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Zinc in PDB 2vcg: Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg was solved by A.Dickmanns, A.Strasser, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.85 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.664, 93.633, 121.664, 90.00, 103.99, 90.00
R / Rfree (%) 15.6 / 20.6

Other elements in 2vcg:

The structure of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Potassium (K) 8 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 (pdb code 2vcg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17, PDB code: 2vcg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2vcg

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Zinc binding site 1 out of 5 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1375

b:14.9
occ:0.50
OD2 A:ASP274 2.0 7.4 1.0
OAE A:S171378 2.0 2.9 0.5
OD1 A:ASP186 2.1 12.4 1.0
ND1 A:HIS188 2.1 8.0 1.0
OAB A:S171378 2.2 4.1 0.5
OD2 A:ASP186 2.4 13.3 1.0
CG A:ASP186 2.6 10.5 1.0
NAR A:S171378 2.7 2.0 0.5
CAU A:S171378 2.7 5.2 0.5
CG A:ASP274 3.0 8.7 1.0
CE1 A:HIS188 3.0 9.6 1.0
CG A:HIS188 3.2 9.7 1.0
OD1 A:ASP274 3.3 9.4 1.0
CB A:HIS188 3.5 9.5 1.0
N A:HIS188 3.9 9.7 1.0
CA A:GLY316 4.0 10.7 1.0
O A:HOH2393 4.0 34.4 1.0
NE2 A:HIS148 4.0 14.2 1.0
CB A:ASP186 4.1 10.0 1.0
CAO A:S171378 4.2 9.0 0.5
NE2 A:HIS188 4.2 8.6 1.0
CB A:ASP274 4.2 8.5 1.0
CD2 A:HIS188 4.3 10.4 1.0
CG1 A:VAL187 4.3 10.5 1.0
CE2 A:TYR318 4.3 11.2 1.0
N A:VAL187 4.3 9.4 1.0
CE1 A:HIS148 4.3 11.4 1.0
CA A:HIS188 4.4 10.4 1.0
N A:GLY316 4.4 10.4 1.0
OH A:TYR318 4.5 14.1 1.0
C A:GLY316 4.7 10.8 1.0
C A:ASP186 4.7 10.0 1.0
CA A:ASP186 4.8 10.3 1.0
N A:GLY317 4.8 11.3 1.0
C A:VAL187 4.9 9.6 1.0
CAM A:S171378 4.9 13.6 0.5
CZ A:TYR318 4.9 12.5 1.0
NE2 A:HIS149 4.9 13.6 1.0

Zinc binding site 2 out of 5 in 2vcg

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Zinc binding site 2 out of 5 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1376

b:11.5
occ:0.50
OD2 B:ASP274 1.9 7.2 1.0
ND1 B:HIS188 2.1 7.2 1.0
OD1 B:ASP186 2.1 6.0 1.0
OAE B:S171379 2.2 2.0 0.5
OAB B:S171379 2.2 5.2 0.5
OD2 B:ASP186 2.4 7.9 1.0
CG B:ASP186 2.5 7.5 1.0
CAU B:S171379 2.7 4.3 0.5
NAR B:S171379 2.8 2.0 0.5
CE1 B:HIS188 2.9 6.3 1.0
CG B:ASP274 2.9 6.8 1.0
CG B:HIS188 3.2 6.5 1.0
OD1 B:ASP274 3.3 7.0 1.0
CB B:HIS188 3.6 6.4 1.0
NE2 B:HIS148 3.9 9.2 1.0
N B:HIS188 3.9 6.5 1.0
O B:HOH2448 4.0 38.4 1.0
CB B:ASP186 4.1 6.5 1.0
NE2 B:HIS188 4.1 5.2 1.0
CA B:GLY316 4.1 9.2 1.0
CAO B:S171379 4.2 9.2 0.5
CB B:ASP274 4.2 6.2 1.0
CD2 B:HIS188 4.2 6.0 1.0
CG1 B:VAL187 4.2 5.5 1.0
N B:VAL187 4.3 6.4 1.0
CE1 B:HIS148 4.4 6.7 1.0
CA B:HIS188 4.4 6.9 1.0
CE1 B:TYR318 4.4 10.2 1.0
N B:GLY316 4.4 9.7 1.0
OH B:TYR318 4.4 12.7 1.0
C B:ASP186 4.7 6.7 1.0
CA B:ASP186 4.8 6.7 1.0
CAM B:S171379 4.8 15.3 0.5
C B:GLY316 4.8 9.9 1.0
NE2 B:HIS149 4.8 10.3 1.0
C B:VAL187 4.9 6.2 1.0
CZ B:TYR318 4.9 11.1 1.0
N B:GLY317 5.0 9.8 1.0

Zinc binding site 3 out of 5 in 2vcg

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Zinc binding site 3 out of 5 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1377

