Calcium in PDB 5v8k: Homodimeric Reaction Center of H. Modesticaldum

The structure of Homodimeric Reaction Center of H. Modesticaldum, PDB code: 5v8k was solved by C.Gisriel, I.Sarrou, B.Ferlez, J.Golbeck, K.E.Redding, R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.08 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.358, 89.714, 111.637, 90.00, 108.15, 90.00
R / Rfree (%)	15.8 / 19.1

The structure of Homodimeric Reaction Center of H. Modesticaldum also contains other interesting chemical elements:

Magnesium	(Mg)	30 atoms
Iron	(Fe)	4 atoms

The binding sites of Calcium atom in the Homodimeric Reaction Center of H. Modesticaldum (pdb code 5v8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Homodimeric Reaction Center of H. Modesticaldum, PDB code: 5v8k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Homodimeric Reaction Center of H. Modesticaldum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Homodimeric Reaction Center of H. Modesticaldum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1032 b:39.5 occ:1.00 OE1 A:GLN517 2.3 36.8 1.0 O A:HOH1253 2.4 35.9 1.0 O A:LEU605 2.4 33.0 1.0 OD2 A:ASP468 2.4 32.1 1.0 O A:HOH1119 2.5 32.5 1.0 CG A:ASP468 3.3 33.6 1.0 HH A:TYR513 3.3 51.9 1.0 C A:VAL608 3.4 42.7 1.0 CD A:GLN517 3.4 36.4 1.0 OD1 A:ASP468 3.5 34.9 1.0 HD21 A:ASN263 3.6 36.2 1.0 C A:LEU605 3.6 34.2 1.0 HZ2 A:TRP464 3.6 32.6 1.0 HE22 A:GLN517 3.7 33.8 1.0 HG23 A:VAL608 3.7 36.7 1.0 HA A:ALA606 3.8 35.0 1.0 NE2 A:GLN517 3.9 35.5 1.0 OH A:TYR513 4.0 44.6 1.0 ND2 A:ASN263 4.1 39.4 1.0 HD22 A:ASN263 4.1 36.2 1.0 H A:VAL608 4.1 34.1 1.0 O A:VAL608 4.1 46.9 1.0 HB3 A:LEU605 4.1 37.0 1.0 O A:HOH1145 4.2 44.9 1.0 HE2 A:TYR513 4.2 33.2 1.0 HA A:LEU605 4.3 27.0 1.0 HG22 A:VAL608 4.4 36.7 1.0 N A:ALA606 4.5 34.1 1.0 CA A:LEU605 4.5 30.9 1.0 CA A:ALA606 4.5 35.9 1.0 CZ2 A:TRP464 4.5 34.5 1.0 CG2 A:VAL608 4.5 39.9 1.0 CA A:VAL608 4.5 42.7 1.0 HG3 A:GLN517 4.5 35.6 1.0 N A:VAL608 4.6 38.7 1.0 HZ2 A:LYS269 4.6 33.8 1.0 CG A:GLN517 4.6 35.6 1.0 CB A:ASP468 4.8 30.8 1.0 C A:ALA606 4.8 37.6 1.0 HE21 A:GLN517 4.8 33.8 1.0 CZ A:TYR513 4.8 36.6 1.0 CE2 A:TYR513 4.8 34.7 1.0 CB A:LEU605 4.8 36.2 1.0 O A:HOH1220 4.8 40.8 1.0 O A:HOH1140 4.9 34.8 1.0 HB3 A:ASP468 4.9 28.7 1.0 HH2 A:TRP464 4.9 32.7 1.0

Calcium binding site 2 out of 2 in the Homodimeric Reaction Center of H. Modesticaldum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Homodimeric Reaction Center of H. Modesticaldum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1033 b:84.3 occ:1.00 HD1 A:HIS51 2.1 36.7 1.0 H41 A:GBF1026 2.7 53.2 1.0 O1A A:GBF1026 2.7 38.1 1.0 HD2 A:PRO65 2.8 39.7 1.0 ND1 A:HIS51 3.0 37.3 1.0 HB3 A:HIS51 3.0 35.3 1.0 HD3 A:PRO65 3.0 39.7 1.0 O A:ALA64 3.0 62.9 1.0 O A:HOH1120 3.1 34.0 1.0 H62 A:GBF1026 3.3 66.8 1.0 CD A:PRO65 3.3 42.4 1.0 HAA2 A:GBF1026 3.4 33.8 1.0 CGA A:GBF1026 3.4 41.6 1.0 C4 A:GBF1026 3.5 53.2 1.0 HBA2 A:GBF1026 3.6 33.8 1.0 CB A:HIS51 3.6 36.2 1.0 HD11 A:ILE47 3.7 46.0 1.0 CG A:HIS51 3.7 38.4 1.0 H42 A:GBF1026 3.7 53.2 1.0 C3 A:GBF1026 3.7 58.2 1.0 HB2 A:HIS51 3.8 35.3 1.0 HG2 A:PRO65 3.9 40.9 1.0 CBA A:GBF1026 3.9 33.8 1.0 CE1 A:HIS51 4.0 39.1 1.0 CAA A:GBF1026 4.0 33.9 1.0 C6 A:GBF1026 4.1 66.8 1.0 HBD A:GBF1026 4.1 38.2 1.0 C A:ALA64 4.1 48.7 1.0 H12 A:GBF1026 4.1 58.4 1.0 HD13 A:ILE47 4.1 46.0 1.0 CG A:PRO65 4.1 43.2 1.0 C2 A:GBF1026 4.1 59.9 1.0 H61 A:GBF1026 4.2 66.8 1.0 HE1 A:HIS51 4.2 39.4 1.0 CD1 A:ILE47 4.3 46.4 1.0 HAA1 A:GBF1026 4.3 33.8 1.0 C5 A:GBF1026 4.3 66.3 1.0 O2A A:GBF1026 4.4 50.7 1.0 H43 A:GBF1026 4.4 53.2 1.0 H23 B:C4D101 4.4 45.0 1.0 C1 A:GBF1026 4.4 58.4 1.0 HG3 A:PRO65 4.5 40.9 1.0 H52 A:GBF1026 4.5 66.3 1.0 N A:PRO65 4.5 49.7 1.0 HD12 A:ILE47 4.6 46.0 1.0 HB3 A:TRP63 4.6 39.0 1.0 H93 A:GBF1026 4.6 70.7 1.0 H2 A:GBF1026 4.7 59.9 1.0 O A:HIS51 4.8 36.1 1.0 H A:ALA66 4.8 34.2 1.0 HBA1 A:GBF1026 4.9 33.8 1.0 HE2 A:PHE46 4.9 48.0 1.0 CD2 A:HIS51 4.9 39.7 1.0 H4 B:C4D101 5.0 49.9 1.0

C.Gisriel, I.Sarrou, B.Ferlez, J.H.Golbeck, K.E.Redding, R.Fromme. Structure of A Symmetric Photosynthetic Reaction Center-Photosystem. Science V. 357 1021 2017.
ISSN: ESSN 1095-9203
PubMed: 28751471
DOI: 10.1126/SCIENCE.AAN5611