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Potassium in PDB 1zz0: Crystal Structure of A Hdac-Like Protein with Acetate Bound

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein with Acetate Bound, PDB code: 1zz0 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) 44.86 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.586, 127.886, 251.681, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.6

Other elements in 1zz0:

The structure of Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound (pdb code 1zz0). 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 Acetate Bound, PDB code: 1zz0:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 1 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1449

b:12.4
occ:1.00
 O A:ASP180 2.5 10.1 1.0
O A:LEU202 2.7 11.1 1.0
O A:HIS182 2.7 9.8 1.0
OG A:SER201 2.8 11.5 1.0
OD2 A:ASP178 2.9 13.5 1.0
O A:ASP178 3.0 11.6 1.0
CG A:ASP178 3.1 12.8 1.0
OD1 A:ASP178 3.5 15.1 1.0
C A:ASP180 3.6 9.3 1.0
C A:ASP178 3.7 12.5 1.0
C A:LEU202 3.7 11.8 1.0
C A:HIS182 3.8 10.3 1.0
N A:ASP180 3.9 9.5 1.0
N A:LEU202 3.9 9.6 1.0
CB A:SER201 3.9 10.8 1.0
CB A:ASP178 3.9 12.1 1.0
CB A:HIS203 4.0 10.7 1.0
N A:GLY184 4.0 10.1 1.0
CA A:SER201 4.2 10.5 1.0
CA A:ASP180 4.2 9.5 1.0
C A:TRP179 4.2 10.2 1.0
CB A:ASP180 4.3 9.0 1.0
C A:SER201 4.3 11.2 1.0
CA A:HIS183 4.3 10.2 1.0
N A:TRP179 4.3 10.7 1.0
ND1 A:HIS203 4.3 12.0 1.0
CA A:TRP179 4.4 11.2 1.0
N A:HIS182 4.4 9.0 1.0
CA A:ASP178 4.4 11.3 1.0
CE1 A:HIS142 4.5 13.4 1.0
ND1 A:HIS142 4.5 12.4 1.0
N A:HIS183 4.5 9.6 1.0
CA A:LEU202 4.5 10.6 1.0
C A:HIS183 4.5 10.2 1.0
N A:HIS203 4.5 10.7 1.0
CA A:HIS203 4.5 10.3 1.0
N A:VAL181 4.6 9.4 1.0
CG A:HIS203 4.7 11.1 1.0
O A:HOH1460 4.7 12.5 1.0
C A:VAL181 4.7 9.2 1.0
CA A:HIS182 4.7 9.1 1.0
CA A:GLY184 4.9 9.1 1.0
OD1 A:ASP180 4.9 10.9 1.0
O A:TRP179 5.0 10.3 1.0
CA A:VAL181 5.0 9.3 1.0

Potassium binding site 2 out of 8 in 1zz0

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Potassium binding site 2 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate Bound


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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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1450

b:11.8
occ:1.00
 O A:VAL197 2.6 11.2 1.0
O A:HOH1463 2.6 13.5 1.0
O A:TRP191 2.7 11.4 1.0
O A:HOH1476 2.9 13.0 1.0
O A:ASP194 2.9 13.7 1.0
O A:TYR226 2.9 10.7 1.0
CB A:TRP191 3.6 10.7 1.0
C A:TRP191 3.6 11.6 1.0
OG1 A:THR199 3.7 13.2 1.0
C A:TYR226 3.8 12.0 1.0
C A:VAL197 3.9 12.0 1.0
C A:ASP194 4.0 13.2 1.0
CB A:TYR226 4.0 11.8 1.0
CA A:TRP191 4.2 10.7 1.0
N A:THR199 4.3 9.7 1.0
CG2 A:THR199 4.4 10.2 1.0
N A:ASN227 4.5 10.6 1.0
CA A:TYR226 4.5 11.5 1.0
N A:ASP194 4.5 13.9 1.0
N A:TRP192 4.5 10.2 1.0
CB A:THR199 4.6 9.9 1.0
CA A:LEU198 4.6 11.4 1.0
N A:LEU198 4.7 11.5 1.0
O A:TRP192 4.7 12.4 1.0
CA A:ASP194 4.7 13.6 1.0
C A:TRP192 4.8 11.7 1.0
CA A:TRP192 4.8 11.0 1.0
CB A:ASN227 4.8 10.3 1.0
CA A:ASN227 4.8 11.1 1.0
CG A:TRP191 4.9 11.1 1.0
CA A:VAL197 4.9 11.3 1.0
C A:LEU198 4.9 11.3 1.0
O A:GLY223 4.9 13.1 1.0
CB A:ASP194 4.9 13.6 1.0
N A:VAL197 4.9 12.4 1.0
N A:PRO195 4.9 13.3 1.0

