Sodium in PDB 6tk2: Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets

The structure of Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets, PDB code: 6tk2 was solved by P.Skopintsev, D.Ehrenberg, T.Weinert, D.James, R.Kar, P.Johnson, D.Ozerov, A.Furrer, I.Martiel, F.Dworkowski, K.Nass, G.Knopp, C.Cirelli, D.Gashi, S.Mous, M.Wranik, T.Gruhl, D.Kekilli, S.Bruenle, X.Deupi, G.F.X.Schertler, R.Benoit, V.Panneels, P.Nogly, I.Schapiro, C.Milne, J.Heberle, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.36 / 2.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	41.540, 84.480, 235.560, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 32.4

The binding sites of Sodium atom in the Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets (pdb code 6tk2). 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 Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets, PDB code: 6tk2:

Sodium binding site 1 out of 1 in the Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Femtosecond to Millisecond Structural Changes in A Light-Driven Sodium Pump: 1MS Structure of KR2 with Extrapolated, Light and Dark Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Na328 b:47.0 occ:1.00 OD1 A:ASN112 2.5 28.9 1.0 OD2 A:ASP251 2.5 38.2 1.0 OD1 A:ASP251 2.9 35.0 1.0 CG A:ASP251 3.0 37.8 1.0 CD2 A:LEU75 3.2 31.6 1.0 NE1 A:TRP113 3.5 25.7 1.0 CG A:ASN112 3.6 36.1 1.0 CE A:LYS255 3.7 25.1 1.0 NH1 A:ARG109 3.7 46.6 1.0 CG A:ARG109 3.8 37.0 1.0 CD1 A:TRP113 3.9 30.5 1.0 CG A:LEU75 4.0 31.4 1.0 CD1 A:LEU75 4.0 29.2 1.0 CB A:ASP251 4.3 27.5 1.0 NZ A:LYS255 4.4 21.5 1.0 CB A:ASN112 4.4 27.6 1.0 C15 A:RET301 4.5 24.7 1.0 O A:ARG109 4.6 33.5 1.0 ND2 A:ASN112 4.6 24.3 1.0 CE2 A:TRP113 4.7 28.7 1.0 CZ A:ARG109 4.7 47.9 1.0 CD A:ARG109 4.7 34.6 1.0 OH A:TYR218 4.8 39.3 1.0 CA A:ARG109 4.9 38.2 1.0 CD A:LYS255 4.9 30.0 1.0 CB A:ARG109 5.0 35.8 1.0

P.Skopintsev, D.Ehrenberg, T.Weinert, D.James, R.Kar, P.Johnson, D.Ozerov, A.Furrer, I.Martiel, F.Dworkowski, K.Nass, G.Knopp, C.Cirelli, D.Gashi, S.Mous, M.Wranik, T.Gruhl, D.Kekilli, S.Bruenle, X.Deupi, G.Schertler, R.Benoit, V.Panneels, P.Nogly, I.Schapiro, C.Milne, J.Heberle, J.Standfuss. Femtosecond-to-Millisecond Structural Changes in A Light-Driven Sodium Pump Nature 2020.
ISSN: ESSN 1476-4687