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Zinc in PDB 3mhj: Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One

Enzymatic activity of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One

All present enzymatic activity of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One:
2.4.2.30;

Protein crystallography data

The structure of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One, PDB code: 3mhj was solved by T.Karlberg, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Kotenyova, N.Markova, M.Moche, P.Nordlund, T.Nyman, C.Persson, M.I.Siponen, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, H.Schuler, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.21 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 90.547, 97.727, 119.126, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.3

Other elements in 3mhj:

The structure of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One (pdb code 3mhj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One, PDB code: 3mhj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mhj

Go back to Zinc Binding Sites List in 3mhj
Zinc binding site 1 out of 2 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:19.8
occ:1.00
 ND1 A:HIS1084 2.1 20.4 1.0
SG A:CYS1089 2.3 19.7 1.0
SG A:CYS1081 2.3 17.8 1.0
SG A:CYS1092 2.3 21.5 1.0
CE1 A:HIS1084 3.0 22.2 1.0
CG A:HIS1084 3.2 22.5 1.0
CB A:CYS1092 3.2 20.1 1.0
CB A:CYS1081 3.2 18.7 1.0
CB A:CYS1089 3.3 17.8 1.0
CB A:HIS1084 3.6 22.0 1.0
N A:HIS1084 3.9 23.1 1.0
N A:CYS1092 4.0 19.1 1.0
O A:HOH95 4.1 32.6 1.0
NE2 A:HIS1084 4.1 21.6 1.0
O A:HOH116 4.2 26.6 1.0
CA A:CYS1092 4.2 19.3 1.0
CD2 A:HIS1084 4.2 23.9 1.0
CA A:HIS1084 4.3 22.0 1.0
CB A:VAL1083 4.4 23.0 1.0
CA A:CYS1081 4.7 19.5 1.0
CA A:CYS1089 4.7 17.1 1.0
C A:VAL1083 4.8 23.3 1.0
CB A:ILE1091 4.8 19.2 1.0
N A:VAL1083 4.8 22.3 1.0
O A:HOH39 4.9 19.7 1.0
CA A:VAL1083 4.9 23.1 1.0
CG1 A:VAL1083 4.9 22.6 1.0

Zinc binding site 2 out of 2 in 3mhj

Go back to Zinc Binding Sites List in 3mhj
Zinc binding site 2 out of 2 in the Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Tankyrase 2 - Catalytic Parp Domain in Complex with 1-Methyl-3- (Trifluoromethyl)-5H-Benzo[C][1,8]Naphtyridine-6-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:21.3
occ:1.00
 ND1 B:HIS1084 2.2 18.9 1.0
SG B:CYS1081 2.3 19.3 1.0
SG B:CYS1089 2.3 19.7 1.0
SG B:CYS1092 2.3 22.7 1.0
CE1 B:HIS1084 3.1 25.5 1.0
CG B:HIS1084 3.2 24.8 1.0
CB B:CYS1081 3.2 20.6 1.0
CB B:CYS1092 3.3 21.0 1.0
CB B:CYS1089 3.3 18.8 1.0
CB B:HIS1084 3.6 24.9 1.0
N B:HIS1084 3.9 24.9 1.0
N B:CYS1092 3.9 20.1 1.0
O B:HOH301 4.2 27.5 1.0
CA B:CYS1092 4.2 19.9 1.0
NE2 B:HIS1084 4.2 26.3 1.0
CD2 B:HIS1084 4.3 25.0 1.0
CA B:HIS1084 4.3 24.0 1.0
CB B:VAL1083 4.4 26.6 1.0
O B:HOH309 4.4 33.7 1.0
CA B:CYS1081 4.6 20.5 1.0
CA B:CYS1089 4.7 18.4 1.0
C B:VAL1083 4.8 26.3 1.0
CB B:ILE1091 4.8 20.8 1.0
O B:HOH75 4.8 24.8 1.0
N B:VAL1083 4.8 25.3 1.0
CA B:VAL1083 4.9 26.4 1.0
CG1 B:VAL1083 4.9 27.5 1.0

Reference:

E.Wahlberg, T.Karlberg, E.Kouznetsova, N.Markova, A.Macchiarulo, A.G.Thorsell, E.Pol, A.Frostell, T.Ekblad, B.Kull, G.M.Robertson, R.Pellicciari, H.Schuler, J.Weigelt. Family-Wide Chemical Profiling and Structural Analysis of Parp and Tankyrase Inhibitors Nat.Biotechnol. V. 30 283 2012.
ISSN: ISSN 1087-0156
PubMed: 22343925
DOI: 10.1038/NBT.2121
Page generated: Sat Oct 26 09:29:50 2024

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