Potassium in PDB 8sfz: High Affinity Nanobodies Against Gfp

The structure of High Affinity Nanobodies Against Gfp, PDB code: 8sfz was solved by N.E.Ketaren, M.P.Rout, J.B.Bonanno, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.649, 101.731, 184.482, 90, 90, 90
R / Rfree (%)	20.7 / 23.1

The structure of High Affinity Nanobodies Against Gfp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Potassium atom in the High Affinity Nanobodies Against Gfp (pdb code 8sfz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the High Affinity Nanobodies Against Gfp, PDB code: 8sfz:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the High Affinity Nanobodies Against Gfp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of High Affinity Nanobodies Against Gfp within 5.0Å range: probe atom residue distance (Å) B Occ B:K201 b:58.5 occ:1.00 OD1 B:ASP101 2.6 41.2 1.0 O B:GLU112 2.6 53.8 1.0 OD1 B:ASP114 2.8 43.4 1.0 OD2 B:ASP101 2.9 40.1 1.0 CG B:ASP101 3.1 43.0 1.0 HB3 B:GLU112 3.2 90.3 1.0 OD2 B:ASP114 3.3 51.4 1.0 CG B:ASP114 3.3 43.7 1.0 C B:GLU112 3.8 55.3 1.0 CB B:GLU112 4.0 75.1 1.0 H B:ASP114 4.1 48.3 1.0 HB2 B:GLU112 4.2 90.3 1.0 HE22 B:GLN109 4.4 55.0 1.0 CA B:GLU112 4.4 63.3 1.0 O B:HOH322 4.4 42.8 1.0 N B:ASP114 4.4 40.1 1.0 HA B:GLU112 4.5 76.0 1.0 CB B:ASP114 4.6 42.0 1.0 HA B:TYR113 4.6 51.5 1.0 CB B:ASP101 4.6 35.3 1.0 HB2 B:ASP114 4.7 50.5 1.0 O B:HOH303 4.8 43.8 1.0 N B:TYR113 4.8 45.1 1.0 HB2 B:ASP101 4.9 42.4 1.0 C B:TYR113 4.9 39.8 1.0 CA B:ASP114 5.0 41.5 1.0 HA B:ASP114 5.0 49.9 1.0 CA B:TYR113 5.0 42.8 1.0

Potassium binding site 2 out of 3 in the High Affinity Nanobodies Against Gfp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of High Affinity Nanobodies Against Gfp within 5.0Å range: probe atom residue distance (Å) B Occ D:K301 b:40.1 occ:1.00 HE D:ARG168 2.4 44.6 1.0 HH21 D:ARG168 2.5 36.4 1.0 O D:HOH448 3.0 37.5 1.0 HB3 D:ASN146 3.1 35.8 1.0 NE D:ARG168 3.2 37.1 1.0 NH2 D:ARG168 3.3 30.3 1.0 CG D:ASN146 3.4 31.7 1.0 OD1 D:ASN146 3.7 26.8 1.0 CZ D:ARG168 3.7 38.3 1.0 CB D:ASN146 3.7 29.7 1.0 ND2 D:ASN146 3.8 30.3 1.0 HH22 D:ARG168 4.0 36.4 1.0 HD21 D:ASN146 4.0 36.5 1.0 HB2 D:ASN146 4.0 35.8 1.0 HD22 D:ASN146 4.1 36.5 1.0 O D:HOH490 4.2 44.0 1.0 HB2 D:ARG168 4.2 41.2 1.0 HD2 D:ARG168 4.3 45.1 1.0 CD D:ARG168 4.4 37.5 1.0 HD21 D:ASN170 4.7 45.0 1.0 HB3 D:ARG168 4.8 41.2 1.0 H D:SER147 4.9 33.8 1.0 CB D:ARG168 4.9 34.3 1.0

Potassium binding site 3 out of 3 in the High Affinity Nanobodies Against Gfp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of High Affinity Nanobodies Against Gfp within 5.0Å range: probe atom residue distance (Å) B Occ F:K301 b:38.1 occ:0.50 HE F:ARG168 2.3 42.6 1.0 HH21 F:ARG168 2.5 40.9 1.0 HB3 F:ASN146 3.1 39.9 1.0 NE F:ARG168 3.1 35.5 1.0 O F:HOH428 3.2 38.5 1.0 NH2 F:ARG168 3.3 34.0 1.0 CG F:ASN146 3.4 40.4 1.0 OD1 F:ASN146 3.6 37.5 1.0 CZ F:ARG168 3.7 38.5 1.0 CB F:ASN146 3.7 33.2 1.0 ND2 F:ASN146 3.8 37.7 1.0 HB2 F:ASN146 4.0 39.9 1.0 HH22 F:ARG168 4.0 40.9 1.0 HD21 F:ASN146 4.0 45.4 1.0 HD22 F:ASN146 4.1 45.4 1.0 HD2 F:ARG168 4.1 44.2 1.0 O F:HOH453 4.1 44.0 1.0 HB2 F:ARG168 4.2 43.7 1.0 CD F:ARG168 4.2 36.8 1.0 HD21 F:ASN170 4.6 52.0 1.0 HD3 F:ARG168 4.9 44.2 1.0 HB3 F:ARG168 4.9 43.7 1.0 CB F:ARG168 4.9 36.3 1.0 H F:SER147 4.9 41.2 1.0

N.E.Ketaren, M.P.Rout, S.Almo. High Affinity Nanobodies Against Gfp To Be Published.