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Zinc in PDB 2gh6: Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6 was solved by T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.507, 94.897, 123.301, 90.00, 104.28, 90.00
R / Rfree (%) 15.8 / 21.4

Other elements in 2gh6:

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Potassium (K) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb code 2gh6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2gh6

Go back to Zinc Binding Sites List in 2gh6
Zinc binding site 1 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9451

b:31.0
occ:0.50
O2 A:CF39452 1.8 17.8 0.5
OD2 A:ASP268 2.0 17.1 1.0
O2 A:CF39452 2.1 14.5 0.5
OD1 A:ASP180 2.2 16.0 1.0
ND1 A:HIS182 2.2 16.8 1.0
OD2 A:ASP180 2.5 15.4 1.0
CG A:ASP180 2.6 17.4 1.0
C13 A:CF39452 2.7 23.5 0.5
C13 A:CF39452 2.8 24.0 0.5
CG A:ASP268 3.1 15.2 1.0
CE1 A:HIS182 3.1 17.5 1.0
CG A:HIS182 3.4 15.8 1.0
C11 A:CF39452 3.4 25.3 0.5
OD1 A:ASP268 3.5 14.0 1.0
F2 A:CF39452 3.6 26.0 1.0
C15 A:CF39452 3.7 23.1 1.0
CB A:HIS182 3.8 16.0 1.0
C11 A:CF39452 3.9 25.6 0.5
C9 A:CF39452 3.9 27.9 1.0
NE2 A:HIS142 4.0 15.6 1.0
N A:HIS182 4.1 16.0 1.0
CA A:GLY310 4.1 17.3 1.0
CB A:ASP180 4.2 15.7 1.0
NE2 A:HIS182 4.3 14.4 1.0
OH A:TYR312 4.3 21.4 1.0
CE2 A:TYR312 4.3 17.3 1.0
CB A:ASP268 4.3 16.8 1.0
CD2 A:HIS182 4.4 12.9 1.0
N A:VAL181 4.4 16.5 1.0
N A:GLY310 4.4 16.9 1.0
CE1 A:HIS142 4.5 16.3 1.0
F1 A:CF39452 4.5 26.7 1.0
CA A:HIS182 4.6 16.5 1.0
CG1 A:VAL181 4.6 14.0 1.0
F3 A:CF39452 4.6 24.6 1.0
NE2 A:HIS143 4.7 17.1 1.0
CZ A:TYR312 4.8 17.3 1.0
C A:GLY310 4.8 17.9 1.0
N A:GLY311 4.8 18.5 1.0
C A:ASP180 4.9 16.5 1.0
CA A:ASP180 4.9 16.0 1.0

Zinc binding site 2 out of 4 in 2gh6

Go back to Zinc Binding Sites List in 2gh6
Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9551

b:26.9
occ:0.50
O2 B:CF39552 1.9 5.5 0.5
OD2 B:ASP268 1.9 17.1 1.0
OD1 B:ASP180 2.0 14.6 1.0
O2 B:CF39552 2.2 6.9 0.5
ND1 B:HIS182 2.3 13.6 1.0
OD2 B:ASP180 2.6 17.3 1.0
CG B:ASP180 2.6 16.1 1.0
C13 B:CF39552 2.7 17.9 0.5
C13 B:CF39552 2.8 17.4 0.5
CG B:ASP268 3.0 16.2 1.0
CE1 B:HIS182 3.1 11.8 1.0
C11 B:CF39552 3.3 20.1 0.5
CG B:HIS182 3.4 15.7 1.0
OD1 B:ASP268 3.4 14.9 1.0
F2 B:CF39552 3.6 18.9 1.0
C11 B:CF39552 3.7 19.2 0.5
C15 B:CF39552 3.7 18.2 1.0
CB B:HIS182 3.8 14.9 1.0
C9 B:CF39552 3.8 23.2 1.0
CB B:ASP180 4.1 15.3 1.0
NE2 B:HIS142 4.1 16.3 1.0
N B:HIS182 4.1 16.9 1.0
CA B:GLY310 4.2 15.7 1.0
CE2 B:TYR312 4.2 22.2 1.0
NE2 B:HIS182 4.3 12.0 1.0
CB B:ASP268 4.3 16.2 1.0
CG1 B:VAL181 4.4 16.9 1.0
N B:VAL181 4.4 17.6 1.0
OH B:TYR312 4.4 18.8 1.0
CD2 B:HIS182 4.4 11.0 1.0
N B:GLY310 4.5 16.0 1.0
CE1 B:HIS142 4.5 13.6 1.0
F1 B:CF39552 4.5 19.7 1.0
CA B:HIS182 4.6 16.6 1.0
NE2 B:HIS143 4.7 19.4 1.0
F3 B:CF39552 4.7 20.6 1.0
CZ B:TYR312 4.8 22.2 1.0
CA B:ASP180 4.8 17.3 1.0
C B:GLY310 4.8 16.2 1.0
C B:ASP180 4.8 17.2 1.0
N B:GLY311 4.9 17.2 1.0

