Calcium in PDB 3kzi: Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II

The structure of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II, PDB code: 3kzi was solved by A.Gabdulkhakov, A.Guskov, M.Broser, J.Kern, A.Zouni, W.Saenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 3.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.890, 224.690, 337.280, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 30.8

The structure of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II also contains other interesting chemical elements:

Magnesium	(Mg)	35 atoms
Manganese	(Mn)	4 atoms
Iron	(Fe)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II (pdb code 3kzi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II, PDB code: 3kzi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca368 b:0.9 occ:1.00 CA1 A:OEC368 0.0 0.9 1.0 OE1 A:GLU189 2.4 0.9 1.0 O A:ALA344 2.4 0.4 1.0 OD1 A:ASP170 2.9 0.5 1.0 MN2 A:OEC368 3.2 0.2 1.0 CD A:GLU189 3.3 0.6 1.0 MN3 A:OEC368 3.3 0.9 1.0 MN1 A:OEC368 3.4 0.2 1.0 C A:ALA344 3.4 0.9 1.0 OE2 A:GLU189 3.4 1.0 1.0 OXT A:ALA344 3.6 0.9 1.0 NE2 A:GLN165 3.8 0.8 1.0 CG A:ASP170 3.8 0.6 1.0 OD2 A:ASP170 4.0 1.0 1.0 MN4 A:OEC368 4.6 0.2 1.0 CG A:GLU189 4.7 0.7 1.0 OH A:TYR161 4.7 0.1 1.0 CA A:ALA344 4.8 0.8 1.0 NH1 C:ARG357 4.8 0.6 1.0 OD1 A:ASP342 4.9 0.2 1.0 CD A:GLN165 5.0 0.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca225 b:0.4 occ:1.00 O F:ARG45 3.2 0.2 1.0 OXT F:ARG45 3.4 0.4 1.0 OE2 V:GLU49 3.6 0.6 1.0 C F:ARG45 3.7 0.7 1.0 OE1 V:GLU49 3.8 0.4 1.0 CD V:GLU49 4.1 0.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca56 b:0.0 occ:1.00 OD2 K:ASP19 2.7 0.9 1.0 OD1 K:ASP23 3.0 0.1 1.0 OD2 K:ASP23 3.0 0.5 1.0 CG K:ASP19 3.3 0.7 1.0 CG K:ASP23 3.3 0.1 1.0 CB K:ASP19 3.8 1.0 1.0 O K:ASP19 4.0 0.0 1.0 OD1 K:ASP19 4.0 0.3 1.0 C K:ASP19 4.1 0.1 1.0 CA K:ASP19 4.3 0.4 1.0 NE2 C:HIS74 4.5 1.0 1.0 N K:PRO20 4.6 0.3 1.0 CB C:ALA73 4.6 0.6 1.0 O C:ALA73 4.6 0.2 1.0 CE1 C:HIS74 4.6 0.9 1.0 CB K:ASP23 4.8 0.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca273 b:0.0 occ:1.00 NE2 O:HIS257 2.7 0.0 1.0 OE1 O:GLU140 2.8 0.5 1.0 OE2 O:GLU140 3.5 0.7 1.0 CD O:GLU140 3.5 0.8 1.0 CD2 O:HIS257 3.6 0.0 1.0 CE1 O:HIS257 3.7 0.0 1.0 OE2 O:GLU81 4.1 0.0 1.0 CD O:GLU81 4.1 0.0 1.0 OE1 O:GLU81 4.3 0.0 1.0 CG O:GLU81 4.7 0.0 1.0 CG O:HIS257 4.8 0.7 1.0 ND1 O:HIS257 4.8 0.0 1.0 SD O:MET136 4.9 0.9 1.0

M.Broser, A.Gabdulkhakov, J.Kern, A.Guskov, F.Muh, W.Saenger, A.Zouni. Crystal Structure of Monomeric Photosystem II From Thermosynechococcus Elongatus at 3.6-A Resolution J.Biol.Chem. V. 285 26255 2010.
ISSN: ISSN 0021-9258
PubMed: 20558739
DOI: 10.1074/JBC.M110.127589