Calcium in PDB 5kaf: Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution:
1.10.3.9;

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, F.Fuller, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, M.S.Hunter, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.12 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.731, 223.815, 330.818, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 30.3

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	70 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution (pdb code 5kaf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:45.8 occ:1.00 CA1 A:OEX601 0.0 45.8 1.0 OD1 A:ASP170 2.3 55.4 1.0 O A:ALA344 2.4 44.6 1.0 O5 A:OEX601 2.5 33.7 1.0 O1 A:OEX601 2.6 40.6 1.0 O2 A:OEX601 2.7 43.1 1.0 O A:HOH706 2.7 32.0 1.0 OE1 A:GLU189 3.1 41.7 1.0 C A:ALA344 3.2 37.7 1.0 OXT A:ALA344 3.2 33.1 1.0 CG A:ASP170 3.2 43.4 1.0 MN2 A:OEX601 3.3 46.2 1.0 OD2 A:ASP170 3.4 42.8 1.0 MN3 A:OEX601 3.4 38.7 1.0 OE2 A:GLU189 3.4 32.4 1.0 MN1 A:OEX601 3.5 37.5 1.0 CD A:GLU189 3.6 32.0 1.0 MN4 A:OEX601 3.8 43.9 1.0 O4 A:OEX601 3.8 41.1 1.0 O3 A:OEX601 4.0 38.7 1.0 OE1 A:GLN165 4.4 44.8 1.0 NH1 C:ARG357 4.4 41.6 1.0 NH2 C:ARG357 4.5 41.6 1.0 CA A:ALA344 4.5 32.2 1.0 CB A:ASP170 4.6 39.8 1.0 O A:HOH701 4.7 28.5 1.0 OH A:TYR161 4.7 29.8 1.0 CZ C:ARG357 4.9 43.9 1.0 O A:HOH702 4.9 47.8 1.0 OD1 A:ASP342 5.0 42.3 1.0 OE2 C:GLU354 5.0 41.3 1.0

Calcium binding site 2 out of 2 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ a:Ca601 b:49.0 occ:1.00 CA1 a:OEX601 0.0 49.0 1.0 OD1 a:ASP170 2.4 41.9 1.0 O a:ALA344 2.4 54.6 1.0 O5 a:OEX601 2.5 45.9 1.0 O1 a:OEX601 2.6 51.1 1.0 O a:HOH711 2.6 34.7 1.0 O2 a:OEX601 2.7 41.6 1.0 OE1 a:GLU189 3.1 58.7 1.0 CG a:ASP170 3.2 45.2 1.0 C a:ALA344 3.2 54.5 1.0 OXT a:ALA344 3.2 52.8 1.0 OD2 a:ASP170 3.3 46.5 1.0 MN2 a:OEX601 3.3 40.8 1.0 MN3 a:OEX601 3.4 44.2 1.0 MN1 a:OEX601 3.5 40.4 1.0 MN4 a:OEX601 3.8 43.7 1.0 O4 a:OEX601 3.8 46.8 1.0 CD a:GLU189 3.9 37.5 1.0 OE2 a:GLU189 4.0 35.2 1.0 O3 a:OEX601 4.0 48.8 1.0 CA a:ALA344 4.6 51.9 1.0 NH1 c:ARG357 4.6 37.5 1.0 CB a:ASP170 4.6 40.7 1.0 OE1 a:GLN165 4.8 45.2 1.0 NH2 c:ARG357 4.8 33.6 1.0 O a:HOH709 4.8 35.6 1.0 OD2 a:ASP342 4.9 51.0 1.0 OH a:TYR161 5.0 30.2 1.0

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161