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Potassium 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:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of A Hdac-Like Protein with Cypx Bound, PDB code: 1zz3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 1 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K1450

b:20.9
occ:1.00
 O A:ASP180 2.4 12.6 1.0
O A:LEU202 2.5 13.0 1.0
O A:HIS182 2.6 12.1 1.0
OG A:SER201 2.6 15.2 1.0
OD2 A:ASP178 2.7 17.1 1.0
O A:ASP178 3.1 15.8 1.0
CG A:ASP178 3.1 15.3 1.0
C A:ASP180 3.5 12.2 1.0
OD1 A:ASP178 3.6 16.3 1.0
C A:LEU202 3.6 14.2 1.0
C A:HIS182 3.7 12.7 1.0
C A:ASP178 3.7 14.7 1.0
CB A:SER201 3.9 15.8 1.0
N A:LEU202 3.9 14.7 1.0
N A:ASP180 3.9 13.2 1.0
CB A:ASP178 4.0 14.1 1.0
CB A:HIS203 4.1 14.7 1.0
N A:GLY184 4.1 14.4 1.0
CA A:ASP180 4.2 12.9 1.0
CA A:SER201 4.2 15.2 1.0
ND1 A:HIS203 4.3 16.0 1.0
C A:TRP179 4.3 12.9 1.0
CA A:HIS183 4.3 14.8 1.0
C A:SER201 4.3 15.3 1.0
N A:HIS182 4.3 11.5 1.0
N A:TRP179 4.4 13.4 1.0
CB A:ASP180 4.4 12.8 1.0
CA A:TRP179 4.4 13.7 1.0
CA A:LEU202 4.4 14.3 1.0
N A:HIS183 4.5 13.3 1.0
N A:HIS203 4.5 14.2 1.0
O A:HOH1453 4.5 13.9 1.0
CE1 A:HIS142 4.5 15.3 1.0
CA A:ASP178 4.5 14.6 1.0
C A:HIS183 4.5 14.7 1.0
CA A:HIS203 4.5 14.2 1.0
ND1 A:HIS142 4.5 14.5 1.0
C A:VAL181 4.6 11.5 1.0
N A:VAL181 4.6 10.8 1.0
CG A:HIS203 4.6 16.3 1.0
CA A:HIS182 4.7 12.5 1.0
OD1 A:ASP180 4.9 12.9 1.0
CA A:VAL181 4.9 11.4 1.0
CA A:GLY184 5.0 14.4 1.0

Potassium binding site 2 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 2 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
A:K1449

b:23.0
occ:1.00
 O A:VAL197 2.6 16.9 1.0
O A:HOH1518 2.7 22.6 1.0
O A:TRP191 2.7 18.9 1.0
O A:ASP194 2.8 21.6 1.0
O A:TYR226 2.9 19.6 1.0
O A:HOH1581 3.1 24.9 1.0
CB A:TRP191 3.5 19.0 1.0
C A:TRP191 3.6 18.4 1.0
C A:TYR226 3.7 19.4 1.0
OG1 A:THR199 3.8 17.2 1.0
C A:VAL197 3.8 16.8 1.0
C A:ASP194 3.9 21.1 1.0
CB A:TYR226 4.0 21.0 1.0
CA A:TRP191 4.2 19.1 1.0
N A:THR199 4.3 16.7 1.0
CA A:TYR226 4.4 19.6 1.0
CG2 A:THR199 4.4 16.8 1.0
N A:TRP192 4.5 18.8 1.0
N A:ASN227 4.5 18.0 1.0
N A:ASP194 4.5 21.5 1.0
CA A:LEU198 4.6 16.3 1.0
CB A:THR199 4.7 16.7 1.0
N A:LEU198 4.7 16.1 1.0
CA A:ASP194 4.7 20.7 1.0
O A:TRP192 4.7 19.4 1.0
CA A:TRP192 4.8 19.2 1.0
C A:TRP192 4.8 19.5 1.0
CA A:VAL197 4.8 17.2 1.0
CB A:ASN227 4.8 17.4 1.0
N A:PRO195 4.8 20.9 1.0
C A:LEU198 4.8 16.8 1.0
CG A:TRP191 4.8 18.4 1.0
O A:GLY223 4.9 22.3 1.0
CA A:ASN227 4.9 17.8 1.0
N A:VAL197 4.9 17.2 1.0
CB A:ASP194 4.9 21.7 1.0
CA A:PRO195 5.0 20.1 1.0

