Calcium in PDB 5y8a: Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)

The structure of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form), PDB code: 5y8a was solved by N.Nakamura, Y.Naoe, M.M.Rahman, Y.Shiro, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.72 / 2.00
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.088, 45.553, 113.002, 90.00, 100.35, 90.00
R / Rfree (%)	20.1 / 26

The structure of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) (pdb code 5y8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form), PDB code: 5y8a:

Calcium binding site 1 out of 1 in the Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Periplasmic Heme-Binding Protein Bhut in Complex with Two Hemes (Holo- 2 Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:42.6 occ:1.00 O B:HOH582 2.6 28.9 1.0 O B:HOH624 2.6 43.5 1.0 O B:ALA271 2.7 29.0 1.0 C B:ALA271 3.8 30.0 1.0 O B:HOH579 4.3 37.9 1.0 CA B:ALA271 4.3 33.2 1.0 CB B:ALA271 4.4 34.2 1.0 O B:HOH592 4.6 32.6 1.0 N B:ARG272 4.9 28.9 1.0

Y.Naoe, N.Nakamura, M.M.Rahman, T.Tosha, S.Nagatoishi, K.Tsumoto, Y.Shiro, H.Sugimoto. Structural Basis For Binding and Transfer of Heme in Bacterial Heme-Acquisition Systems Proteins V. 85 2217 2017.
ISSN: ESSN 1097-0134
PubMed: 28913898
DOI: 10.1002/PROT.25386