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Calcium in PDB 7m78: Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I

Enzymatic activity of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I

All present enzymatic activity of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I:
1.97.1.12;

Protein crystallography data

The structure of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I, PDB code: 7m78 was solved by S.M.Keable, P.S.Simon, A.Kolsch, J.Kern, V.K.Yachandra, A.Zouni, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.63 / 3.00
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 284.864, 284.864, 166.177, 90, 90, 120
R / Rfree (%) 33.4 / 35

Other elements in 7m78:

The structure of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I also contains other interesting chemical elements:

Magnesium (Mg) 96 atoms
Iron (Fe) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I (pdb code 7m78). 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 Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I, PDB code: 7m78:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7m78

Go back to Calcium Binding Sites List in 7m78
Calcium binding site 1 out of 2 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I


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 Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:43.8
occ:1.00
 HE1 B:HIS205 1.6 38.1 1.0
CE1 B:HIS205 2.3 21.5 1.0
HD1 B:HIS205 2.4 33.8 1.0
O B:HOH906 2.4 88.8 1.0
OE2 B:GLU200 2.5 13.3 1.0
OD2 B:ASP133 2.6 27.1 1.0
ND1 B:HIS205 2.6 17.9 1.0
HB2 B:ARG129 3.5 50.1 1.0
HED1 B:CLA814 3.5 47.0 1.0
NE2 B:HIS205 3.5 25.6 1.0
H B:ARG129 3.6 52.0 1.0
CG B:ASP133 3.7 32.5 1.0
CD B:GLU200 3.7 34.4 1.0
O B:GLY127 4.0 22.1 1.0
CG B:HIS205 4.0 50.9 1.0
HED3 B:CLA814 4.1 47.0 1.0
CED B:CLA814 4.1 28.9 1.0
OD1 B:ASP133 4.2 18.5 1.0
O2D B:CLA814 4.2 19.8 1.0
HG22 B:THR130 4.2 42.5 1.0
CB B:ARG129 4.3 31.5 1.0
N B:ARG129 4.4 33.1 1.0
HG3 B:ARG129 4.4 24.3 1.0
OE1 B:GLU200 4.4 32.3 1.0
CD2 B:HIS205 4.4 35.9 1.0
HA B:MET128 4.4 49.9 1.0
HG2 B:ARG129 4.4 24.3 1.0
CG B:ARG129 4.6 10.1 1.0
HG3 B:GLU200 4.7 70.5 1.0
H B:THR130 4.7 34.1 1.0
CG B:GLU200 4.9 48.6 1.0
CA B:ARG129 4.9 34.0 1.0
HB2 B:HIS205 5.0 80.9 1.0
CB B:ASP133 5.0 39.3 1.0

Calcium binding site 2 out of 2 in 7m78

Go back to Calcium Binding Sites List in 7m78
Calcium binding site 2 out of 2 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I


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 Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca203

b:2.0
occ:1.00
 OD2 L:ASP70 1.9 8.3 1.0
O L:HOH301 2.3 62.0 1.0
OD1 L:ASP70 2.4 2.0 1.0
CG L:ASP70 2.4 5.4 1.0
O L:PRO67 2.8 12.4 1.0
HE21 A:GLN472 3.2 5.3 1.0
CB L:ASP70 3.8 2.0 1.0
C L:PRO67 3.9 2.0 1.0
OD2 A:ASP473 3.9 2.0 1.0
HB2 L:ASP70 4.0 2.0 1.0
HA L:PRO67 4.0 4.6 1.0
NE2 A:GLN472 4.0 2.0 1.0
OD1 A:ASP473 4.1 2.0 1.0
H L:ASP70 4.2 14.5 1.0
HB3 L:ASP70 4.3 2.0 1.0
HG3 A:GLN472 4.4 2.0 1.0
CA L:PRO67 4.4 2.0 1.0
HE22 A:GLN472 4.5 5.3 1.0
CG A:ASP473 4.5 2.0 1.0
HH12 L:ARG69 4.5 9.7 1.0
O L:ASP70 4.5 9.0 1.0
HB2 L:PRO67 4.5 2.0 1.0
HG2 A:GLN472 4.6 2.0 1.0
HA L:LEU68 4.7 4.4 1.0
CA L:ASP70 4.8 2.0 1.0
CG A:GLN472 4.8 2.0 1.0
N L:ASP70 4.9 2.0 1.0
NH1 L:ARG69 4.9 2.0 1.0
CB L:PRO67 4.9 2.0 1.0
C L:ASP70 4.9 2.0 1.0
CD A:GLN472 5.0 2.0 1.0

Reference:

S.M.Keable, A.Kolsch, P.S.Simon, M.Dasgupta, R.Chatterjee, S.K.Subramanian, R.Hussein, M.Ibrahim, I.S.Kim, I.Bogacz, H.Makita, C.C.Pham, F.D.Fuller, S.Gul, D.Paley, L.Lassalle, K.D.Sutherlin, A.Bhowmick, N.W.Moriarty, I.D.Young, J.P.Blaschke, C.De Lichtenberg, P.Chernev, M.H.Cheah, S.Park, G.Park, J.Kim, S.J.Lee, J.Park, K.Tono, S.Owada, M.S.Hunter, A.Batyuk, R.Oggenfuss, M.Sander, S.Zerdane, D.Ozerov, K.Nass, H.Lemke, R.Mankowsky, A.S.Brewster, J.Messinger, N.K.Sauter, V.K.Yachandra, J.Yano, A.Zouni, J.Kern. Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I. Sci Rep V. 11 21787 2021.
ISSN: ESSN 2045-2322
PubMed: 34750381
DOI: 10.1038/S41598-021-00236-3
Page generated: Fri Jul 19 01:56:03 2024

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