Potassium binding site 3 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 3 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
B:K1550

b:14.3
occ:1.00
 O B:ASP180 2.5 10.2 1.0
O B:LEU202 2.6 10.7 1.0
O B:HIS182 2.7 11.5 1.0
OG B:SER201 2.7 13.0 1.0
OD1 B:ASP178 2.8 12.5 1.0
O B:ASP178 3.0 12.0 1.0
CG B:ASP178 3.2 14.7 1.0
OD2 B:ASP178 3.5 13.2 1.0
C B:ASP180 3.6 10.2 1.0
C B:LEU202 3.7 11.0 1.0
C B:ASP178 3.7 11.3 1.0
C B:HIS182 3.7 11.4 1.0
CB B:SER201 3.9 12.4 1.0
N B:LEU202 3.9 11.4 1.0
CB B:ASP178 4.0 12.4 1.0
N B:ASP180 4.0 10.8 1.0
N B:GLY184 4.0 11.3 1.0
CB B:HIS203 4.1 11.9 1.0
CA B:SER201 4.1 12.2 1.0
CA B:ASP180 4.3 10.2 1.0
C B:SER201 4.3 12.2 1.0
C B:TRP179 4.3 10.1 1.0
N B:TRP179 4.3 11.7 1.0
CA B:HIS183 4.3 12.8 1.0
CA B:TRP179 4.3 11.7 1.0
CD2 B:HIS203 4.4 11.7 1.0
CB B:ASP180 4.4 10.4 1.0
N B:HIS182 4.4 10.9 1.0
CE1 B:HIS142 4.4 9.6 1.0
CA B:ASP178 4.4 12.4 1.0
N B:HIS183 4.5 11.5 1.0
ND1 B:HIS142 4.5 11.9 1.0
CA B:LEU202 4.5 11.5 1.0
C B:HIS183 4.5 11.1 1.0
N B:HIS203 4.5 11.0 1.0
CA B:HIS203 4.6 11.4 1.0
O B:HOH1556 4.6 11.3 1.0
CG B:HIS203 4.6 12.3 1.0
C B:VAL181 4.7 9.4 1.0
N B:VAL181 4.7 9.3 1.0
CA B:HIS182 4.7 10.3 1.0
OD1 B:ASP180 4.9 10.0 1.0
CA B:GLY184 4.9 11.7 1.0
CA B:VAL181 5.0 9.2 1.0
O B:TRP179 5.0 10.8 1.0

Potassium binding site 4 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 4 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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
B:K1549

b:22.5
occ:1.00
 O B:VAL197 2.5 15.1 1.0
O B:HOH1633 2.6 18.1 1.0
O B:TRP191 2.7 16.1 1.0
O B:ASP194 2.8 17.4 1.0
O B:HOH1679 2.9 20.3 1.0
O B:TYR226 3.1 13.3 1.0
CB B:TRP191 3.5 14.9 1.0
C B:TRP191 3.6 15.6 1.0
C B:VAL197 3.7 15.2 1.0
C B:ASP194 3.9 17.8 1.0
C B:TYR226 3.9 14.8 1.0
OG1 B:THR199 3.9 14.7 1.0
CB B:TYR226 4.1 15.7 1.0
CA B:TRP191 4.2 15.2 1.0
N B:THR199 4.4 13.6 1.0
CG2 B:THR199 4.5 15.4 1.0
N B:ASP194 4.5 17.9 1.0
N B:TRP192 4.5 15.9 1.0
CA B:LEU198 4.5 14.3 1.0
N B:LEU198 4.6 15.1 1.0
CA B:TYR226 4.6 15.2 1.0
CA B:ASP194 4.6 17.0 1.0
N B:ASN227 4.7 13.7 1.0
O B:TRP192 4.7 15.1 1.0
CA B:VAL197 4.7 15.0 1.0
CB B:THR199 4.8 15.0 1.0
C B:TRP192 4.8 16.1 1.0
CA B:TRP192 4.8 15.7 1.0
CG B:TRP191 4.8 14.7 1.0
N B:VAL197 4.8 15.3 1.0
C B:LEU198 4.8 14.3 1.0
N B:PRO195 4.8 17.9 1.0
O B:GLY223 4.9 16.9 1.0
CA B:PRO195 4.9 17.6 1.0
CB B:VAL197 4.9 15.3 1.0
CB B:ASP194 4.9 17.0 1.0
CB B:ASN227 5.0 13.6 1.0