Zinc binding site 3 out of 4 in 2gh6

Go back to Zinc Binding Sites List in 2gh6
Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9651

b:31.3
occ:0.50
O2 C:CF39652 1.8 16.3 0.5
OD2 C:ASP268 2.0 16.2 1.0
O2 C:CF39652 2.1 12.0 0.5
OD1 C:ASP180 2.1 17.9 1.0
ND1 C:HIS182 2.3 20.4 1.0
OD2 C:ASP180 2.6 18.6 1.0
C13 C:CF39652 2.7 23.6 0.5
CG C:ASP180 2.7 18.4 1.0
C13 C:CF39652 2.7 22.1 0.5
CE1 C:HIS182 3.2 21.4 1.0
CG C:ASP268 3.2 16.4 1.0
F2 C:CF39652 3.3 24.9 1.0
CG C:HIS182 3.3 20.2 1.0
C15 C:CF39652 3.6 22.0 1.0
OD1 C:ASP268 3.7 16.6 1.0
C11 C:CF39652 3.7 23.6 0.5
C11 C:CF39652 3.7 25.1 0.5
CB C:HIS182 3.7 17.9 1.0
NE2 C:HIS142 3.9 15.1 1.0
C9 C:CF39652 3.9 27.5 1.0
CA C:GLY310 4.1 17.5 1.0
CB C:ASP180 4.2 17.1 1.0
OH C:TYR312 4.3 20.4 1.0
CE2 C:TYR312 4.3 18.4 1.0
N C:HIS182 4.3 18.7 1.0
NE2 C:HIS182 4.3 19.9 1.0
N C:GLY310 4.4 17.4 1.0
F1 C:CF39652 4.4 23.6 1.0
CB C:ASP268 4.4 17.3 1.0
CD2 C:HIS182 4.4 20.2 1.0
CE1 C:HIS142 4.4 16.2 1.0
N C:VAL181 4.5 17.7 1.0
F3 C:CF39652 4.5 23.8 1.0
CG1 C:VAL181 4.5 16.7 1.0
NE2 C:HIS143 4.5 14.9 1.0
CA C:HIS182 4.7 18.1 1.0
CZ C:TYR312 4.8 18.7 1.0
C C:GLY310 4.8 17.8 1.0
N C:GLY311 4.9 18.1 1.0
CA C:ASP180 5.0 17.3 1.0

Zinc binding site 4 out of 4 in 2gh6

Go back to Zinc Binding Sites List in 2gh6
Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn9751

b:29.7
occ:0.50
O2 D:CF39752 1.9 15.4 0.5
OD2 D:ASP268 2.0 15.7 1.0
OD1 D:ASP180 2.1 23.4 1.0
O2 D:CF39752 2.1 16.3 0.5
ND1 D:HIS182 2.3 21.4 1.0
OD2 D:ASP180 2.5 21.7 1.0
CG D:ASP180 2.6 20.9 1.0
C13 D:CF39752 2.8 23.0 0.5
C13 D:CF39752 2.8 23.3 0.5
CG D:ASP268 3.1 15.9 1.0
CE1 D:HIS182 3.2 21.8 1.0
CG D:HIS182 3.3 20.1 1.0
OD1 D:ASP268 3.5 15.9 1.0
F2 D:CF39752 3.5 24.9 1.0
CB D:HIS182 3.6 17.7 1.0
C15 D:CF39752 3.7 23.7 1.0
C11 D:CF39752 3.7 26.0 0.5
C11 D:CF39752 3.8 25.9 0.5
NE2 D:HIS142 3.9 21.1 1.0
C9 D:CF39752 3.9 28.4 1.0
N D:HIS182 4.1 17.4 1.0
CB D:ASP180 4.1 18.8 1.0
CA D:GLY310 4.2 18.1 1.0
CB D:ASP268 4.3 15.4 1.0
N D:VAL181 4.3 18.3 1.0
NE2 D:HIS182 4.3 19.9 1.0
CE2 D:TYR312 4.3 16.7 1.0
CE1 D:HIS142 4.4 18.1 1.0
OH D:TYR312 4.4 20.4 1.0
CD2 D:HIS182 4.4 22.1 1.0
CG1 D:VAL181 4.4 16.5 1.0
F1 D:CF39752 4.4 23.3 1.0
N D:GLY310 4.5 17.9 1.0
CA D:HIS182 4.5 17.6 1.0
NE2 D:HIS143 4.6 17.7 1.0
F3 D:CF39752 4.7 24.8 1.0
C D:ASP180 4.8 19.2 1.0
CA D:ASP180 4.8 19.4 1.0
CZ D:TYR312 4.9 18.1 1.0
C D:GLY310 4.9 18.3 1.0
N D:GLY311 5.0 18.4 1.0
C D:VAL181 5.0 17.3 1.0

Reference:

T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner. Complex Structure of A Bacterial Class 2 Histone Deacetylase Homologue with A Trifluoromethylketone Inhibitor. Acta Crystallogr.,Sect.F V. 63 270 2007.
ISSN: ESSN 1744-3091
PubMed: 17401192
DOI: 10.1107/S1744309107012377
Page generated: Wed Dec 16 03:29:27 2020

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