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Zinc in PDB 5ebt: Tankyrase 1 with Phthalazinone 2

Enzymatic activity of Tankyrase 1 with Phthalazinone 2

All present enzymatic activity of Tankyrase 1 with Phthalazinone 2:
2.4.2.30;

Protein crystallography data

The structure of Tankyrase 1 with Phthalazinone 2, PDB code: 5ebt was solved by S.L.Kazmirski, J.Johannes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.35 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.733, 151.189, 57.224, 90.00, 96.28, 90.00
R / Rfree (%) 17.1 / 20.8

Other elements in 5ebt:

The structure of Tankyrase 1 with Phthalazinone 2 also contains other interesting chemical elements:

Fluorine (F) 20 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tankyrase 1 with Phthalazinone 2 (pdb code 5ebt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tankyrase 1 with Phthalazinone 2, PDB code: 5ebt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ebt

Go back to Zinc Binding Sites List in 5ebt
Zinc binding site 1 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1403

b:31.9
occ:1.00
ND1 A:HIS1237 2.2 33.5 1.0
SG A:CYS1245 2.2 28.4 1.0
SG A:CYS1234 2.3 29.8 1.0
SG A:CYS1242 2.3 32.2 1.0
CE1 A:HIS1237 3.1 33.7 1.0
CG A:HIS1237 3.2 32.2 1.0
CB A:CYS1234 3.3 24.8 1.0
CB A:CYS1245 3.3 23.9 1.0
CB A:CYS1242 3.3 26.8 1.0
CB A:HIS1237 3.6 29.0 1.0
N A:HIS1237 3.8 29.4 1.0
N A:CYS1245 4.1 23.7 1.0
CA A:HIS1237 4.3 29.2 1.0
NE2 A:HIS1237 4.3 35.3 1.0
CA A:CYS1245 4.3 24.1 1.0
CB A:THR1236 4.3 37.0 1.0
CD2 A:HIS1237 4.4 35.5 1.0
CA A:CYS1234 4.7 25.5 1.0
C A:THR1236 4.7 35.4 1.0
CA A:CYS1242 4.7 25.7 1.0
CA A:THR1236 4.9 32.4 1.0

Zinc binding site 2 out of 4 in 5ebt

Go back to Zinc Binding Sites List in 5ebt
Zinc binding site 2 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1402

b:25.4
occ:1.00
ND1 B:HIS1237 2.1 28.4 1.0
SG B:CYS1245 2.2 27.0 1.0
SG B:CYS1234 2.2 29.8 1.0
SG B:CYS1242 2.3 24.5 1.0
CE1 B:HIS1237 3.1 27.1 1.0
CG B:HIS1237 3.2 28.1 1.0
CB B:CYS1234 3.3 24.4 1.0
CB B:CYS1242 3.3 19.6 1.0
CB B:CYS1245 3.4 22.2 1.0
CB B:HIS1237 3.5 26.1 1.0
N B:HIS1237 3.8 26.4 1.0
N B:CYS1245 4.0 21.4 1.0
NE2 B:HIS1237 4.3 28.7 1.0
CA B:HIS1237 4.3 27.0 1.0
CA B:CYS1245 4.3 21.2 1.0
CD2 B:HIS1237 4.3 29.5 1.0
CB B:THR1236 4.4 37.7 1.0
CA B:CYS1234 4.7 24.0 1.0
C B:THR1236 4.7 29.8 1.0
CA B:CYS1242 4.7 19.0 1.0
CA B:THR1236 4.9 27.0 1.0
CB B:ILE1244 5.0 24.0 1.0

Zinc binding site 3 out of 4 in 5ebt

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Zinc binding site 3 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1403

b:22.6
occ:1.00
ND1 C:HIS1237 2.1 25.6 1.0
SG C:CYS1234 2.2 22.9 1.0
SG C:CYS1245 2.2 26.8 1.0
SG C:CYS1242 2.3 20.0 1.0
CE1 C:HIS1237 3.1 25.0 1.0
CG C:HIS1237 3.2 25.4 1.0
CB C:CYS1234 3.3 19.3 1.0
CB C:CYS1245 3.3 22.1 1.0
CB C:CYS1242 3.3 15.3 1.0
CB C:HIS1237 3.6 22.3 1.0
N C:HIS1237 3.8 24.8 1.0
N C:CYS1245 4.0 21.7 1.0
CA C:CYS1245 4.3 22.2 1.0
NE2 C:HIS1237 4.3 26.5 1.0
CA C:HIS1237 4.3 23.3 1.0
CD2 C:HIS1237 4.3 27.6 1.0
CB C:THR1236 4.4 30.4 1.0
O C:HOH1553 4.7 44.2 1.0
CA C:CYS1234 4.7 21.1 1.0
O C:HOH1529 4.7 16.3 1.0
CA C:CYS1242 4.7 16.4 1.0
C C:THR1236 4.8 29.8 1.0
CA C:THR1236 4.9 26.8 1.0
CB C:ILE1244 5.0 25.1 1.0

Zinc binding site 4 out of 4 in 5ebt

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Zinc binding site 4 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1401

b:35.0
occ:1.00
SG D:CYS1245 2.2 34.4 1.0
SG D:CYS1242 2.2 31.7 1.0
ND1 D:HIS1237 2.2 38.7 1.0
SG D:CYS1234 2.3 33.7 1.0
CE1 D:HIS1237 3.1 38.9 1.0
CB D:CYS1245 3.2 29.2 1.0
CB D:CYS1234 3.3 29.2 1.0
CB D:CYS1242 3.3 26.6 1.0
CG D:HIS1237 3.3 38.0 1.0
CB D:HIS1237 3.7 34.4 1.0
N D:CYS1245 3.9 30.1 1.0
O D:HOH1557 3.9 27.2 1.0
N D:HIS1237 4.0 35.1 1.0
CA D:CYS1245 4.1 29.9 1.0
NE2 D:HIS1237 4.3 40.8 1.0
CB D:THR1236 4.4 47.1 1.0
CD2 D:HIS1237 4.4 41.1 1.0
CA D:HIS1237 4.4 34.7 1.0
O D:HOH1510 4.5 37.3 1.0
CA D:CYS1234 4.7 30.4 1.0
CA D:CYS1242 4.7 26.8 1.0
CB D:ILE1244 4.8 33.6 1.0
C D:THR1236 4.9 40.7 1.0

Reference:

J.W.Johannes, L.Almeida, K.Daly, A.D.Ferguson, S.E.Grosskurth, H.Guan, T.Howard, S.Ioannidis, S.Kazmirski, M.L.Lamb, N.A.Larsen, P.D.Lyne, K.Mikule, C.Ogoe, B.Peng, P.Petteruti, J.A.Read, N.Su, M.Sylvester, S.Throner, W.Wang, X.Wang, J.Wu, Q.Ye, Y.Yu, X.Zheng, D.A.Scott. Discovery of AZ0108, An Orally Bioavailable Phthalazinone Parp Inhibitor That Blocks Centrosome Clustering. Bioorg.Med.Chem.Lett. V. 25 5743 2015.
ISSN: ESSN 1464-3405
PubMed: 26546219
DOI: 10.1016/J.BMCL.2015.10.079
Page generated: Wed Dec 16 06:09:22 2020

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