Potassium binding site 5 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 5 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of A Hdac-Like Protein with Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1650

b:18.4
occ:1.00
 O C:ASP180 2.5 10.2 1.0
O C:LEU202 2.5 12.9 1.0
OD2 C:ASP178 2.6 13.6 1.0
O C:HIS182 2.6 12.2 1.0
OG C:SER201 2.7 12.4 1.0
O C:ASP178 3.1 13.4 1.0
CG C:ASP178 3.1 13.7 1.0
C C:ASP180 3.5 10.9 1.0
C C:LEU202 3.6 12.2 1.0
OD1 C:ASP178 3.6 13.5 1.0
C C:ASP178 3.7 13.1 1.0
C C:HIS182 3.7 11.5 1.0
CB C:SER201 3.9 12.1 1.0
N C:LEU202 3.9 12.0 1.0
N C:ASP180 3.9 11.7 1.0
CB C:ASP178 4.0 12.4 1.0
CB C:HIS203 4.1 11.4 1.0
N C:GLY184 4.1 12.7 1.0
CA C:SER201 4.1 12.4 1.0
CA C:ASP180 4.1 11.3 1.0
CB C:ASP180 4.2 11.9 1.0
C C:SER201 4.3 12.9 1.0
CD2 C:HIS203 4.3 10.2 1.0
C C:TRP179 4.3 11.4 1.0
N C:HIS182 4.3 10.8 1.0
N C:TRP179 4.3 12.5 1.0
CA C:HIS183 4.4 12.8 1.0
CA C:TRP179 4.4 12.5 1.0
CA C:LEU202 4.4 13.3 1.0
N C:HIS203 4.4 11.7 1.0
CA C:ASP178 4.4 12.7 1.0
N C:HIS183 4.5 11.5 1.0
CA C:HIS203 4.5 11.6 1.0
CE1 C:HIS142 4.5 11.8 1.0
ND1 C:HIS142 4.5 12.4 1.0
O C:HOH1653 4.5 11.0 1.0
CG C:HIS203 4.5 13.3 1.0
C C:HIS183 4.6 11.8 1.0
N C:VAL181 4.6 10.3 1.0
C C:VAL181 4.6 9.9 1.0
CA C:HIS182 4.7 11.2 1.0
OD1 C:ASP180 4.8 11.1 1.0
CA C:VAL181 4.9 10.2 1.0
O C:TRP179 4.9 12.2 1.0
CA C:GLY184 5.0 11.8 1.0

Potassium binding site 6 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 6 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of A Hdac-Like Protein with Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1649

b:19.3
occ:1.00
 O C:VAL197 2.6 14.9 1.0
O C:TRP191 2.6 15.6 1.0
O C:HOH1744 2.7 20.6 1.0
O C:ASP194 2.8 17.8 1.0
O C:HOH1754 2.9 18.9 1.0
O C:TYR226 3.0 15.5 1.0
C C:TRP191 3.5 15.9 1.0
CB C:TRP191 3.5 14.7 1.0
C C:TYR226 3.8 16.0 1.0
OG1 C:THR199 3.8 15.1 1.0
C C:VAL197 3.9 13.8 1.0
C C:ASP194 3.9 18.0 1.0
CB C:TYR226 4.0 17.6 1.0
CA C:TRP191 4.2 15.8 1.0
N C:THR199 4.4 14.1 1.0
CG2 C:THR199 4.4 15.1 1.0
N C:ASP194 4.4 17.6 1.0
N C:TRP192 4.5 16.4 1.0
CA C:TYR226 4.5 16.6 1.0
N C:ASN227 4.5 14.6 1.0
CA C:ASP194 4.6 17.6 1.0
CA C:LEU198 4.6 14.1 1.0
N C:LEU198 4.7 14.3 1.0
CB C:THR199 4.7 14.1 1.0
O C:TRP192 4.7 16.8 1.0
CA C:TRP192 4.8 16.3 1.0
C C:TRP192 4.8 16.9 1.0
CB C:ASP194 4.8 17.3 1.0
CG C:TRP191 4.8 15.8 1.0
CB C:ASN227 4.8 14.7 1.0
CA C:VAL197 4.8 14.3 1.0
O C:GLY223 4.8 19.5 1.0
N C:PRO195 4.9 18.1 1.0
CA C:ASN227 4.9 13.8 1.0
C C:LEU198 4.9 14.1 1.0
N C:VAL197 4.9 14.2 1.0
CA C:PRO195 5.0 17.5 1.0

