Atomistry » Calcium » PDB 7m43-7mg7 » 7m78
Atomistry »
  Calcium »
    PDB 7m43-7mg7 »
      7m78 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy