Chlorine 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:

Magnesium (Mg) 2 atoms
Iron (Fe) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3, PDB code: 6t0h:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6t0h

Go back to Chlorine Binding Sites List in 6t0h
Chlorine binding site 1 out of 3 in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl515

b:26.0
occ:0.50
O A:HOH1205 2.6 36.4 0.5
O A:HOH1249 2.7 36.8 0.5
O A:HOH992 2.8 21.7 1.0
NH2 A:ARG397 2.8 14.6 1.0
O A:HOH1249 2.9 37.7 0.5
O A:HOH1038 3.5 37.4 0.5
CG A:ARG398 3.6 18.5 0.5
CZ A:ARG397 3.8 13.7 1.0
NH1 A:ARG397 3.8 14.2 1.0
O A:HOH1225 3.9 51.5 1.0
CG A:ARG398 4.0 11.4 0.5
CD A:ARG398 4.0 18.4 0.5
O A:HOH1156 4.3 17.8 1.0
O A:HOH1269 4.4 41.5 1.0
O A:HOH784 4.4 18.7 1.0
CB A:ARG398 4.9 11.5 0.5
CB A:ARG398 4.9 17.3 0.5
NE A:ARG397 5.0 12.8 1.0

Chlorine binding site 2 out of 3 in 6t0h

Go back to Chlorine Binding Sites List in 6t0h
Chlorine binding site 2 out of 3 in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl516

b:16.5
occ:0.35
O A:HOH710 2.8 16.6 1.0
N A:ASP158 3.0 13.1 1.0
OD1 A:ASP158 3.1 14.4 1.0
N A:PRO157 3.1 14.3 1.0
CD A:PRO157 3.2 15.7 1.0
CG A:ASP158 3.3 14.3 1.0
C A:ASN156 3.5 13.2 1.0
CB A:ASP158 3.7 14.1 1.0
CB A:PRO157 3.7 15.5 1.0
CA A:ASN156 3.7 12.8 1.0
CA A:PRO157 3.8 14.7 1.0
CG A:PRO157 3.8 15.7 1.0
C A:PRO157 3.9 13.9 1.0
OD2 A:ASP158 3.9 14.5 1.0
O A:HOH1218 3.9 25.4 0.5
CA A:ASP158 3.9 13.9 1.0
O A:ASN156 4.4 12.9 1.0
O A:HOH1218 4.4 19.9 0.5
CB A:ASN156 4.4 12.9 1.0
O A:ASN155 4.6 13.7 1.0
OD1 A:ASN156 4.8 13.3 1.0
O A:HOH1204 4.9 41.5 0.5
N A:ASN156 4.9 12.9 1.0
C A:ASP158 4.9 14.2 1.0

Chlorine binding site 3 out of 3 in 6t0h

Go back to Chlorine Binding Sites List in 6t0h
Chlorine binding site 3 out of 3 in the Crystal Structure of CYP124 in Complex with 1-Alpha-Hydroxy-Vitamin D3


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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:Cl517

b:20.8
occ:0.75
O A:HOH1080 3.0 14.9 1.0
ND2 A:ASN12 3.1 12.5 1.0
NE2 A:GLN289 3.2 14.5 1.0
O A:HOH1189 3.7 46.0 1.0
O A:HOH1157 3.7 40.5 1.0
CB A:GLU288 3.7 14.4 0.6
CB A:ASN12 3.8 12.5 1.0
CG A:GLN289 3.8 12.8 1.0
CB A:GLU288 3.9 14.3 0.4
CG A:ASN12 4.0 12.2 1.0
CD A:GLN289 4.0 13.3 1.0
O A:HOH1041 4.2 20.7 1.0
CG A:GLU288 4.3 19.1 0.6
N A:GLN289 4.3 11.7 1.0
CB A:TYR286 4.5 11.7 1.0
O A:HOH601 4.5 32.5 0.6
CA A:GLU288 4.6 12.3 0.6
C A:GLU288 4.6 11.9 0.6
N A:GLU288 4.7 11.3 0.6
O A:HOH601 4.7 21.3 0.4
CG A:GLU288 4.7 19.3 0.4
CA A:GLU288 4.7 12.6 0.4
C A:GLU288 4.8 11.9 0.4
N A:GLU288 4.9 12.1 0.4
CB A:GLN289 5.0 12.0 1.0
O A:HOH1083 5.0 34.6 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: Sat Dec 12 13:41:28 2020

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