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Calcium in PDB 5ijs: Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog

Enzymatic activity of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog

All present enzymatic activity of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog, PDB code: 5ijs was solved by J.Hausmann, R.P.Joosten, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.750, 63.450, 70.550, 99.33, 105.91, 99.51
R / Rfree (%) 20.3 / 23.9

Other elements in 5ijs:

The structure of Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Vanadium (V) 1 atom
Iodine (I) 6 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog (pdb code 5ijs). 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 Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog, PDB code: 5ijs:

Calcium binding site 1 out of 1 in 5ijs

Go back to Calcium Binding Sites List in 5ijs
Calcium binding site 1 out of 1 in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog


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 Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:29.4
occ:1.00
OD1 A:ASP747 2.2 35.2 1.0
O A:LEU745 2.3 26.7 1.0
OD1 A:ASN741 2.3 30.6 1.0
O A:HOH1062 2.4 30.8 1.0
OD1 A:ASP739 2.4 26.9 1.0
OD1 A:ASP743 2.5 29.4 1.0
CG A:ASN741 3.4 30.9 1.0
C A:LEU745 3.4 29.8 1.0
CG A:ASP743 3.4 31.7 1.0
CG A:ASP747 3.5 38.4 1.0
CG A:ASP739 3.5 27.7 1.0
OD2 A:ASP743 3.7 34.3 1.0
ND2 A:ASN741 3.8 32.3 1.0
N A:ASP747 3.9 34.5 1.0
CA A:ASP739 3.9 30.7 1.0
N A:LEU745 4.0 28.3 1.0
C A:ARG746 4.0 33.9 1.0
CA A:ASP747 4.1 36.9 1.0
CA A:LEU745 4.1 29.7 1.0
O A:ARG746 4.2 35.5 1.0
CB A:ASP739 4.2 28.6 1.0
OE1 A:GLU751 4.2 48.4 1.0
OD2 A:ASP747 4.3 38.5 1.0
CB A:ASP747 4.4 38.9 1.0
N A:ASP743 4.4 30.4 1.0
O A:PHE738 4.4 34.9 1.0
C A:ASP739 4.4 31.6 1.0
CB A:LEU745 4.4 29.6 1.0
N A:ARG746 4.5 31.5 1.0
OD2 A:ASP739 4.5 26.8 1.0
N A:ASN741 4.5 31.6 1.0
CB A:ASN741 4.7 32.4 1.0
CB A:ASP743 4.7 30.6 1.0
CA A:ARG746 4.7 32.2 1.0
N A:TYR740 4.7 31.2 1.0
N A:TYR742 4.7 31.0 1.0
N A:GLY744 4.8 28.1 1.0
CA A:ASP743 4.9 29.8 1.0
CA A:ASN741 4.9 32.0 1.0
C A:ASN741 4.9 31.2 1.0
N A:ASP739 5.0 32.8 1.0

Reference:

J.Hausmann, W.J.Keune, A.L.Hipgrave Ederveen, L.Van Zeijl, R.P.Joosten, A.Perrakis. Structural Snapshots of the Catalytic Cycle of the Phosphodiesterase Autotaxin. J.Struct.Biol. V. 195 199 2016.
ISSN: ESSN 1095-8657
PubMed: 27268273
DOI: 10.1016/J.JSB.2016.06.002
Page generated: Wed Oct 28 09:15:28 2020

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