Zinc in PDB 7kkm: Structure of the Catalytic Domain of Tankyrase 1

Protein crystallography data

The structure of Structure of the Catalytic Domain of Tankyrase 1, PDB code: 7kkm 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) 22.82 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.03, 114.93, 80.52, 90, 91.48, 90
R / Rfree (%) 19.5 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Catalytic Domain of Tankyrase 1 (pdb code 7kkm). 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, PDB code: 7kkm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7kkm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9001

b:20.4
occ:0.90
ND1 A:HIS1237 2.1 25.1 1.0
SG A:CYS1242 2.3 20.5 1.0
SG A:CYS1234 2.3 21.2 1.0
SG A:CYS1245 2.3 22.4 1.0
CE1 A:HIS1237 3.1 24.5 1.0
CG A:HIS1237 3.2 23.4 1.0
CB A:CYS1234 3.2 18.1 1.0
CB A:CYS1242 3.3 17.5 1.0
CB A:CYS1245 3.4 19.1 1.0
CB A:HIS1237 3.5 20.1 1.0
N A:HIS1237 3.9 19.4 1.0
N A:CYS1245 3.9 19.8 1.0
NE2 A:HIS1237 4.2 24.2 1.0
CA A:CYS1245 4.3 19.1 1.0
CD2 A:HIS1237 4.3 24.4 1.0
CA A:HIS1237 4.3 19.5 1.0
CB A:THR1236 4.5 27.7 1.0
O A:HOH9129 4.5 24.6 1.0
CA A:CYS1234 4.7 17.8 1.0
CA A:CYS1242 4.7 16.8 1.0
CB A:ILE1244 4.7 22.2 1.0
O A:HOH9140 4.8 19.8 1.0
C A:THR1236 4.9 22.7 1.0

Zinc binding site 2 out of 4 in 7kkm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9001

b:22.1
occ:0.90
ND1 B:HIS1237 2.1 28.1 1.0
SG B:CYS1242 2.2 24.4 1.0
SG B:CYS1234 2.3 22.5 1.0
SG B:CYS1245 2.4 25.7 1.0
CE1 B:HIS1237 3.0 27.3 1.0
CB B:CYS1234 3.2 20.2 1.0
CG B:HIS1237 3.2 26.9 1.0
CB B:CYS1242 3.2 20.2 1.0
CB B:CYS1245 3.3 22.0 1.0
CB B:HIS1237 3.6 24.2 1.0
N B:HIS1237 3.9 23.1 1.0
O B:HOH9262 3.9 44.9 1.0
N B:CYS1245 4.0 19.7 1.0
NE2 B:HIS1237 4.2 27.7 1.0
CA B:CYS1245 4.3 20.8 1.0
CD2 B:HIS1237 4.3 28.0 1.0
CA B:HIS1237 4.3 23.5 1.0
O B:HOH9161 4.4 27.7 1.0
CB B:THR1236 4.6 28.6 1.0
CA B:CYS1242 4.6 19.7 1.0
CA B:CYS1234 4.7 20.8 1.0
C B:THR1236 4.8 29.1 1.0
CB B:ILE1244 4.8 26.9 1.0
O B:HOH9170 4.9 25.1 1.0
O B:HOH9289 5.0 39.6 1.0

Zinc binding site 3 out of 4 in 7kkm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9001

b:20.8
occ:0.90
ND1 C:HIS1237 2.1 24.5 1.0
SG C:CYS1245 2.3 22.6 1.0
SG C:CYS1234 2.3 23.2 1.0
SG C:CYS1242 2.3 21.6 1.0
CE1 C:HIS1237 3.1 23.3 1.0
CG C:HIS1237 3.2 24.0 1.0
CB C:CYS1234 3.2 20.7 1.0
CB C:CYS1245 3.3 19.7 1.0
CB C:CYS1242 3.3 18.5 1.0
CB C:HIS1237 3.6 22.0 1.0
N C:CYS1245 3.9 19.2 1.0
N C:HIS1237 4.0 23.2 1.0
CA C:CYS1245 4.2 19.8 1.0
NE2 C:HIS1237 4.3 23.3 1.0
CD2 C:HIS1237 4.3 24.0 1.0
CA C:HIS1237 4.4 21.9 1.0
O C:HOH9157 4.4 28.1 1.0
CA C:CYS1234 4.7 20.8 1.0
CA C:CYS1242 4.7 18.6 1.0
CB C:THR1236 4.7 34.0 1.0
CB C:ILE1244 4.8 22.6 1.0
O C:HOH9128 4.9 19.7 1.0
C C:THR1236 5.0 28.8 1.0

Zinc binding site 4 out of 4 in 7kkm

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn9001

b:27.9
occ:0.90
SG D:CYS1234 2.2 30.5 1.0
SG D:CYS1242 2.2 28.3 1.0
ND1 D:HIS1237 2.3 39.1 1.0
SG D:CYS1245 2.4 30.1 1.0
CB D:CYS1234 3.2 27.1 1.0
CE1 D:HIS1237 3.2 38.6 1.0
CB D:CYS1242 3.2 24.7 1.0
CB D:CYS1245 3.3 25.4 1.0
CG D:HIS1237 3.3 37.5 1.0
CB D:HIS1237 3.6 34.4 1.0
N D:CYS1245 3.9 22.4 1.0
N D:HIS1237 4.0 35.4 1.0
CA D:CYS1245 4.2 23.8 1.0
NE2 D:HIS1237 4.4 38.9 1.0
CA D:HIS1237 4.4 34.0 1.0
CD2 D:HIS1237 4.4 39.4 1.0
CA D:CYS1234 4.6 27.5 1.0
CA D:CYS1242 4.7 24.7 1.0
CB D:THR1236 4.7 41.8 1.0
CB D:ILE1244 4.7 26.9 1.0
O D:HOH9142 4.9 28.4 1.0
C D:THR1236 4.9 39.0 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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