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Calcium in PDB 7m76: 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: 7m76 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) 25.23 / 3.00
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 284.269, 284.269, 165.746, 90, 90, 120
R / Rfree (%) 26.8 / 27.8

Other elements in 7m76:

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 7m76). 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: 7m76:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7m76

Go back to Calcium Binding Sites List in 7m76
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:Ca3002

b:70.0
occ:1.00
 HE1 B:HIS205 2.2 64.2 1.0
HD1 B:HIS205 2.3 59.9 1.0
CE1 B:HIS205 2.6 47.7 1.0
OD2 B:ASP133 2.6 53.3 1.0
ND1 B:HIS205 2.6 44.1 1.0
OE2 B:GLU200 2.6 39.5 1.0
O B:HOH3107 2.8 88.8 1.0
CG B:ASP133 3.4 58.6 1.0
OD1 B:ASP133 3.6 44.7 1.0
HB2 B:ARG129 3.6 76.2 1.0
H B:ARG129 3.7 78.1 1.0
CD B:GLU200 3.8 60.6 1.0
NE2 B:HIS205 3.8 51.8 1.0
CG B:HIS205 3.9 77.1 1.0
HG22 B:THR130 4.0 68.7 1.0
OE1 B:GLU200 4.2 58.4 1.0
O B:GLY127 4.3 48.2 1.0
HG3 B:ARG129 4.4 50.5 1.0
CD2 B:HIS205 4.4 62.0 1.0
O B:VAL206 4.5 73.9 1.0
CB B:ARG129 4.5 57.7 1.0
N B:ARG129 4.5 59.3 1.0
HA B:MET128 4.6 76.1 1.0
HB2 B:HIS205 4.6 107.0 1.0
HG2 B:ARG129 4.6 50.5 1.0
HED3 B:CLA3015 4.6 73.1 1.0
H B:VAL206 4.7 105.2 1.0
CG B:ARG129 4.7 36.2 1.0
H B:THR130 4.8 60.3 1.0
CB B:ASP133 4.8 65.5 1.0
CB B:HIS205 4.8 83.4 1.0
HG21 B:THR130 4.8 68.7 1.0
CG2 B:THR130 4.9 51.4 1.0
HB3 B:ASP133 4.9 85.6 1.0
HED1 B:CLA3015 4.9 73.1 1.0
O1D B:CLA3015 4.9 60.0 1.0
HA3 B:GLY207 4.9 99.8 1.0
O2D B:CLA3015 4.9 46.0 1.0
HG3 B:GLU200 5.0 96.7 1.0
HA B:HIS205 5.0 98.5 1.0

Calcium binding site 2 out of 2 in 7m76

Go back to Calcium Binding Sites List in 7m76
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:27.5
occ:1.00
 OD1 L:ASP70 2.4 14.9 1.0
O A:HOH901 2.4 62.0 1.0
O L:HOH302 2.6 46.4 1.0
O L:PRO67 2.7 38.6 1.0
OD2 L:ASP70 2.8 34.4 1.0
CG L:ASP70 2.9 31.5 1.0
HE21 A:GLN472 3.6 31.5 1.0
C L:PRO67 3.8 19.9 1.0
HA L:PRO67 4.0 30.8 1.0
H L:ASP70 4.2 40.7 1.0
HH12 L:ARG69 4.3 35.8 1.0
NE2 A:GLN472 4.4 20.4 1.0
CA L:PRO67 4.4 19.8 1.0
OD1 A:ASP473 4.4 21.1 1.0
CB L:ASP70 4.4 7.8 1.0
OD2 A:ASP473 4.4 8.0 1.0
HB2 L:PRO67 4.5 27.8 1.0
HA L:LEU68 4.6 30.6 1.0
O L:ASP70 4.6 35.2 1.0
HE22 A:GLN472 4.7 31.5 1.0
NH1 L:ARG69 4.7 24.0 1.0
HB2 L:ASP70 4.8 16.4 1.0
HG3 A:GLN472 4.9 22.2 1.0
CG A:ASP473 4.9 12.7 1.0
CB L:PRO67 4.9 17.3 1.0
HB3 L:ASP70 4.9 16.4 1.0
N L:LEU68 4.9 17.9 1.0
N L:ASP70 5.0 28.0 1.0
HH11 L:ARG69 5.0 35.8 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 01:56:04 2024

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