Magnesium in PDB 6kmd: Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin

All present enzymatic activity of Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin:
1.3.7.4;

The structure of Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin, PDB code: 6kmd was solved by M.Sugishima, K.Wada, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.48 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.925, 63.925, 158.426, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.2

The structure of Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin (pdb code 6kmd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin, PDB code: 6kmd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.6 occ:1.00 O A:HOH571 2.0 28.2 1.0 O A:HOH625 2.1 33.9 1.0 O A:HOH580 2.1 30.3 1.0 OD1 A:ASP91 2.2 52.2 1.0 CG A:ASP91 3.2 47.8 1.0 OD2 A:ASP91 3.6 51.5 1.0 O A:SER88 4.0 32.4 1.0 O A:MSE89 4.3 34.7 1.0 CB A:ASP91 4.6 43.1 1.0 O A:HOH604 4.7 47.2 1.0 CB A:LEU87 4.7 33.6 1.0 CA A:ASP91 4.9 39.0 1.0 C A:MSE89 4.9 38.7 1.0 CA A:MSE89 5.0 39.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Semet-Phytochromobilin Synthase From Tomato in Complex with Biliverdin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:67.4 occ:1.00 O A:HOH502 2.1 67.6 1.0 OE2 A:GLU67 3.5 42.5 1.0 OE1 A:GLU67 3.8 38.9 1.0 CD A:GLU67 4.0 38.7 1.0 OG1 A:THR70 4.5 27.6 1.0 CG2 A:THR70 4.8 27.0 1.0

M.Sugishima, K.Wada, K.Fukuyama, K.Yamamoto. Crystal Structure of Phytochromobilin Synthase in Complex with Biliverdin IX Alpha , A Key Enzyme in the Biosynthesis of Phytochrome. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31822504
DOI: 10.1074/JBC.RA119.011431