Sodium in PDB 5mad: Gfp-Binding Darpin 3G61

The structure of Gfp-Binding Darpin 3G61, PDB code: 5mad was solved by S.Hansen, J.Stueber, P.Ernst, A.Koch, D.Bojar, A.Batyuk, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 1.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.420, 83.070, 162.000, 90.00, 94.59, 90.00
R / Rfree (%)	17.1 / 19.9

The binding sites of Sodium atom in the Gfp-Binding Darpin 3G61 (pdb code 5mad). 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 Gfp-Binding Darpin 3G61, PDB code: 5mad:

Sodium binding site 1 out of 1 in the Gfp-Binding Darpin 3G61


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gfp-Binding Darpin 3G61 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na202 b:31.0 occ:0.76 O E:GLY145 2.4 34.0 1.0 O E:HOH350 2.4 33.5 1.0 O H:HOH432 2.4 31.7 1.0 O H:HOH454 2.4 35.9 1.0 O E:HOH339 2.5 36.5 1.0 O E:HOH404 2.5 37.0 1.0 HZ2 H:LYS107 2.9 40.5 1.0 C E:GLY145 3.3 33.6 1.0 HA3 E:GLY145 3.3 41.5 1.0 NZ H:LYS107 3.7 33.7 1.0 O H:HOH312 3.8 48.5 1.0 O H:HOH482 3.8 40.7 1.0 HZ1 H:LYS107 3.8 40.5 1.0 CA E:GLY145 3.8 34.6 1.0 HA E:LYS146 3.9 36.8 1.0 O E:HOH316 4.1 33.6 1.0 HG2 E:LYS146 4.1 46.7 1.0 HE2 H:LYS107 4.2 40.8 1.0 HD21 H:ASN105 4.2 39.9 1.0 N E:LYS146 4.3 30.6 1.0 HZ3 H:LYS107 4.3 40.5 1.0 O H:HOH512 4.3 46.1 1.0 HA2 E:GLY145 4.3 41.5 1.0 CE H:LYS107 4.5 34.0 1.0 O E:PHE144 4.5 38.8 1.0 CA E:LYS146 4.5 30.7 1.0 OD2 E:ASP150 4.6 34.2 1.0 HE3 H:LYS107 4.7 40.8 1.0 ND2 H:ASN105 4.8 33.3 1.0 HG3 E:LYS146 4.8 46.7 1.0 CG E:LYS146 4.9 38.9 1.0 O E:HOH371 4.9 38.0 1.0 N E:GLY145 5.0 34.4 1.0

S.Hansen, J.C.Stuber, P.Ernst, A.Koch, D.Bojar, A.Batyuk, A.Pluckthun. Design and Applications of A Clamp For Green Fluorescent Protein with Picomolar Affinity. Sci Rep V. 7 16292 2017.
ISSN: ESSN 2045-2322
PubMed: 29176615
DOI: 10.1038/S41598-017-15711-Z