Calcium in PDB 4fby: Fs X-Ray Diffraction of Photosystem II

All present enzymatic activity of Fs X-Ray Diffraction of Photosystem II:
1.10.3.9;

The structure of Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby was solved by J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Gloeckner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.-C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.89 / 6.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.783, 227.764, 308.630, 90.00, 90.00, 90.00
R / Rfree (%)	36.6 / 38.5

The structure of Fs X-Ray Diffraction of Photosystem II also contains other interesting chemical elements:

Magnesium	(Mg)	70 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Fs X-Ray Diffraction of Photosystem II (pdb code 4fby). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca412 b:0.5 occ:1.00 CA1 A:OEC412 0.0 0.5 1.0 MN1 A:OEC412 2.9 0.9 1.0 OE1 A:GLU189 2.9 0.9 1.0 MN3 A:OEC412 3.0 0.2 1.0 OD1 A:ASP170 3.1 0.1 1.0 OD2 A:ASP170 3.1 0.5 1.0 O A:ALA344 3.4 0.9 1.0 CG A:ASP170 3.4 0.6 1.0 MN4 A:OEC412 3.6 0.1 1.0 CD A:GLU189 3.7 0.3 1.0 MN2 A:OEC412 3.7 0.5 1.0 OE2 A:GLU189 3.8 0.4 1.0 OXT A:ALA344 4.2 0.7 1.0 C A:ALA344 4.2 0.1 1.0 NE2 A:GLN165 4.4 0.5 1.0 CG1 A:VAL185 4.8 0.7 1.0 CB A:ASP170 4.8 0.9 1.0 OH A:TYR161 4.8 0.8 1.0

Calcium binding site 2 out of 4 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca301 b:0.3 occ:1.00 CD O:GLU81 3.2 0.7 1.0 OE1 O:GLU140 3.3 0.8 1.0 NE2 O:HIS257 3.3 0.6 1.0 OE2 O:GLU81 3.4 0.3 1.0 OE1 O:GLU81 3.4 0.6 1.0 CG O:GLU81 3.5 0.8 1.0 OE2 O:GLU140 3.9 0.6 1.0 CD O:GLU140 4.0 0.0 1.0 CD2 O:HIS257 4.1 0.1 1.0 CE1 O:HIS257 4.3 0.6 1.0 CB O:GLU81 4.9 0.0 1.0

Calcium binding site 3 out of 4 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca413 b:0.4 occ:1.00 CA1 G:OEC413 0.0 0.4 1.0 OE1 G:GLU189 2.9 0.9 1.0 MN3 G:OEC413 2.9 0.2 1.0 MN1 G:OEC413 2.9 0.5 1.0 OD1 G:ASP170 3.0 0.2 1.0 OD2 G:ASP170 3.1 0.9 1.0 CG G:ASP170 3.4 0.7 1.0 MN2 G:OEC413 3.4 0.8 1.0 O G:ALA344 3.4 0.2 1.0 CD G:GLU189 3.7 0.3 1.0 MN4 G:OEC413 3.7 92.0 1.0 OE2 G:GLU189 3.8 0.3 1.0 C G:ALA344 4.3 0.1 1.0 OXT G:ALA344 4.3 0.8 1.0 NE2 G:GLN165 4.4 0.2 1.0 CB G:ASP170 4.7 0.3 1.0 CG1 G:VAL185 4.7 0.4 1.0 OH G:TYR161 4.8 0.1 1.0 OE1 G:GLU333 5.0 0.6 1.0

Calcium binding site 4 out of 4 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ f:Ca301 b:0.2 occ:1.00 NE2 f:HIS257 3.2 0.1 1.0 OE1 f:GLU140 3.2 0.7 1.0 CD f:GLU81 3.4 0.5 1.0 OE1 f:GLU81 3.6 0.8 1.0 OE2 f:GLU81 3.7 0.4 1.0 OE2 f:GLU140 3.7 0.8 1.0 CG f:GLU81 3.7 0.6 1.0 CD f:GLU140 3.8 0.1 1.0 CD2 f:HIS257 4.0 0.1 1.0 CE1 f:HIS257 4.2 0.5 1.0

J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Glockner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra. Room Temperature Femtosecond X-Ray Diffraction of Photosystem II Microcrystals. Proc.Natl.Acad.Sci.Usa V. 109 9721 2012.
ISSN: ISSN 0027-8424
PubMed: 22665786
DOI: 10.1073/PNAS.1204598109