b:11.1
occ:0.50
OD2 C:ASP274 1.9 5.7 1.0
OD1 C:ASP186 2.1 6.4 1.0
OAE C:S171380 2.1 2.0 0.5
OAB C:S171380 2.2 2.0 0.5
ND1 C:HIS188 2.2 6.9 1.0
OD2 C:ASP186 2.4 6.3 1.0
CG C:ASP186 2.5 7.7 1.0
NAR C:S171380 2.7 2.0 0.5
CAU C:S171380 2.7 2.3 0.5
CG C:ASP274 3.0 5.8 1.0
CE1 C:HIS188 3.1 5.7 1.0
CG C:HIS188 3.3 6.8 1.0
OD1 C:ASP274 3.4 5.0 1.0
CB C:HIS188 3.6 6.3 1.0
N C:HIS188 4.0 6.6 1.0
CB C:ASP186 4.0 6.9 1.0
NE2 C:HIS148 4.0 8.0 1.0
O C:HOH2409 4.0 31.6 1.0
CA C:GLY316 4.1 5.8 1.0
CAO C:S171380 4.2 5.8 0.5
CB C:ASP274 4.2 5.4 1.0
NE2 C:HIS188 4.3 5.2 1.0
N C:VAL187 4.3 6.9 1.0
CE1 C:HIS148 4.4 7.6 1.0
CD2 C:HIS188 4.4 2.4 1.0
N C:GLY316 4.4 6.3 1.0
CE2 C:TYR318 4.4 16.1 1.0
CG1 C:VAL187 4.4 4.5 1.0
OH C:TYR318 4.4 13.4 1.0
CA C:HIS188 4.4 7.2 1.0
CAM C:S171380 4.7 10.0 0.5
C C:GLY316 4.7 7.6 1.0
C C:ASP186 4.7 7.2 1.0
CA C:ASP186 4.7 7.3 1.0
NE2 C:HIS149 4.9 9.2 1.0
CZ C:TYR318 4.9 14.7 1.0
O C:HOH2224 4.9 32.4 1.0
N C:GLY317 4.9 7.7 1.0
C C:VAL187 5.0 7.0 1.0

Zinc binding site 4 out of 5 in 2vcg

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Zinc binding site 4 out of 5 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


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 Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1377

b:12.5
occ:0.50
OD2 D:ASP274 1.9 8.4 1.0
OD1 D:ASP186 2.0 8.9 1.0
OAE D:S171381 2.0 2.0 0.5
ND1 D:HIS188 2.1 9.4 1.0
OAB D:S171381 2.2 2.0 0.5
OD2 D:ASP186 2.4 9.3 1.0
CG D:ASP186 2.5 10.0 1.0
NAR D:S171381 2.7 2.0 0.5
CAU D:S171381 2.7 2.0 0.5
CG D:ASP274 2.9 10.4 1.0
CE1 D:HIS188 3.0 9.5 1.0
CG D:HIS188 3.2 9.7 1.0
OD1 D:ASP274 3.4 8.3 1.0
CB D:HIS188 3.6 9.2 1.0
O D:HOH2444 3.9 30.6 1.0
NE2 D:HIS148 4.0 9.9 1.0
N D:HIS188 4.0 9.6 1.0
CB D:ASP186 4.0 9.6 1.0
CA D:GLY316 4.0 9.7 1.0
CB D:ASP274 4.2 9.5 1.0
NE2 D:HIS188 4.2 8.5 1.0
CAO D:S171381 4.2 2.7 0.5
CD2 D:HIS188 4.3 8.9 1.0
CE1 D:HIS148 4.3 12.0 1.0
N D:VAL187 4.3 9.5 1.0
CE1 D:TYR318 4.4 10.3 1.0
N D:GLY316 4.4 9.2 1.0
CG1 D:VAL187 4.4 9.4 1.0
CA D:HIS188 4.5 9.7 1.0
OH D:TYR318 4.5 12.8 1.0
CAM D:S171381 4.7 7.6 0.5
C D:ASP186 4.7 9.7 1.0
CA D:ASP186 4.7 9.6 1.0
C D:GLY316 4.8 10.2 1.0
N D:GLY317 4.8 10.8 1.0
NE2 D:HIS149 4.9 8.0 1.0
CZ D:TYR318 5.0 12.0 1.0
C D:VAL187 5.0 9.6 1.0

Zinc binding site 5 out of 5 in 2vcg

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Zinc binding site 5 out of 5 in the Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Hdac-Like Protein Hdah From Bordetella Sp. with the Bound Inhibitor St-17 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1378

b:21.6
occ:1.00
NE2 D:HIS6 2.0 20.3 1.0
ND1 D:HIS4 2.0 28.5 1.0
ND1 D:HIS64 2.1 14.8 1.0
CL D:CL1382 2.3 21.4 1.0
CD2 D:HIS6 2.9 22.1 1.0
CG D:HIS4 3.0 27.7 1.0
CG D:HIS64 3.0 14.7 1.0
CE1 D:HIS6 3.0 21.4 1.0
CE1 D:HIS64 3.1 15.0 1.0
CE1 D:HIS4 3.1 29.6 1.0
CB D:HIS4 3.2 27.7 1.0
CB D:HIS64 3.3 13.6 1.0
CA D:HIS64 3.8 13.6 1.0
CA D:HIS4 3.9 27.2 1.0
CG2 D:VAL337 4.0 17.0 1.0
O D:HOH2441 4.0 53.0 1.0
CG D:HIS6 4.1 22.6 1.0
ND1 D:HIS6 4.1 23.1 1.0
CD2 D:HIS4 4.1 28.4 1.0
NE2 D:HIS64 4.2 14.4 1.0
NE2 D:HIS4 4.2 29.8 1.0
CD2 D:HIS64 4.2 15.0 1.0
O D:HOH2117 4.5 32.1 1.0
N D:HIS5 4.6 26.3 1.0
N D:HIS64 4.8 14.0 1.0
C D:HIS4 4.8 26.7 1.0
O D:HIS64 4.8 12.6 1.0
C D:HIS64 4.8 13.1 1.0
O D:GLU63 4.8 15.9 1.0

Reference:

S.Schaefer, L.Saunders, E.Eliseeva, A.Velena, M.Jung, A.Schwienhorst, A.Strasser, A.Dickmanns, R.Ficner, S.Schlimme, W.Sippl, E.Verdin, M.Jung. Phenylalanine-Containing Hydroxamic Acids As Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs). Bioorg.Med.Chem. V. 16 2011 2008.
ISSN: ISSN 0968-0896
PubMed: 18054239
DOI: 10.1016/J.BMC.2007.10.092
Page generated: Wed Dec 16 03:54:58 2020

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