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Magnesium in PDB 7zb9: Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)

Enzymatic activity of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)

All present enzymatic activity of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo):
1.14.15.14; 1.14.15.28;

Protein crystallography data

The structure of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo), PDB code: 7zb9 was solved by S.Bukhdruker, T.Varaksa, E.Marin, 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) 29.50 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.54, 75.08, 56.56, 90, 106.96, 90
R / Rfree (%) 13 / 15.7

Other elements in 7zb9:

The structure of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Iron (Fe) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) (pdb code 7zb9). 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 Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo), PDB code: 7zb9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7zb9

Go back to Magnesium Binding Sites List in 7zb9
Magnesium binding site 1 out of 2 in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)


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 Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:11.2
occ:1.00
 O A:HOH1247 2.0 14.2 1.0
O A:HOH1501 2.0 15.7 1.0
O A:HOH1206 2.1 11.4 1.0
O A:HOH868 2.1 11.6 1.0
O A:HOH806 2.1 10.0 1.0
O A:HOH1464 2.1 13.8 1.0
O A:HOH727 4.0 10.7 1.0
O A:HOH1240 4.1 18.7 1.0
O A:HOH1008 4.2 15.7 1.0
O A:HOH1184 4.2 27.9 1.0
OD1 A:ASP178 4.3 8.9 1.0
O A:HOH1433 4.3 30.5 1.0
O A:HOH1525 4.3 33.2 1.0
O A:HOH1407 4.3 18.4 1.0
O A:HOH1053 4.3 14.3 1.0
O A:HOH1524 4.3 36.2 1.0
O A:ASP178 4.5 8.7 1.0
O A:ILE182 4.5 8.5 1.0
CA A:GLY181 4.6 9.0 1.0
CA A:ASP178 4.7 7.8 1.0
C A:GLY181 4.8 7.8 1.0
CG A:ASP178 4.8 9.0 1.0
O A:HOH782 4.9 19.7 1.0
CB A:ASP178 5.0 8.9 1.0

Magnesium binding site 2 out of 2 in 7zb9

Go back to Magnesium Binding Sites List in 7zb9
Magnesium binding site 2 out of 2 in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)


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 Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:14.4
occ:0.50
 O A:HOH1251 1.9 20.7 1.0
O A:HOH1349 1.9 19.2 0.5
O A:HOH678 2.0 18.0 1.0
O A:HOH1280 2.0 28.5 0.7
O A:HOH1517 2.1 17.3 0.5
O A:HOH673 2.3 21.3 1.0
O A:HOH1499 2.5 23.3 0.1
O A:HOH1349 2.6 29.9 0.5
O A:HOH602 2.9 25.5 0.5
O A:HOH1280 2.9 16.7 0.1
O A:HOH1227 4.1 17.4 0.5
O A:HOH602 4.1 13.3 0.5
OD1 A:ASN156 4.2 10.0 1.0
OE2 A:GLU166 4.2 14.0 1.0
O A:HOH1400 4.2 19.1 0.5
O A:GLN160 4.2 11.6 0.5
O A:HOH688 4.2 19.7 1.0
O A:HOH1229 4.4 29.1 1.0
O A:HOH773 4.4 10.6 0.8
O A:GLN160 4.5 11.7 0.5
O A:HOH1360 4.6 27.5 0.5
CA A:ALA161 4.7 10.6 1.0
N A:ASP162 4.9 9.7 1.0
C A:GLN160 5.0 12.2 0.5

Reference:

S.Bukhdruker, T.Varaksa, P.Orekhov, I.Grabovec, E.Marin, I.Kapranov, K.Kovalev, R.Astashkin, L.Kaluzhskiy, A.Ivanov, A.Mishin, A.Rogachev, V.Gordeliy, A.Gilep, N.Strushkevich, V.Borshchevskiy. Structural Insights Into the Effects of Glycerol on Ligand Binding to Cytochrome P450 Acta Crystallogr.,Sect.D V. 79 66 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322011019
Page generated: Thu Oct 3 16:21:35 2024

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