda-Molina, J.A.Gavira, T.Krell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.308 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	226.350, 45.850, 51.180, 90.00, 95.81, 90.00
R / Rfree (%)	20.88 / 25.13

The binding sites of Sodium atom in the X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate (pdb code 2yfa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate, PDB code: 2yfa:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1284 b:47.5 occ:1.00 O B:HOH2207 3.5 33.5 1.0 NH2 B:ARG147 3.8 42.0 1.0 ND2 B:ASN235 3.9 35.9 1.0 CZ B:ARG147 4.8 47.0 1.0 CB B:ASN235 4.8 32.9 1.0 CG B:ASN235 4.8 38.5 1.0 NE B:ARG147 4.9 47.7 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Mcps Ligand Binding Domain in Complex with Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1285 b:47.3 occ:1.00 NH2 B:ARG147 3.8 42.0 1.0 NH1 B:ARG147 4.1 42.8 1.0 CZ B:ARG147 4.4 47.0 1.0

E.Pineda-Molina, J.Reyes-Darias, J.Lacal, J.L.Ramos, J.M.Garcia-Ruiz, J.A.Gavira, T.Krell. Evidence For Chemoreceptors with Bimodular Ligand-Binding Regions Harboring Two Signal-Binding Sites. Proc.Natl.Acad.Sci.Usa V. 109 18926 2012.
ISSN: ISSN 0027-8424
PubMed: 23112148
DOI: 10.1073/PNAS.1201400109