Atomistry » Calcium » PDB 5kai-5klg » 5kai
Atomistry »
  Calcium »
    PDB 5kai-5klg »
      5kai »

Calcium in PDB 5kai: NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

Enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

All present enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai 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) 43.57 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.911, 224.268, 330.996, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 30

Other elements in 5kai:

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution 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 NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution (pdb code 5kai). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5kai

Go back to Calcium Binding Sites List in 5kai
Calcium binding site 1 out of 2 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution 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
OD1 A:ASP170 2.3 54.0 1.0
O A:ALA344 2.4 55.8 1.0
O5 A:OEX601 2.5 56.4 1.0
O A:HOH703 2.6 41.1 1.0
O1 A:OEX601 2.6 56.5 1.0
O2 A:OEX601 2.7 48.5 1.0
OE1 A:GLU189 3.1 47.5 1.0
MN2 A:OEX601 3.3 51.3 1.0
C A:ALA344 3.3 47.6 1.0
OE2 A:GLU189 3.4 49.8 1.0
CG A:ASP170 3.4 50.0 1.0
MN3 A:OEX601 3.4 59.5 1.0
MN1 A:OEX601 3.5 54.3 1.0
OXT A:ALA344 3.5 48.8 1.0
CD A:GLU189 3.6 47.3 1.0
MN4 A:OEX601 3.8 60.4 1.0
O4 A:OEX601 3.8 52.8 1.0
OD2 A:ASP170 3.9 52.0 1.0
O3 A:OEX601 4.0 56.4 1.0
O A:HOH707 4.2 47.7 1.0
OE1 A:GLN165 4.4 44.4 1.0
NH1 C:ARG357 4.5 40.7 1.0
CB A:ASP170 4.5 44.1 1.0
OH A:TYR161 4.6 39.4 1.0
CA A:ALA344 4.7 45.6 1.0
O A:HOH705 4.9 40.4 1.0
OE2 C:GLU354 4.9 55.9 1.0
OD2 A:ASP342 4.9 50.2 1.0
O A:HOH710 4.9 47.8 1.0
OE1 C:GLU354 5.0 51.0 1.0

Calcium binding site 2 out of 2 in 5kai

Go back to Calcium Binding Sites List in 5kai
Calcium binding site 2 out of 2 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca702

b:47.9
occ:1.00
CA1 a:OEX702 0.0 47.9 1.0
OD1 a:ASP170 2.3 56.5 1.0
O a:ALA344 2.4 58.6 1.0
O5 a:OEX702 2.5 52.6 1.0
O1 a:OEX702 2.6 60.2 1.0
O2 a:OEX702 2.7 53.0 1.0
O a:HOH808 2.9 49.7 1.0
OE1 a:GLU189 3.1 55.3 1.0
CG a:ASP170 3.2 49.1 1.0
MN2 a:OEX702 3.3 59.4 1.0
OD2 a:ASP170 3.3 54.2 1.0
C a:ALA344 3.3 51.8 1.0
MN3 a:OEX702 3.4 51.0 1.0
OXT a:ALA344 3.5 50.5 1.0
MN1 a:OEX702 3.5 48.3 1.0
MN4 a:OEX702 3.8 56.0 1.0
O4 a:OEX702 3.8 44.7 1.0
O3 a:OEX702 4.0 58.2 1.0
CD a:GLU189 4.0 46.9 1.0
OE2 a:GLU189 4.3 53.5 1.0
CB a:ASP170 4.5 44.2 1.0
NH1 c:ARG357 4.5 35.4 1.0
OH a:TYR161 4.7 41.7 1.0
OE1 a:GLN165 4.7 54.9 1.0
CA a:ALA344 4.8 46.9 1.0
NH2 c:ARG357 4.8 45.0 1.0
OE2 c:GLU354 5.0 52.5 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: Wed Jul 9 07:22:22 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy