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Zinc in PDB 1zz3: Crystal Structure of A Hdac-Like Protein with Cypx Bound

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein with Cypx Bound, PDB code: 1zz3 was solved by T.K.Nielsen, C.Hildmann, A.Dickmanns, A.Schwienhorst, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.77 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.098, 94.486, 122.632, 90.00, 104.27, 90.00
R / Rfree (%) 15.6 / 19.1

Other elements in 1zz3:

The structure of Crystal Structure of A Hdac-Like Protein with Cypx Bound also contains other interesting chemical elements:

Potassium (K) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Hdac-Like Protein with Cypx Bound (pdb code 1zz3). 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 Cypx Bound, PDB code: 1zz3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1zz3

Go back to Zinc Binding Sites List in 1zz3
Zinc binding site 1 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1451

b:22.4
occ:0.50
OD2 A:ASP268 2.0 11.6 1.0
OAB A:3YP1452 2.0 25.3 1.0
OD1 A:ASP180 2.1 12.9 1.0
OAA A:3YP1452 2.2 15.7 1.0
ND1 A:HIS182 2.3 14.0 1.0
OD2 A:ASP180 2.3 13.7 1.0
CG A:ASP180 2.5 13.7 1.0
NAI A:3YP1452 2.7 14.4 1.0
CAJ A:3YP1452 2.8 2.0 1.0
CG A:ASP268 3.0 12.7 1.0
CE1 A:HIS182 3.1 15.1 1.0
CG A:HIS182 3.3 12.9 1.0
OD1 A:ASP268 3.4 12.3 1.0
CB A:HIS182 3.7 11.8 1.0
NE2 A:HIS142 4.0 16.6 1.0
N A:HIS182 4.0 11.5 1.0
CB A:ASP180 4.1 12.8 1.0
CA A:GLY310 4.1 12.8 1.0
CAE A:3YP1452 4.2 22.9 1.0
CB A:ASP268 4.3 11.6 1.0
CE2 A:TYR312 4.3 12.6 1.0
CG1 A:VAL181 4.3 11.9 1.0
NE2 A:HIS182 4.3 13.3 1.0
CAH A:3YP1452 4.4 28.2 1.0
N A:GLY310 4.4 12.7 1.0
N A:VAL181 4.4 10.8 1.0
CE1 A:HIS142 4.4 15.3 1.0
CD2 A:HIS182 4.4 13.6 1.0
OH A:TYR312 4.4 15.0 1.0
CA A:HIS182 4.5 12.5 1.0
C A:ASP180 4.8 12.2 1.0
NE2 A:HIS143 4.8 15.1 1.0
CA A:ASP180 4.8 12.9 1.0
C A:GLY310 4.8 12.7 1.0
N A:GLY311 4.9 12.2 1.0
CZ A:TYR312 4.9 11.3 1.0

Zinc binding site 2 out of 4 in 1zz3

Go back to Zinc Binding Sites List in 1zz3
Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1551

b:19.2
occ:0.50
OD2 B:ASP268 2.0 9.5 1.0
OAB B:3YP1552 2.0 17.0 1.0
OD1 B:ASP180 2.1 10.0 1.0
OAA B:3YP1552 2.1 18.4 1.0
ND1 B:HIS182 2.2 12.9 1.0
OD2 B:ASP180 2.4 13.5 1.0
CG B:ASP180 2.5 10.2 1.0
NAI B:3YP1552 2.8 2.0 1.0
CAJ B:3YP1552 2.8 2.0 1.0
CG B:ASP268 3.1 11.5 1.0
CE1 B:HIS182 3.1 15.1 1.0
CG B:HIS182 3.3 10.1 1.0
OD1 B:ASP268 3.5 11.1 1.0
CB B:HIS182 3.6 9.7 1.0
NE2 B:HIS142 3.9 12.6 1.0
N B:HIS182 4.0 10.9 1.0
CB B:ASP180 4.0 10.4 1.0
CA B:GLY310 4.1 10.7 1.0
CAE B:3YP1552 4.2 24.9 1.0
NE2 B:HIS182 4.3 12.3 1.0
CE1 B:HIS142 4.3 9.6 1.0
CB B:ASP268 4.3 10.5 1.0
CE1 B:TYR312 4.4 11.8 1.0
CD2 B:HIS182 4.4 13.4 1.0
CG1 B:VAL181 4.4 8.1 1.0
N B:VAL181 4.4 9.3 1.0
CAG B:3YP1552 4.4 41.3 1.0
OH B:TYR312 4.4 15.4 1.0
N B:GLY310 4.4 10.0 1.0
CA B:HIS182 4.5 10.3 1.0
NE2 B:HIS143 4.6 17.0 1.0
C B:ASP180 4.7 10.2 1.0
CA B:ASP180 4.8 10.2 1.0
C B:GLY310 4.8 11.8 1.0
CAH B:3YP1552 4.9 31.9 1.0
N B:GLY311 4.9 12.1 1.0
CZ B:TYR312 4.9 12.8 1.0
C B:VAL181 5.0 9.4 1.0

Zinc binding site 3 out of 4 in 1zz3

Go back to Zinc Binding Sites List in 1zz3
Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1651

b:19.8
occ:0.50
OD2 C:ASP268 2.0 9.1 1.0
OD1 C:ASP180 2.1 11.1 1.0
OAA C:3YP1652 2.1 21.0 1.0
OAB C:3YP1652 2.1 16.0 1.0
ND1 C:HIS182 2.2 11.0 1.0
OD2 C:ASP180 2.4 11.8 1.0
CG C:ASP180 2.5 9.9 1.0
CAJ C:3YP1652 2.8 17.9 1.0
NAI C:3YP1652 2.8 2.0 1.0
CG C:ASP268 3.0 11.3 1.0
CE1 C:HIS182 3.1 11.7 1.0
CG C:HIS182 3.2 11.6 1.0
OD1 C:ASP268 3.4 12.2 1.0
CB C:HIS182 3.6 11.3 1.0
N C:HIS182 4.0 10.8 1.0
NE2 C:HIS142 4.0 14.3 1.0
CB C:ASP180 4.0 11.9 1.0
CA C:GLY310 4.2 10.1 1.0
CAE C:3YP1652 4.2 32.1 1.0
NE2 C:HIS182 4.2 10.0 1.0
CB C:ASP268 4.3 10.4 1.0
N C:VAL181 4.3 10.3 1.0
CD2 C:HIS182 4.3 10.9 1.0
CG1 C:VAL181 4.3 10.4 1.0
CE1 C:HIS142 4.3 11.8 1.0
CE2 C:TYR312 4.4 13.2 1.0
CA C:HIS182 4.4 11.2 1.0
N C:GLY310 4.4 9.3 1.0
CAH C:3YP1652 4.6 38.2 1.0
OH C:TYR312 4.6 13.9 1.0
C C:ASP180 4.7 10.9 1.0
CA C:ASP180 4.7 11.3 1.0
NE2 C:HIS143 4.8 13.1 1.0
C C:GLY310 4.8 11.6 1.0
N C:GLY311 4.9 11.6 1.0
CAK C:3YP1652 4.9 42.5 1.0
C C:VAL181 4.9 9.9 1.0
CZ C:TYR312 5.0 14.6 1.0

Zinc binding site 4 out of 4 in 1zz3

Go back to Zinc Binding Sites List in 1zz3
Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1751

b:20.9
occ:0.50
OAB D:3YP1752 1.7 27.3 1.0
OD2 D:ASP268 2.0 14.0 1.0
OD1 D:ASP180 2.1 10.4 1.0
OAA D:3YP1752 2.1 18.5 1.0
ND1 D:HIS182 2.3 16.8 1.0
OD2 D:ASP180 2.3 12.1 1.0
CG D:ASP180 2.5 13.0 1.0
NAI D:3YP1752 2.5 18.3 1.0
CAJ D:3YP1752 2.7 2.0 1.0
CG D:ASP268 3.0 13.8 1.0
CE1 D:HIS182 3.1 15.9 1.0
CG D:HIS182 3.4 13.2 1.0
OD1 D:ASP268 3.4 12.8 1.0
CB D:HIS182 3.8 12.6 1.0
CA D:GLY310 4.0 12.9 1.0
NE2 D:HIS142 4.0 15.1 1.0
CB D:ASP180 4.0 11.2 1.0
CAE D:3YP1752 4.1 21.4 1.0
N D:HIS182 4.2 12.6 1.0
CE1 D:TYR312 4.3 14.8 1.0
CB D:ASP268 4.3 12.8 1.0
NE2 D:HIS182 4.3 16.2 1.0
N D:GLY310 4.3 12.1 1.0
CE1 D:HIS142 4.3 14.0 1.0
N D:VAL181 4.4 10.7 1.0
CD2 D:HIS182 4.4 15.5 1.0
OH D:TYR312 4.4 13.5 1.0
CG1 D:VAL181 4.4 13.9 1.0
CA D:HIS182 4.6 13.0 1.0
C D:GLY310 4.7 13.0 1.0
CAG D:3YP1752 4.7 36.6 1.0
C D:ASP180 4.8 11.8 1.0
NE2 D:HIS143 4.8 14.4 1.0
N D:GLY311 4.8 13.5 1.0
CA D:ASP180 4.8 11.7 1.0
CAH D:3YP1752 4.8 28.0 1.0
CZ D:TYR312 4.8 13.5 1.0

Reference:

T.K.Nielsen, C.Hildmann, A.Dickmanns, A.Schwienhorst, R.Ficner. Crystal Structure of A Bacterial Class 2 Histone Deacetylase Homologue J.Mol.Biol. V. 354 107 2005.
ISSN: ISSN 0022-2836
PubMed: 16242151
DOI: 10.1016/J.JMB.2005.09.065
Page generated: Wed Dec 16 03:16:23 2020

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