Zinc in PDB 7kkp: Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib

The structure of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib, PDB code: 7kkp was solved by K.S.Gajiwala, K.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.78 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.37, 74.08, 151.76, 90, 90, 90
R / Rfree (%)	18.7 / 20.8

The binding sites of Zinc atom in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib (pdb code 7kkp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib, PDB code: 7kkp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:10.5 occ:0.80 ND1 A:HIS1237 2.0 17.6 1.0 SG A:CYS1245 2.3 15.8 1.0 SG A:CYS1242 2.3 11.5 1.0 SG A:CYS1234 2.3 12.9 1.0 CE1 A:HIS1237 3.0 16.6 1.0 CG A:HIS1237 3.1 16.4 1.0 CB A:CYS1234 3.2 10.5 1.0 CB A:CYS1245 3.3 12.8 1.0 CB A:CYS1242 3.3 9.5 1.0 CB A:HIS1237 3.5 13.9 1.0 N A:HIS1237 3.9 15.4 1.0 N A:CYS1245 4.0 10.5 1.0 NE2 A:HIS1237 4.1 17.5 1.0 CD2 A:HIS1237 4.2 17.8 1.0 CA A:CYS1245 4.3 11.6 1.0 O A:HOH1569 4.3 13.7 1.0 CA A:HIS1237 4.4 13.7 1.0 O A:HOH1523 4.4 21.9 1.0 CB A:THR1236 4.5 23.6 1.0 CB A:ILE1244 4.6 14.1 1.0 CA A:CYS1234 4.7 10.7 1.0 CA A:CYS1242 4.7 8.9 1.0 C A:THR1236 4.9 19.6 1.0 O A:HOH1584 4.9 13.4 1.0 N A:THR1236 5.0 16.9 1.0 CA A:THR1236 5.0 16.9 1.0

Zinc binding site 2 out of 2 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Niraparib within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1401 b:11.6 occ:0.80 ND1 B:HIS1237 2.1 16.1 1.0 SG B:CYS1242 2.2 13.4 1.0 SG B:CYS1245 2.3 16.3 1.0 SG B:CYS1234 2.3 14.4 1.0 CE1 B:HIS1237 3.0 16.1 1.0 CG B:HIS1237 3.1 16.7 1.0 CB B:CYS1234 3.2 12.0 1.0 CB B:CYS1242 3.3 10.2 1.0 CB B:CYS1245 3.4 13.2 1.0 CB B:HIS1237 3.5 14.9 1.0 N B:HIS1237 3.9 16.6 1.0 N B:CYS1245 4.0 11.6 1.0 NE2 B:HIS1237 4.2 17.1 1.0 CD2 B:HIS1237 4.3 17.1 1.0 CA B:CYS1245 4.3 12.4 1.0 CA B:HIS1237 4.3 14.7 1.0 O B:HOH1627 4.3 16.6 1.0 O B:HOH1511 4.4 25.6 1.0 CB B:THR1236 4.5 20.3 1.0 CB B:ILE1244 4.6 13.3 1.0 CA B:CYS1242 4.6 9.2 1.0 CA B:CYS1234 4.7 13.3 1.0 C B:THR1236 4.8 20.5 1.0 O B:HOH1550 4.8 13.5 1.0 N B:THR1236 5.0 18.1 1.0 CA B:THR1236 5.0 17.2 1.0

K.Ryan, B.Bolanos, M.Smith, P.Palde, P.D.Cuenca, T.L.Vanarsdale, S.Niessen, L.Zhang, D.Behenna, M.A.Ornelas, K.T.Tran, S.Kaiser, L.Lum, A.Stewart, K.S.Gajiwala. Dissecting the Molecular Determinants of Clinical PARP1 Inhibitor Selectivity For TANKYRASE1. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33361107
DOI: 10.1074/JBC.RA120.016573