Calcium in PDB 5tis: Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

Enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

All present enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.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.V.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.Braeuer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, 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.Watermann, 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, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.870, 223.140, 310.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 5tis:

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex (pdb code 5tis). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5tis

Go back to Calcium Binding Sites List in 5tis
Calcium binding site 1 out of 2 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:41.3
occ:1.00
CA1 A:OEX601 0.0 41.3 1.0
O A:ALA344 2.4 34.8 1.0
O A:HOH714 2.5 38.0 1.0
O1 A:OEX601 2.5 32.1 1.0
O A:HOH772 2.6 29.4 1.0
O5 A:OEX601 2.7 39.1 1.0
OD1 A:ASP170 2.7 39.1 1.0
O2 A:OEX601 2.7 32.2 1.0
OE1 A:GLU189 3.2 41.5 1.0
CG A:ASP170 3.2 35.1 1.0
C A:ALA344 3.3 41.2 1.0
MN2 A:OEX601 3.4 35.1 1.0
OXT A:ALA344 3.4 34.6 1.0
OD2 A:ASP170 3.5 35.6 1.0
MN3 A:OEX601 3.5 34.4 1.0
MN1 A:OEX601 3.5 33.4 1.0
OE2 A:GLU189 3.8 40.3 1.0
O4 A:OEX601 3.9 36.2 1.0
CD A:GLU189 3.9 35.6 1.0
MN4 A:OEX601 3.9 40.5 1.0
O3 A:OEX601 4.1 34.4 0.8
NH1 C:ARG357 4.4 34.1 1.0
CB A:ASP170 4.4 33.0 1.0
O A:HOH780 4.5 47.0 1.0
O A:HOH746 4.5 35.7 1.0
OE1 A:GLN165 4.6 43.6 1.0
NH2 C:ARG357 4.6 33.0 1.0
CA A:ALA344 4.6 32.4 1.0
OH A:TYR161 4.7 33.0 1.0
O A:HOH723 4.7 36.2 1.0
OE2 C:GLU354 5.0 38.2 1.0
CZ C:ARG357 5.0 36.6 1.0

Calcium binding site 2 out of 2 in 5tis

Go back to Calcium Binding Sites List in 5tis
Calcium binding site 2 out of 2 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:42.4
occ:1.00
CA1 a:OEX601 0.0 42.4 1.0
O a:HOH738 2.4 33.9 1.0
O5 a:OEX601 2.5 33.6 1.0
O2 a:OEX601 2.5 28.8 1.0
O a:ALA344 2.5 38.1 1.0
O1 a:OEX601 2.6 31.2 1.0
O a:HOH779 2.6 33.5 1.0
OD1 a:ASP170 2.8 37.4 1.0
OE1 a:GLU189 3.1 38.8 1.0
CG a:ASP170 3.3 36.2 1.0
MN2 a:OEX601 3.4 32.6 1.0
MN3 a:OEX601 3.4 32.9 1.0
OD2 a:ASP170 3.4 34.3 1.0
MN1 a:OEX601 3.4 32.4 1.0
C a:ALA344 3.5 34.7 1.0
OE2 a:GLU189 3.6 37.3 1.0
OXT a:ALA344 3.7 32.4 1.0
CD a:GLU189 3.7 35.4 1.0
MN4 a:OEX601 3.8 35.8 1.0
O3 a:OEX601 4.0 33.5 1.0
O4 a:OEX601 4.1 35.4 1.0
O a:HOH717 4.3 28.8 1.0
NH1 c:ARG357 4.5 28.8 1.0
CB a:ASP170 4.5 29.8 1.0
O a:HOH739 4.5 40.0 1.0
O a:HOH772 4.7 37.6 1.0
OH a:TYR161 4.8 33.6 1.0
NH2 c:ARG357 4.8 33.9 1.0
OE1 a:GLN165 4.8 33.6 1.0
CA a:ALA344 4.8 33.3 1.0

Reference:

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
Page generated: Sat Dec 12 05:44:37 2020

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