Calcium in PDB 5joo: Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature

The structure of Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature, PDB code: 5joo was solved by J.L.Thomaston, R.A.Woldeyes, J.S.Fraser, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.25 / 1.41
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	30.051, 30.051, 67.399, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.7

The structure of Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature (pdb code 5joo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature, PDB code: 5joo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:34.0 occ:1.00 OD1 A:ASP24 2.4 18.6 1.0 O A:HOH202 2.4 38.6 1.0 O A:HOH207 2.4 25.4 1.0 CG A:ASP24 3.4 19.4 1.0 OD2 A:ASP24 3.7 20.2 1.0 HD2 A:PRO25 4.0 21.0 1.0 O A:HOH217 4.1 61.3 1.0 O A:HOH203 4.1 19.0 1.0 CB A:ASP24 4.6 13.1 1.0 HB2 A:ASP24 4.7 15.7 1.0 HA A:ASP24 4.7 16.7 1.0 CD A:PRO25 4.9 17.5 1.0 HD3 A:PRO25 4.9 21.0 1.0

Calcium binding site 2 out of 2 in the Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xfel Structure of Influenza A M2 Wild Type Tm Domain at Low pH in the Lipidic Cubic Phase at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:14.3 occ:0.25 O A:SER22 2.4 13.5 1.0 O A:HOH204 2.4 17.1 1.0 H A:SER22 3.6 15.3 1.0 C A:SER22 3.6 12.8 1.0 HG A:SER22 3.8 19.2 1.0 HA A:SER23 3.9 14.8 1.0 N A:SER22 4.3 12.8 1.0 O A:HOH218 4.5 35.0 0.2 OG A:SER22 4.5 16.0 1.0 CA A:SER22 4.5 13.5 1.0 N A:SER23 4.5 12.7 1.0 CA A:SER23 4.6 12.3 1.0 HG A:SER23 4.8 15.1 1.0 O A:HOH211 4.8 36.1 1.0

J.L.Thomaston, R.A.Woldeyes, T.Nakane, A.Yamashita, T.Tanaka, K.Koiwai, A.S.Brewster, B.A.Barad, Y.Chen, T.Lemmin, M.Uervirojnangkoorn, T.Arima, J.Kobayashi, T.Masuda, M.Suzuki, M.Sugahara, N.K.Sauter, R.Tanaka, O.Nureki, K.Tono, Y.Joti, E.Nango, S.Iwata, F.Yumoto, J.S.Fraser, W.F.Degrado. Xfel Structures of the Influenza M2 Proton Channel: Room Temperature Water Networks and Insights Into Proton Conduction. Proc. Natl. Acad. Sci. V. 114 13357 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28835537
DOI: 10.1073/PNAS.1705624114