Magnesium in PDB 3dmi: Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution

The structure of Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution, PDB code: 3dmi was solved by H.Akazaki, F.Kawai, M.Hosokawa, T.Hama, T.Hirano, B.-K.Lim, N.Sakurai, W.Hakamata, S.-Y.Park, T.Nishio, T.Oku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	80.385, 80.385, 80.385, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.2

The structure of Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution (pdb code 3dmi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution, PDB code: 3dmi:

Magnesium binding site 1 out of 1 in the Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystallization and Structural Analysis of Cytochrome C6 From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg134 b:13.1 occ:1.00 O A:HOH246 2.0 15.2 1.0 OD2 A:ASP114 2.0 12.9 1.0 O A:HOH147 2.1 13.3 1.0 O A:HOH192 2.1 14.4 1.0 O A:HOH182 2.1 17.0 1.0 O A:HOH177 2.1 15.0 1.0 CG A:ASP114 2.9 9.4 1.0 OD1 A:ASP114 3.1 12.0 1.0 O A:HOH202 4.1 27.1 1.0 O A:HOH176 4.1 17.3 1.0 O A:HOH239 4.1 12.3 1.0 O A:HOH158 4.2 7.5 1.0 CB A:ASP114 4.3 8.1 1.0 O A:HOH210 4.3 21.7 1.0

H.Akazaki, F.Kawai, M.Hosokawa, T.Hama, H.Chida, T.Hirano, B.K.Lim, N.Sakurai, W.Hakamata, S.Y.Park, T.Nishio, T.Oku. Crystallization and Structural Analysis of Cytochrome C(6) From the Diatom Phaeodactylum Tricornutum at 1.5 A Resolution. Biosci.Biotechnol.Biochem. V. 73 189 2009.
ISSN: ISSN 0916-8451
PubMed: 19129656
DOI: 10.1271/BBB.80472