Potassium in PDB 5vnv: Crystal Structure of Nb.B201

The structure of Crystal Structure of Nb.B201, PDB code: 5vnv was solved by A.C.Kruse, C.Mcmahon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 1.40
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.751, 106.751, 52.232, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.4

The binding sites of Potassium atom in the Crystal Structure of Nb.B201 (pdb code 5vnv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Nb.B201, PDB code: 5vnv:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of Nb.B201


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Nb.B201 within 5.0Å range: probe atom residue distance (Å) B Occ A:K204 b:17.9 occ:1.00 O A:ASN73 2.6 18.1 1.0 OD1 A:ASN76 2.7 17.7 1.0 O A:HOH327 2.7 22.9 1.0 O A:HOH378 2.8 24.5 1.0 O A:ILE28 2.8 18.4 1.0 O A:HOH332 3.1 19.8 1.0 CE1 A:TYR27 3.2 21.0 1.0 CD1 A:TYR27 3.4 20.7 1.0 CG A:ASN76 3.7 17.0 1.0 C A:ASN73 3.7 15.4 1.0 OD1 A:ASP30 3.7 20.2 1.0 C A:ILE28 3.9 18.7 1.0 N A:ILE28 4.1 16.6 1.0 CZ A:TYR27 4.2 21.4 1.0 ND2 A:ASN76 4.3 21.0 1.0 O A:HOH387 4.5 18.2 1.0 CA A:ASN73 4.5 15.4 1.0 CG A:TYR27 4.5 19.6 1.0 CA A:ILE28 4.5 17.0 1.0 O A:HOH417 4.6 30.2 1.0 N A:ALA74 4.7 15.4 1.0 N A:ASN76 4.7 16.4 1.0 O A:ALA74 4.7 20.6 1.0 CA A:ALA74 4.7 16.9 1.0 OH A:TYR27 4.7 26.5 1.0 CA A:ASN76 4.8 15.9 1.0 C A:ALA74 4.8 17.5 1.0 CB A:ASN76 4.8 16.1 1.0 CB A:ASN73 4.8 16.6 1.0 CG A:ASP30 4.8 22.1 1.0 CB A:ILE28 4.9 16.1 1.0 N A:SER29 5.0 16.8 1.0 C A:TYR27 5.0 18.0 1.0 CA A:TYR27 5.0 18.6 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Nb.B201


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Nb.B201 within 5.0Å range: probe atom residue distance (Å) B Occ A:K205 b:23.5 occ:0.44 O A:THR57 2.6 15.5 1.0 O A:HOH358 2.7 22.3 1.0 O A:HOH303 3.6 49.2 1.0 C A:THR57 3.7 13.4 1.0 OG1 A:THR57 3.9 15.9 1.0 O1 A:FMT208 4.0 21.1 1.0 O2 A:FMT208 4.1 26.3 1.0 N A:THR57 4.4 14.1 1.0 C A:FMT208 4.5 25.0 1.0 CA A:THR57 4.5 12.9 1.0 N A:TYR58 4.6 12.9 1.0 CA A:TYR58 4.7 13.2 1.0 O A:HOH406 4.7 40.3 1.0 CB A:THR57 4.9 14.7 1.0 O A:HOH330 4.9 19.9 1.0 CD1 A:TYR58 5.0 15.4 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Nb.B201


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Nb.B201 within 5.0Å range: probe atom residue distance (Å) B Occ A:K206 b:44.3 occ:1.00 O A:GLU120 2.6 34.7 1.0 OE1 A:GLN13 3.0 39.3 1.0 C A:GLU120 3.2 43.3 1.0 CA A:GLU120 3.3 50.7 1.0 CD A:GLN13 3.7 33.2 1.0 CB A:GLU120 3.7 56.0 1.0 NE2 A:GLN13 4.1 29.4 1.0 O A:LEU119 4.7 35.6 1.0 N A:GLU120 4.7 50.0 1.0 CG A:GLN13 4.8 28.0 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Nb.B201


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Nb.B201 within 5.0Å range: probe atom residue distance (Å) B Occ A:K207 b:22.1 occ:1.00 O A:HIS53 2.7 16.1 1.0 OG1 A:THR55 2.7 15.5 1.0 O A:HOH414 2.8 35.0 1.0 OD1 A:ASN56 2.9 18.8 1.0 C A:HIS53 3.9 14.5 1.0 CG A:ASN56 3.9 16.2 1.0 CB A:THR55 4.0 14.7 1.0 N A:THR55 4.1 12.6 1.0 CB A:HIS53 4.1 15.4 1.0 ND2 A:ASN56 4.3 16.6 1.0 CG2 A:THR55 4.4 17.2 1.0 CA A:THR55 4.5 14.2 1.0 N A:ASN56 4.6 13.9 1.0 CA A:HIS53 4.7 13.2 1.0 C A:THR55 4.7 15.7 1.0 O A:HOH390 4.8 33.8 1.0 N A:GLY54 4.9 14.3 1.0

C.Mcmahon, A.S.Baier, R.Pascolutti, M.Wegrecki, S.Zheng, J.X.Ong, S.C.Erlandson, D.Hilger, S.G.F.Rasmussen, A.M.Ring, A.Manglik, A.C.Kruse. Yeast Surface Display Platform For Rapid Discovery of Conformationally Selective Nanobodies. Nat. Struct. Mol. Biol. V. 25 289 2018.
ISSN: ESSN 1545-9985
PubMed: 29434346
DOI: 10.1038/S41594-018-0028-6