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Calcium in PDB 7g49: Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49 was solved by M.Stihle, J.Benz, D.Hunziker, E.Goetschi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.899, 92.064, 119.722, 90, 90, 90
R / Rfree (%) 16 / 20.8

Other elements in 7g49:

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Fluorine (F) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One (pdb code 7g49). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49:

Calcium binding site 1 out of 1 in 7g49

Go back to Calcium Binding Sites List in 7g49
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:17.6
occ:1.00
 OD1 A:ASP747 2.2 17.2 1.0
O A:LEU745 2.3 17.8 1.0
OD1 A:ASP739 2.3 16.8 1.0
OD1 A:ASN741 2.3 18.8 1.0
OD1 A:ASP743 2.4 18.3 1.0
O A:HOH1451 2.4 23.4 1.0
HA A:ASP739 3.0 19.5 1.0
CG A:ASP743 3.3 21.6 1.0
CG A:ASN741 3.4 21.9 1.0
H A:LEU745 3.4 21.5 1.0
C A:LEU745 3.4 18.7 1.0
H A:ASP743 3.4 25.9 1.0
HD22 A:ASN741 3.5 31.2 1.0
CG A:ASP739 3.5 23.0 1.0
CG A:ASP747 3.5 20.7 1.0
HA A:ASP747 3.6 23.5 1.0
H A:ASN741 3.7 21.8 1.0
OD2 A:ASP743 3.7 23.5 1.0
HB2 A:LEU745 3.8 20.9 1.0
ND2 A:ASN741 3.8 26.0 1.0
CA A:ASP739 3.9 16.3 1.0
N A:ASP747 4.0 18.1 1.0
N A:LEU745 4.0 17.9 1.0
C A:ARG746 4.1 17.8 1.0
CA A:ASP747 4.1 19.6 1.0
O A:ARG746 4.1 15.2 1.0
H A:ASP747 4.2 21.7 1.0
CB A:ASP739 4.2 18.4 1.0
CA A:LEU745 4.2 18.9 1.0
N A:ASP743 4.3 21.6 1.0
OD2 A:ASP747 4.3 22.5 1.0
HB2 A:ASP739 4.4 22.1 1.0
OD2 A:ASP739 4.4 18.0 1.0
CB A:ASP747 4.4 18.7 1.0
O A:PHE738 4.4 15.6 1.0
C A:ASP739 4.4 14.8 1.0
N A:ASN741 4.5 18.1 1.0
N A:ARG746 4.5 15.8 1.0
CB A:LEU745 4.5 17.4 1.0
H A:GLY744 4.5 20.7 1.0
CB A:ASP743 4.5 17.9 1.0
H A:TYR742 4.5 21.4 1.0
H A:TYR740 4.5 20.3 1.0
OE2 A:GLU751 4.6 29.6 1.0
CB A:ASN741 4.6 23.1 1.0
HD21 A:ASN741 4.7 31.2 1.0
N A:TYR740 4.7 16.9 1.0
N A:TYR742 4.7 17.9 1.0
CA A:ARG746 4.7 17.5 0.5
O A:HOH1374 4.7 33.2 1.0
CA A:ARG746 4.7 17.5 0.6
HB3 A:ASP743 4.8 21.5 1.0
CA A:ASP743 4.8 20.4 1.0
HA A:ARG746 4.8 21.0 0.5
C A:ASN741 4.8 24.1 1.0
N A:GLY744 4.9 17.3 1.0
CA A:ASN741 4.9 19.3 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 15:43:13 2025

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