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Sodium 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
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Autotaxin with Orthovanadate Bound As A Trigonal Bipyramidal Intermediate Analog, PDB code: 5ijs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ijs

Go back to Sodium Binding Sites List in 5ijs
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na913

b:55.6
occ:1.00
O A:HOH1106 2.4 54.7 1.0
O A:MET675 2.5 51.8 1.0
O A:TYR669 2.6 55.0 1.0
O A:ASP672 2.8 56.4 1.0
O A:HOH1145 2.8 45.3 1.0
C A:MET675 3.7 46.1 1.0
O A:LYS673 3.8 59.9 1.0
C A:TYR669 3.8 54.2 1.0
C A:ASP672 4.0 58.4 1.0
C A:LYS673 4.1 58.9 1.0
CA A:LYS673 4.2 60.9 1.0
CA A:SER676 4.4 41.2 1.0
N A:SER676 4.5 43.0 1.0
N A:LYS673 4.5 58.8 1.0
N A:MET675 4.6 50.1 1.0
CA A:LYS670 4.7 62.8 1.0
N A:LYS670 4.7 58.4 1.0
CA A:TYR669 4.8 50.1 1.0
CA A:MET675 4.8 46.6 1.0
CB A:SER676 4.8 40.1 1.0
O A:LYS670 4.8 68.1 1.0
CB A:TYR669 5.0 47.7 1.0
C A:LYS670 5.0 64.0 1.0

Sodium binding site 2 out of 2 in 5ijs

Go back to Sodium Binding Sites List in 5ijs
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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:Na914

b:41.9
occ:1.00
O A:SER804 2.4 31.3 1.0
OG A:SER807 2.4 31.9 1.0
O A:ASN801 2.7 29.3 1.0
C A:SER804 3.5 32.1 1.0
C A:ASN801 3.6 29.2 1.0
CB A:SER807 3.7 31.1 1.0
CA A:ASP802 3.9 32.1 1.0
N A:ASP802 4.2 29.9 1.0
CA A:CYS805 4.2 35.1 1.0
N A:SER807 4.2 31.1 1.0
O A:ASP802 4.3 32.8 1.0
N A:CYS805 4.3 32.8 1.0
C A:ASP802 4.3 32.6 1.0
C A:CYS805 4.4 33.5 1.0
O A:CYS805 4.4 36.5 1.0
CA A:SER804 4.5 30.5 1.0
CA A:SER807 4.5 32.8 1.0
N A:SER804 4.6 29.9 1.0
CB A:ASN801 4.6 30.2 1.0
CA A:ASN801 4.7 29.9 1.0
OD1 A:ASP802 4.7 42.8 1.0
O A:HOH1097 4.8 37.1 1.0
CB A:SER804 4.9 30.9 1.0
N A:ALA806 5.0 31.4 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: Tue Dec 15 11:06:07 2020

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