Sodium in PDB 5ma5: Gfp-Binding Darpin Fusion GC_K11

The structure of Gfp-Binding Darpin Fusion GC_K11, PDB code: 5ma5 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)	44.25 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.710, 60.280, 90.240, 86.94, 79.13, 89.35
R / Rfree (%)	15.4 / 18.4

The binding sites of Sodium atom in the Gfp-Binding Darpin Fusion GC_K11 (pdb code 5ma5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Gfp-Binding Darpin Fusion GC_K11, PDB code: 5ma5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Gfp-Binding Darpin Fusion GC_K11


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 Fusion GC_K11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:37.7 occ:1.00 O A:HOH733 2.2 40.2 1.0 O1 A:CIT401 2.3 43.0 1.0 O A:GLY58 2.3 30.9 1.0 O7 A:CIT401 2.3 43.3 1.0 HO7 A:CIT401 3.0 51.9 1.0 C1 A:CIT401 3.3 43.9 1.0 H A:LEU60 3.3 36.3 1.0 C3 A:CIT401 3.4 42.8 1.0 H42 A:CIT401 3.5 53.3 1.0 C A:GLY58 3.5 29.9 1.0 C2 A:CIT401 3.8 43.4 1.0 O4 A:CIT401 3.8 45.1 1.0 HB2 A:LEU60 3.8 38.9 1.0 C4 A:CIT401 3.8 44.4 1.0 HB3 A:LEU60 3.9 38.9 1.0 O A:HOH643 4.0 42.9 1.0 HA A:HIS59 4.0 36.0 1.0 C5 A:CIT401 4.0 45.1 1.0 H21 A:CIT401 4.1 52.1 1.0 N A:LEU60 4.1 30.3 1.0 HA3 A:GLY58 4.1 35.8 1.0 CB A:LEU60 4.3 32.4 1.0 CA A:GLY58 4.3 29.8 1.0 O2 A:CIT401 4.4 43.3 1.0 HD11 A:ILE95 4.4 36.4 1.0 O A:HOH597 4.4 41.6 1.0 HA2 A:GLY58 4.4 35.8 1.0 N A:HIS59 4.5 28.7 1.0 CA A:HIS59 4.6 30.0 1.0 C6 A:CIT401 4.7 37.7 1.0 H22 A:CIT401 4.8 52.1 1.0 HD12 A:ILE95 4.9 36.4 1.0 H41 A:CIT401 4.9 53.3 1.0 CA A:LEU60 4.9 30.8 1.0 C A:HIS59 4.9 29.4 1.0 O3 A:CIT401 4.9 44.4 1.0 O5 A:CIT401 5.0 34.3 1.0

Sodium binding site 2 out of 2 in the Gfp-Binding Darpin Fusion GC_K11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gfp-Binding Darpin Fusion GC_K11 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:35.4 occ:1.00 O C:GLY58 2.2 26.4 1.0 O7 C:CIT402 2.3 39.3 1.0 O1 C:CIT402 2.3 35.8 1.0 O C:HOH616 2.4 51.7 1.0 HO7 C:CIT402 2.9 47.1 1.0 H C:LEU60 3.1 28.6 1.0 C1 C:CIT402 3.4 37.4 1.0 C3 C:CIT402 3.4 40.0 1.0 C C:GLY58 3.5 26.9 1.0 HB2 C:LEU60 3.6 31.2 1.0 H42 C:CIT402 3.7 53.1 1.0 HB3 C:LEU60 3.7 31.2 1.0 C2 C:CIT402 3.8 39.0 1.0 O3 C:CIT402 3.8 46.8 1.0 HA C:HIS59 3.9 30.7 1.0 N C:LEU60 3.9 23.8 1.0 H21 C:CIT402 3.9 46.8 1.0 O C:HOH519 3.9 34.6 1.0 C4 C:CIT402 3.9 44.2 1.0 CB C:LEU60 4.1 26.0 1.0 C5 C:CIT402 4.2 46.6 1.0 HA3 C:GLY58 4.2 33.4 1.0 CA C:GLY58 4.3 27.9 1.0 N C:HIS59 4.4 25.4 1.0 HD11 C:ILE95 4.4 36.5 1.0 HA2 C:GLY58 4.4 33.4 1.0 CA C:HIS59 4.5 25.6 1.0 O2 C:CIT402 4.5 36.7 1.0 O C:HOH565 4.5 43.6 1.0 CA C:LEU60 4.6 25.5 1.0 C6 C:CIT402 4.7 35.6 1.0 C C:HIS59 4.7 23.8 1.0 H22 C:CIT402 4.8 46.8 1.0 O5 C:CIT402 4.9 33.4 1.0 HD1 C:HIS59 4.9 32.9 1.0 H41 C:CIT402 5.0 53.1 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