Potassium binding site 7 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 7 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of A Hdac-Like Protein with Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1750

b:16.9
occ:1.00
 O D:ASP180 2.5 10.9 1.0
O D:LEU202 2.6 14.9 1.0
O D:HIS182 2.7 12.6 1.0
OG D:SER201 2.7 13.7 1.0
OD1 D:ASP178 2.7 13.2 1.0
O D:ASP178 3.0 14.6 1.0
CG D:ASP178 3.1 15.3 1.0
OD2 D:ASP178 3.5 14.0 1.0
C D:ASP180 3.6 11.8 1.0
C D:ASP178 3.7 14.5 1.0
C D:LEU202 3.7 14.6 1.0
C D:HIS182 3.7 13.4 1.0
N D:LEU202 3.8 14.4 1.0
CB D:SER201 3.8 14.3 1.0
N D:GLY184 4.0 12.9 1.0
N D:ASP180 4.0 12.7 1.0
CB D:ASP178 4.0 14.2 1.0
CB D:HIS203 4.1 14.6 1.0
CA D:SER201 4.1 14.3 1.0
C D:SER201 4.3 14.3 1.0
CA D:ASP180 4.3 11.7 1.0
N D:TRP179 4.3 13.4 1.0
CA D:HIS183 4.3 13.8 1.0
C D:TRP179 4.4 12.3 1.0
ND1 D:HIS203 4.4 15.8 1.0
CB D:ASP180 4.4 11.2 1.0
N D:HIS182 4.4 12.6 1.0
CA D:TRP179 4.4 13.2 1.0
ND1 D:HIS142 4.4 12.6 1.0
CE1 D:HIS142 4.4 14.0 1.0
CA D:ASP178 4.4 14.2 1.0
C D:HIS183 4.5 12.3 1.0
CA D:LEU202 4.5 14.4 1.0
N D:HIS183 4.5 12.9 1.0
N D:HIS203 4.5 13.9 1.0
CA D:HIS203 4.6 14.5 1.0
O D:HOH1759 4.6 13.6 1.0
N D:VAL181 4.7 10.7 1.0
C D:VAL181 4.7 11.9 1.0
CG D:HIS203 4.7 14.7 1.0
CA D:HIS182 4.7 13.0 1.0
CA D:GLY184 4.9 12.7 1.0
OD1 D:ASP180 4.9 10.4 1.0

Potassium binding site 8 out of 8 in 1zz3

Go back to Potassium Binding Sites List in 1zz3
Potassium binding site 8 out of 8 in the Crystal Structure of A Hdac-Like Protein with Cypx Bound


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of A Hdac-Like Protein with Cypx Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1749

b:23.3
occ:1.00
 O D:HOH1791 2.5 18.7 1.0
O D:VAL197 2.5 16.6 1.0
O D:TRP191 2.6 16.4 1.0
O D:ASP194 2.9 17.6 1.0
O D:HOH1801 2.9 21.5 1.0
O D:TYR226 2.9 16.5 1.0
C D:TRP191 3.5 16.8 1.0
CB D:TRP191 3.5 16.9 1.0
C D:VAL197 3.8 16.7 1.0
C D:TYR226 3.8 16.7 1.0
OG1 D:THR199 3.9 15.9 1.0
C D:ASP194 4.0 17.6 1.0
CB D:TYR226 4.0 17.1 1.0
CA D:TRP191 4.2 16.6 1.0
N D:THR199 4.4 15.9 1.0
N D:TRP192 4.5 16.7 1.0
CA D:TYR226 4.5 16.4 1.0
CG2 D:THR199 4.5 15.0 1.0
N D:ASN227 4.5 15.5 1.0
N D:ASP194 4.6 17.5 1.0
CA D:LEU198 4.6 15.9 1.0
N D:LEU198 4.6 16.1 1.0
CA D:VAL197 4.7 16.6 1.0
CA D:ASP194 4.7 17.7 1.0
CB D:THR199 4.8 14.4 1.0
O D:TRP192 4.8 17.8 1.0
O D:GLY223 4.8 18.9 1.0
CA D:TRP192 4.8 17.3 1.0
CG D:TRP191 4.8 17.3 1.0
C D:TRP192 4.8 17.8 1.0
N D:VAL197 4.9 16.8 1.0
C D:LEU198 4.9 16.9 1.0
CB D:ASN227 4.9 15.3 1.0
N D:PRO195 4.9 17.1 1.0
CB D:VAL197 4.9 17.4 1.0
CA D:PRO195 4.9 17.1 1.0
CA D:ASN227 4.9 15.7 1.0
CB D:ASP194 5.0 17.3 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: Sat Aug 9 03:02:20 2025

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