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Zinc in PDB 5ohi: Crystal Structure of Autotaxin in Complex with Bi-2545

Enzymatic activity of Crystal Structure of Autotaxin in Complex with Bi-2545

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with Bi-2545:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin in Complex with Bi-2545, PDB code: 5ohi was solved by S.Hoerer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.82 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.057, 93.779, 75.695, 90.00, 94.91, 90.00
R / Rfree (%) 17 / 20

Other elements in 5ohi:

The structure of Crystal Structure of Autotaxin in Complex with Bi-2545 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Potassium (K) 1 atom
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with Bi-2545 (pdb code 5ohi). 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 in Complex with Bi-2545, PDB code: 5ohi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5ohi

Go back to Zinc Binding Sites List in 5ohi
Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with Bi-2545


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 in Complex with Bi-2545 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn912

b:23.8
occ:1.00
NE2 A:HIS315 2.0 23.9 1.0
N29 A:9V8920 2.1 30.6 1.0
NE2 A:HIS474 2.1 19.4 1.0
OD1 A:ASP311 2.1 25.8 1.0
OD2 A:ASP311 2.5 25.8 1.0
O A:HOH1002 2.5 35.4 1.0
CG A:ASP311 2.6 23.8 1.0
CD2 A:HIS315 3.0 24.2 1.0
N30 A:9V8920 3.0 31.3 1.0
CE1 A:HIS315 3.0 24.1 1.0
CD2 A:HIS474 3.0 19.8 1.0
C28 A:9V8920 3.1 31.6 1.0
CE1 A:HIS474 3.1 19.0 1.0
C25 A:9V8920 3.6 34.6 1.0
CG A:HIS315 4.1 25.2 1.0
CB A:ASP311 4.1 24.1 1.0
ND1 A:HIS315 4.2 26.2 1.0
N31 A:9V8920 4.2 32.9 1.0
CG A:HIS474 4.2 18.8 1.0
CE1 A:HIS359 4.2 20.1 1.0
ND1 A:HIS474 4.2 19.4 1.0
C27 A:9V8920 4.3 33.0 1.0
OG1 A:THR209 4.4 37.7 1.0
CE A:MET361 4.4 20.6 1.0
NE2 A:HIS359 4.5 20.1 1.0
OD1 A:ASP171 4.5 30.5 1.0
O A:HOH1157 4.5 42.0 1.0
ZN A:ZN913 4.6 29.2 0.6
O A:ASP311 4.9 26.8 1.0
CA A:ASP311 5.0 23.0 1.0

Zinc binding site 2 out of 2 in 5ohi

Go back to Zinc Binding Sites List in 5ohi
Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with Bi-2545


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 in Complex with Bi-2545 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn913

b:29.2
occ:0.56
OD1 A:ASP171 1.9 30.5 1.0
OD2 A:ASP358 2.1 22.9 1.0
O A:HOH1002 2.1 35.4 1.0
NE2 A:HIS359 2.3 20.1 1.0
CG A:ASP171 2.6 32.4 1.0
OG1 A:THR209 2.7 37.7 1.0
OD2 A:ASP171 2.8 41.6 1.0
CG A:ASP358 2.9 22.5 1.0
CG2 A:THR209 3.0 26.7 1.0
CB A:THR209 3.1 28.6 1.0
CE1 A:HIS359 3.2 20.1 1.0
CD2 A:HIS359 3.2 20.5 1.0
OD1 A:ASP358 3.2 22.5 1.0
CA A:THR209 3.3 18.9 1.0
N A:THR209 3.8 19.0 1.0
CB A:ASP171 4.0 22.7 1.0
C25 A:9V8920 4.1 34.6 1.0
OD1 A:ASP311 4.2 25.8 1.0
N A:GLY172 4.2 20.9 1.0
ND1 A:HIS359 4.3 20.9 1.0
CG A:HIS359 4.3 19.9 1.0
CB A:ASP358 4.3 19.5 1.0
CA A:ASP171 4.4 20.6 1.0
C A:THR209 4.5 21.6 1.0
CE1 A:HIS474 4.5 19.0 1.0
CG A:ASP311 4.6 23.8 1.0
ZN A:ZN912 4.6 23.8 1.0
C28 A:9V8920 4.6 31.6 1.0
C A:LYS208 4.7 21.3 1.0
C A:ASP171 4.7 23.8 1.0
C24 A:9V8920 4.7 36.3 1.0
NE2 A:HIS474 4.7 19.4 1.0
N29 A:9V8920 4.8 30.6 1.0
O A:THR209 4.8 22.0 1.0
OD2 A:ASP311 5.0 25.8 1.0

Reference:

C.A.Kuttruff, M.Ferrara, T.Bretschneider, S.Hoerer, S.Handschuh, B.Nosse, H.Romig, P.Nicklin, G.J.Roth. Discovery of Bi-2545: A Novel Autotaxin Inhibitor That Significantly Reduces Lpa Levels in Vivo. Acs Med Chem Lett V. 8 1252 2017.
ISSN: ISSN 1948-5875
PubMed: 29259743
DOI: 10.1021/ACSMEDCHEMLETT.7B00312
Page generated: Wed Dec 16 06:38:31 2020

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