Calcium in PDB 5g38: Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6

The structure of Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6, PDB code: 5g38 was solved by M.Bommer, A.N.Bondar, A.Zouni, H.Dobbek, H.Dau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.45 / 1.15
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.436, 54.436, 191.759, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 18.4

The binding sites of Calcium atom in the Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6 (pdb code 5g38). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6, PDB code: 5g38:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca191 b:12.1 occ:1.00 O A:HOH2120 2.3 14.6 1.0 OD1 A:ASN151 2.4 12.8 1.0 O A:VAL152 2.4 13.2 1.0 O A:HOH2118 2.4 12.7 1.0 O A:THR131 2.4 13.6 1.0 O A:HOH2119 2.4 15.2 1.0 O A:HOH2133 2.5 14.6 1.0 HA A:SER132 3.3 15.9 1.0 CG A:ASN151 3.5 12.4 1.0 C A:VAL152 3.5 11.6 1.0 HA A:ALA153 3.5 14.5 1.0 C A:THR131 3.6 12.7 1.0 HD22 A:ASN151 3.8 17.9 1.0 ND2 A:ASN151 4.0 14.9 1.0 CA A:SER132 4.2 13.3 1.0 N A:VAL152 4.3 11.6 1.0 N A:SER132 4.3 13.1 1.0 HB A:THR131 4.3 16.9 1.0 CA A:ALA153 4.4 12.1 1.0 N A:ALA153 4.4 11.8 1.0 C A:ASN151 4.4 11.8 1.0 H A:VAL152 4.4 13.9 1.0 O A:HOH2124 4.4 14.8 1.0 CA A:VAL152 4.5 10.9 1.0 HA A:THR131 4.5 15.5 1.0 HA A:ASN151 4.6 13.8 1.0 HB A:VAL152 4.6 14.3 1.0 CA A:THR131 4.6 12.9 1.0 HB3 A:ALA153 4.6 17.0 1.0 O A:THR133 4.7 12.8 1.0 O A:HOH2134 4.7 18.6 1.0 CB A:ASN151 4.7 12.1 1.0 C A:SER132 4.7 12.8 1.0 OD1 A:ASP134 4.8 14.9 1.0 CA A:ASN151 4.8 11.5 1.0 O A:ASN151 4.8 11.6 1.0 HD21 A:ASN151 4.9 17.9 1.0 O A:HOH2122 4.9 14.0 1.0 CB A:THR131 5.0 14.1 1.0

Calcium binding site 2 out of 3 in the Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:22.0 occ:0.65 CA A:CA202 1.7 23.9 0.3 O A:HOH2155 2.2 39.0 1.0 O A:HOH2160 2.3 36.8 1.0 O A:HOH2154 2.3 24.9 1.0 O A:HOH2159 2.4 36.9 1.0 O A:HOH2156 2.4 27.1 1.0 O A:HOH2158 2.6 21.1 1.0 O A:HOH2157 2.9 31.3 1.0 O A:HOH2066 2.9 36.4 1.0 HG3 A:GLU57 4.0 19.6 1.0 OE2 A:GLU57 4.2 23.0 1.0 O A:HOH2067 4.5 27.0 1.0 CG A:GLU57 4.8 16.3 1.0 O A:HOH2068 4.8 27.2 1.0 CD A:GLU57 4.8 19.1 1.0

Calcium binding site 3 out of 3 in the Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Psbo Subunit of Photosystem II, Beta Barrel Domain at 100K, pH 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:23.9 occ:0.35 CA A:CA201 1.7 22.0 0.7 O A:HOH2066 2.1 36.4 1.0 OE2 A:GLU57 2.5 23.0 1.0 O A:HOH2156 2.6 27.1 1.0 O A:HOH2154 2.6 24.9 1.0 O A:HOH2158 2.7 21.1 1.0 HG3 A:GLU57 3.1 19.6 1.0 O A:HOH2160 3.2 36.8 1.0 O A:HOH2159 3.2 36.9 1.0 CD A:GLU57 3.3 19.1 1.0 O A:HOH2067 3.4 27.0 1.0 CG A:GLU57 3.6 16.3 1.0 O A:HOH2155 3.7 39.0 1.0 HG2 A:GLU57 3.9 19.6 1.0 OE1 A:GLU57 4.4 18.1 1.0 O A:HOH2157 4.4 31.3 1.0 O A:HOH2064 4.6 25.2 1.0 O A:HOH2065 4.8 17.8 1.0 O A:HOH2068 5.0 27.2 1.0

M.Bommer, A.N.Bondar, A.Zouni, H.Dobbek, H.Dau. Crystallographic and Computational Analysis of the Barrel Part of the Psbo Protein of Photosystem II -Carboxylate-Water Clusters As Putative Proton Transfer Relays and Structural Switches Biochemistry V. 55 4626 2016.
ISSN: ISSN 0006-2960
PubMed: 27454911
DOI: 10.1021/ACS.BIOCHEM.6B00441