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Zinc 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:

Vanadium (V) 1 atom
Iodine (I) 6 atoms
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5ijs

Go back to Zinc Binding Sites List in 5ijs
Zinc 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 Zinc with other atoms in the Zn 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:Zn904

b:28.9
occ:1.00
O3 A:6BR209 1.9 35.5 1.0
NE2 A:HIS315 2.1 26.6 1.0
NE2 A:HIS474 2.1 24.1 1.0
OD1 A:ASP311 2.3 30.1 1.0
OD2 A:ASP311 2.6 32.1 1.0
O1 A:6BR209 2.8 37.8 1.0
CG A:ASP311 2.8 29.8 1.0
CE1 A:HIS315 3.0 28.9 1.0
CE1 A:HIS474 3.0 24.6 1.0
CD2 A:HIS474 3.1 23.4 1.0
CD2 A:HIS315 3.1 28.0 1.0
V A:6BR209 3.2 36.4 1.0
O A:HOH1100 3.6 56.5 1.0
CE1 A:HIS359 4.1 26.7 1.0
O2 A:6BR209 4.1 32.6 1.0
ND1 A:HIS315 4.1 28.8 1.0
ND1 A:HIS474 4.1 23.3 1.0
CG A:HIS474 4.2 22.7 1.0
CG A:HIS315 4.2 29.0 1.0
CB A:ASP311 4.3 30.6 1.0
ZN A:ZN905 4.3 32.2 1.0
OG1 A:6BR209 4.4 31.9 1.0
NE2 A:HIS359 4.4 25.4 1.0
O4 A:6BR209 4.4 40.5 1.0
OD1 A:ASP171 4.6 31.4 1.0
CE A:MET361 4.6 23.3 1.0
O A:ASP311 5.0 28.6 1.0

Zinc binding site 2 out of 2 in 5ijs

Go back to Zinc Binding Sites List in 5ijs
Zinc 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 Zinc with other atoms in the Zn 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:Zn905

b:32.2
occ:1.00
OG1 A:6BR209 1.9 31.9 1.0
OD1 A:ASP171 2.0 31.4 1.0
NE2 A:HIS359 2.1 25.4 1.0
OD2 A:ASP358 2.2 24.1 1.0
O3 A:6BR209 2.6 35.5 1.0
CG A:ASP171 2.7 29.6 1.0
OD2 A:ASP171 2.8 29.3 1.0
CB A:6BR209 3.0 26.3 1.0
CE1 A:HIS359 3.0 26.7 1.0
CD2 A:HIS359 3.1 26.2 1.0
V A:6BR209 3.2 36.4 1.0
CG A:ASP358 3.2 24.5 1.0
CA A:6BR209 3.3 24.9 1.0
CG2 A:6BR209 3.5 27.2 1.0
OD1 A:ASP358 3.5 27.0 1.0
N A:6BR209 3.8 25.3 1.0
O2 A:6BR209 4.1 32.6 1.0
CB A:ASP171 4.1 30.0 1.0
ND1 A:HIS359 4.1 26.2 1.0
OD1 A:ASP311 4.1 30.1 1.0
CG A:HIS359 4.1 25.6 1.0
O4 A:6BR209 4.1 40.5 1.0
CG A:ASP311 4.3 29.8 1.0
ZN A:ZN904 4.3 28.9 1.0
N A:GLY172 4.3 26.5 1.0
CE1 A:HIS474 4.3 24.6 1.0
CB A:ASP358 4.5 23.6 1.0
CA A:ASP171 4.5 29.6 1.0
NE2 A:HIS474 4.6 24.1 1.0
OD2 A:ASP311 4.6 32.1 1.0
C A:LYS208 4.6 25.4 1.0
C A:6BR209 4.7 24.4 1.0
C A:ASP171 4.7 29.8 1.0
O1 A:6BR209 4.8 37.8 1.0
CB A:ASP311 4.8 30.6 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 Dec 16 06:22:11 2020

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