Potassium binding site 3 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 3 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1549

b:13.8
occ:1.00
 O B:ASP180 2.6 10.7 1.0
O B:HIS182 2.6 11.1 1.0
O B:LEU202 2.7 12.5 1.0
OD2 B:ASP178 2.8 13.9 1.0
OG B:SER201 2.8 12.5 1.0
O B:ASP178 3.0 11.6 1.0
CG B:ASP178 3.1 13.9 1.0
OD1 B:ASP178 3.4 14.7 1.0
C B:ASP180 3.6 10.5 1.0
C B:ASP178 3.7 12.3 1.0
C B:LEU202 3.7 13.1 1.0
C B:HIS182 3.7 10.2 1.0
CB B:SER201 3.9 13.3 1.0
N B:LEU202 3.9 13.0 1.0
N B:ASP180 3.9 11.4 1.0
CB B:ASP178 4.0 12.3 1.0
N B:GLY184 4.0 11.4 1.0
CB B:HIS203 4.0 11.0 1.0
CA B:SER201 4.1 13.1 1.0
CA B:ASP180 4.2 10.5 1.0
C B:SER201 4.3 13.5 1.0
C B:TRP179 4.3 11.6 1.0
CB B:ASP180 4.3 9.8 1.0
CA B:HIS183 4.3 11.0 1.0
N B:TRP179 4.4 11.2 1.0
CA B:TRP179 4.4 11.8 1.0
ND1 B:HIS203 4.4 12.9 1.0
N B:HIS182 4.4 9.7 1.0
CA B:ASP178 4.4 12.1 1.0
ND1 B:HIS142 4.5 13.2 1.0
CE1 B:HIS142 4.5 14.9 1.0
N B:HIS183 4.5 10.3 1.0
C B:HIS183 4.5 10.9 1.0
CA B:LEU202 4.5 13.4 1.0
CA B:HIS203 4.5 10.5 1.0
N B:HIS203 4.6 11.2 1.0
O B:HOH1559 4.7 13.8 1.0
C B:VAL181 4.7 9.9 1.0
CG B:HIS203 4.7 13.2 1.0
N B:VAL181 4.7 9.4 1.0
CA B:HIS182 4.7 9.5 1.0
CA B:GLY184 4.9 11.2 1.0
O B:TRP179 5.0 11.4 1.0

Potassium binding site 4 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 4 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1550

b:13.0
occ:1.00
 O B:VAL197 2.7 12.2 1.0
O B:TRP191 2.7 11.2 1.0
O B:HOH1584 2.8 14.4 1.0
O B:ASP194 2.8 14.5 1.0
O B:HOH1555 2.8 12.5 1.0
O B:TYR226 2.8 13.0 1.0
CB B:TRP191 3.6 11.6 1.0
C B:TRP191 3.6 11.7 1.0
C B:TYR226 3.7 12.8 1.0
OG1 B:THR199 3.7 13.5 1.0
C B:VAL197 3.9 12.4 1.0
C B:ASP194 3.9 15.0 1.0
CB B:TYR226 4.0 14.5 1.0
CA B:TRP191 4.3 11.1 1.0
N B:THR199 4.3 12.0 1.0
CG2 B:THR199 4.4 13.9 1.0
N B:ASN227 4.5 12.5 1.0
CA B:TYR226 4.5 14.6 1.0
N B:ASP194 4.5 14.9 1.0
N B:TRP192 4.6 11.6 1.0
CA B:LEU198 4.6 12.3 1.0
CB B:THR199 4.6 12.1 1.0
CA B:ASP194 4.7 14.6 1.0
N B:LEU198 4.7 12.2 1.0
O B:TRP192 4.7 13.0 1.0
CB B:ASN227 4.8 12.1 1.0
CA B:TRP192 4.8 12.6 1.0
C B:TRP192 4.8 12.5 1.0
CA B:ASN227 4.8 12.0 1.0
CA B:VAL197 4.8 11.9 1.0
O B:GLY223 4.8 15.2 1.0
CG B:TRP191 4.9 9.6 1.0
C B:LEU198 4.9 13.3 1.0
N B:PRO195 4.9 14.8 1.0
CB B:ASP194 4.9 15.0 1.0
N B:VAL197 5.0 12.0 1.0
CA B:PRO195 5.0 14.8 1.0

