Zinc in PDB 7kkq: Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib

Protein crystallography data

The structure of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib, PDB code: 7kkq 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) 79.55 / 1.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.19, 159.1, 84.27, 90, 90, 90
R / Rfree (%) 20.4 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib (pdb code 7kkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib, PDB code: 7kkq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7kkq

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Zinc binding site 1 out of 4 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib


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 Veliparib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9002

b:30.2
occ:0.90
ND1 A:HIS1237 2.1 38.7 1.0
SG A:CYS1242 2.3 30.2 1.0
SG A:CYS1234 2.4 33.2 1.0
SG A:CYS1245 2.4 32.5 1.0
CE1 A:HIS1237 3.1 38.2 1.0
CG A:HIS1237 3.2 37.4 1.0
CB A:CYS1234 3.3 30.8 1.0
CB A:CYS1242 3.3 26.1 1.0
CB A:CYS1245 3.3 28.1 1.0
CB A:HIS1237 3.6 34.0 1.0
N A:CYS1245 3.9 25.6 1.0
N A:HIS1237 4.0 34.7 1.0
O B:HOH9195 4.1 30.1 1.0
CA A:CYS1245 4.2 26.3 1.0
NE2 A:HIS1237 4.2 38.6 1.0
CD2 A:HIS1237 4.3 38.8 1.0
CA A:HIS1237 4.4 33.7 1.0
O A:HOH9189 4.6 40.2 1.0
CA A:CYS1242 4.7 25.4 1.0
CB A:ILE1244 4.7 30.3 1.0
CA A:CYS1234 4.7 32.0 1.0
CB A:THR1236 4.7 42.7 1.0
O A:HOH9128 4.8 29.0 1.0
C A:THR1236 4.9 38.7 1.0

Zinc binding site 2 out of 4 in 7kkq

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Zinc binding site 2 out of 4 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib


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 Veliparib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9002

b:35.6
occ:0.90
ND1 B:HIS1237 2.2 46.1 1.0
SG B:CYS1245 2.2 36.2 1.0
SG B:CYS1242 2.3 35.5 1.0
SG B:CYS1234 2.3 40.5 1.0
CE1 B:HIS1237 3.1 45.7 1.0
CB B:CYS1234 3.2 38.0 1.0
CB B:CYS1245 3.2 31.3 1.0
CB B:CYS1242 3.2 31.3 1.0
CG B:HIS1237 3.3 44.8 1.0
CB B:HIS1237 3.6 41.4 1.0
N B:CYS1245 3.9 28.4 1.0
N B:HIS1237 4.0 41.3 1.0
CA B:CYS1245 4.2 29.4 1.0
NE2 B:HIS1237 4.3 46.1 1.0
CD2 B:HIS1237 4.4 46.5 1.0
CA B:HIS1237 4.4 41.0 1.0
O B:HOH9166 4.4 50.7 1.0
O B:HOH9140 4.5 38.5 1.0
CA B:CYS1234 4.6 38.9 1.0
CB B:THR1236 4.7 50.9 1.0
CA B:CYS1242 4.7 30.2 1.0
CB B:ILE1244 4.9 30.9 1.0
C B:THR1236 4.9 45.9 1.0

Zinc binding site 3 out of 4 in 7kkq

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Zinc binding site 3 out of 4 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9002

b:23.7
occ:0.90
ND1 C:HIS1237 2.1 30.8 1.0
SG C:CYS1245 2.3 27.0 1.0
SG C:CYS1242 2.4 25.9 1.0
SG C:CYS1234 2.4 27.0 1.0
CE1 C:HIS1237 3.0 30.6 1.0
CG C:HIS1237 3.2 29.2 1.0
CB C:CYS1234 3.2 24.1 1.0
CB C:CYS1245 3.3 23.4 1.0
CB C:CYS1242 3.3 22.0 1.0
CB C:HIS1237 3.6 26.2 1.0
O D:HOH9167 4.1 25.6 1.0
N C:HIS1237 4.1 27.8 1.0
N C:CYS1245 4.1 22.0 1.0
NE2 C:HIS1237 4.2 30.9 1.0
O C:HOH9136 4.2 32.9 1.0
CD2 C:HIS1237 4.3 31.7 1.0
CA C:CYS1245 4.3 22.8 1.0
CA C:HIS1237 4.5 26.7 1.0
CA C:CYS1234 4.7 24.9 1.0
CA C:CYS1242 4.7 22.2 1.0
CB C:THR1236 4.8 38.4 1.0

Zinc binding site 4 out of 4 in 7kkq

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Zinc binding site 4 out of 4 in the Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Catalytic Domain of Tankyrase 1 in Complex with Veliparib within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn9002

b:25.7
occ:0.90
ND1 D:HIS1237 2.1 32.6 1.0
SG D:CYS1242 2.3 29.8 1.0
SG D:CYS1234 2.3 31.6 1.0
SG D:CYS1245 2.3 29.4 1.0
CE1 D:HIS1237 3.0 32.4 1.0
CB D:CYS1234 3.2 28.7 1.0
CG D:HIS1237 3.3 31.7 1.0
CB D:CYS1242 3.3 25.6 1.0
CB D:CYS1245 3.3 25.2 1.0
CB D:HIS1237 3.7 29.1 1.0
N D:CYS1245 4.1 23.1 1.0
N D:HIS1237 4.1 29.7 1.0
O C:HOH9151 4.2 28.7 1.0
NE2 D:HIS1237 4.2 32.8 1.0
CA D:CYS1245 4.3 23.8 1.0
O D:HOH9168 4.3 40.9 1.0
CD2 D:HIS1237 4.3 32.9 1.0
CA D:HIS1237 4.5 29.2 1.0
CA D:CYS1234 4.6 29.4 1.0
CA D:CYS1242 4.6 25.1 1.0
CB D:THR1236 4.9 35.2 1.0

Reference:

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
Page generated: Mon Jan 25 16:46:11 2021

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