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Magnesium in PDB 6t0h: Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3

Enzymatic activity of Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3

All present enzymatic activity of Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3:
1.14.15.14; 1.14.15.28;

Protein crystallography data

The structure of Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3, PDB code: 6t0h was solved by S.Bukhdruker, E.Marin, T.Varaksa, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 1.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.560, 74.970, 56.630, 90.00, 106.95, 90.00
R / Rfree (%) 15.6 / 18.1

Other elements in 6t0h:

The structure of Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3 also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3 (pdb code 6t0h). 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 CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3, PDB code: 6t0h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6t0h

Go back to Magnesium Binding Sites List in 6t0h
Magnesium binding site 1 out of 2 in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3


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 CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg513

b:18.7
occ:0.80
O A:HOH1305 2.0 25.1 1.0
O A:HOH825 2.0 17.1 1.0
O A:HOH818 2.1 20.1 1.0
O A:HOH1109 2.1 22.3 1.0
O A:HOH1287 2.1 25.9 1.0
O A:HOH1138 2.1 24.9 1.0
O A:HOH1133 4.0 29.7 1.0
O A:HOH738 4.0 16.8 1.0
O A:HOH745 4.1 25.9 1.0
O A:HOH1118 4.2 43.5 1.0
O A:HOH977 4.2 18.5 0.5
OD1 A:ASP178 4.3 13.6 1.0
O A:HOH1263 4.3 48.8 1.0
O A:HOH1244 4.3 28.6 1.0
O A:ASP178 4.5 12.3 1.0
O A:ILE182 4.6 13.2 1.0
CA A:GLY181 4.6 12.0 1.0
O A:HOH977 4.7 27.8 0.5
CA A:ASP178 4.8 12.4 1.0
C A:GLY181 4.8 12.4 1.0
O A:HOH741 4.8 27.2 1.0
CG A:ASP178 4.8 13.3 1.0
CB A:ASP178 5.0 13.0 1.0

Magnesium binding site 2 out of 2 in 6t0h

Go back to Magnesium Binding Sites List in 6t0h
Magnesium binding site 2 out of 2 in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3


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 CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg514

b:32.5
occ:1.00
O A:HOH1127 1.9 32.6 1.0
O A:HOH1314 2.0 58.0 1.0
O A:HOH790 2.2 18.3 1.0
O A:HOH1190 2.2 20.9 0.7
O A:HOH1204 2.3 41.4 0.5
O A:HOH655 2.5 22.5 1.0
O A:HOH1204 2.6 41.5 0.5
O A:HOH1190 3.0 19.1 0.3
O A:HOH942 3.2 19.4 0.5
O A:HOH1218 3.7 19.9 0.5
O A:HOH1254 3.8 46.4 1.0
O A:HOH1324 3.9 36.8 1.0
O A:HOH1198 4.0 48.7 0.4
O A:HOH1198 4.2 48.7 0.6
O A:HOH942 4.3 19.1 0.5
O A:HOH709 4.3 19.7 1.0
OD1 A:ASN156 4.3 13.3 1.0
O A:HOH1226 4.4 19.3 0.5
OE2 A:GLU166 4.4 14.2 1.0
O A:HOH710 4.4 16.6 1.0
O A:HOH1218 4.5 25.4 0.5
O A:GLN160 4.5 14.4 1.0
O A:HOH1208 4.8 26.9 0.5
CA A:ALA161 4.9 13.5 1.0
N A:ASP162 5.0 12.5 1.0

Reference:

T.Varaksa, S.Bukhdruker, I.Grabovec, E.Marin, A.Kavaleuski, A.Gusach, K.Kovalev, I.Maslov, A.Luginina, D.Zabelskiy, R.Astashkin, M.Shevtsov, S.Smolskaya, A.Kavaleuskaya, P.Shabunya, A.Baranovsky, V.Dolgopalets, Y.Charnou, A.Savachka, R.Litvinovskaya, E.Shevchenko, A.Rogachev, A.Mishin, V.Gordeliy, A.Gabrielian, D.E.Hurt, B.Nikonenko, K.Majorov, A.Apt, A.Rosenthal, A.Gilep, V.Borshchevskiy, N.Strushkevich. Metabolic Fate of Human Immunoactive Oxysterols in Mycobacterium Tuberculosis. To Be Published.
Page generated: Tue Oct 1 18:32:34 2024

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