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Magnesium in PDB 6kme: Crystal Structure of Phytochromobilin Synthase From Tomato in Complex with Biliverdin

Enzymatic activity of Crystal Structure of Phytochromobilin Synthase From Tomato in Complex with Biliverdin

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

Protein crystallography data

The structure of Crystal Structure of Phytochromobilin Synthase From Tomato in Complex with Biliverdin, PDB code: 6kme 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) 49.85 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.130, 64.130, 158.490, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.7

Other elements in 6kme:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phytochromobilin Synthase From Tomato in Complex with Biliverdin (pdb code 6kme). 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 Crystal Structure of Phytochromobilin Synthase From Tomato in Complex with Biliverdin, PDB code: 6kme:

Magnesium binding site 1 out of 1 in 6kme

Go back to Magnesium Binding Sites List in 6kme
Magnesium binding site 1 out of 1 in the Crystal Structure of 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 Phytochromobilin Synthase From Tomato in Complex with Biliverdin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:37.7
occ:1.00
O A:HOH654 2.1 32.8 1.0
O A:HOH522 2.1 29.0 1.0
O A:HOH619 2.1 33.4 1.0
OD1 A:ASP91 2.3 37.9 1.0
CG A:ASP91 3.4 44.5 1.0
OD2 A:ASP91 3.7 46.0 1.0
O A:SER88 4.2 31.3 1.0
O A:MET89 4.3 33.2 1.0
O A:HOH674 4.6 44.7 1.0
CB A:ASP91 4.7 44.4 1.0
CB A:LEU87 4.8 31.4 1.0
C A:MET89 4.9 38.4 1.0

Reference:

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
Page generated: Tue Oct 1 07:16:54 2024

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