Potassium binding site 5 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 5 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1649

b:14.4
occ:1.00
 O C:ASP180 2.5 10.7 1.0
O C:LEU202 2.6 14.7 1.0
O C:HIS182 2.7 12.3 1.0
OG C:SER201 2.7 13.3 1.0
OD2 C:ASP178 2.8 15.1 1.0
O C:ASP178 3.0 13.0 1.0
CG C:ASP178 3.1 15.9 1.0
OD1 C:ASP178 3.5 16.4 1.0
C C:ASP180 3.6 11.1 1.0
C C:ASP178 3.7 12.5 1.0
C C:LEU202 3.7 13.5 1.0
C C:HIS182 3.7 12.1 1.0
N C:LEU202 3.9 12.8 1.0
CB C:SER201 3.9 14.1 1.0
CB C:ASP178 3.9 14.4 1.0
N C:ASP180 4.0 11.2 1.0
N C:GLY184 4.1 12.8 1.0
CB C:HIS203 4.1 11.9 1.0
CA C:SER201 4.1 12.9 1.0
CA C:ASP180 4.2 10.9 1.0
C C:SER201 4.3 12.9 1.0
C C:TRP179 4.3 12.2 1.0
CA C:HIS183 4.3 11.4 1.0
CB C:ASP180 4.3 11.8 1.0
ND1 C:HIS203 4.3 15.1 1.0
N C:TRP179 4.3 12.4 1.0
N C:HIS182 4.4 11.2 1.0
CA C:TRP179 4.4 12.1 1.0
CA C:ASP178 4.4 13.5 1.0
CE1 C:HIS142 4.4 14.3 1.0
N C:HIS183 4.5 11.1 1.0
ND1 C:HIS142 4.5 13.1 1.0
CA C:LEU202 4.5 13.6 1.0
C C:HIS183 4.5 12.1 1.0
N C:HIS203 4.5 12.4 1.0
CA C:HIS203 4.5 11.4 1.0
O C:HOH1655 4.7 14.4 1.0
C C:VAL181 4.7 10.6 1.0
CG C:HIS203 4.7 11.8 1.0
N C:VAL181 4.7 10.3 1.0
CA C:HIS182 4.7 11.6 1.0
CA C:GLY184 4.9 11.3 1.0
OD1 C:ASP180 4.9 12.8 1.0

Potassium binding site 6 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 6 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1650

b:15.0
occ:1.00
 O C:HOH1671 2.7 15.9 1.0
O C:VAL197 2.7 14.4 1.0
O C:TRP191 2.8 12.4 1.0
O C:ASP194 2.8 16.8 1.0
O C:HOH1658 2.9 14.5 1.0
O C:TYR226 2.9 14.0 1.0
CB C:TRP191 3.6 13.3 1.0
C C:TRP191 3.6 13.1 1.0
C C:TYR226 3.7 14.7 1.0
OG1 C:THR199 3.7 14.0 1.0
C C:VAL197 3.9 13.7 1.0
C C:ASP194 4.0 16.8 1.0
CB C:TYR226 4.0 15.4 1.0
CA C:TRP191 4.3 12.9 1.0
N C:THR199 4.3 12.8 1.0
CG2 C:THR199 4.5 13.8 1.0
CA C:TYR226 4.5 15.2 1.0
N C:ASN227 4.5 14.1 1.0
N C:ASP194 4.6 17.1 1.0
N C:TRP192 4.6 14.0 1.0
CA C:LEU198 4.6 13.2 1.0
CB C:THR199 4.6 12.8 1.0
O C:TRP192 4.7 14.3 1.0
CA C:ASP194 4.7 16.6 1.0
N C:LEU198 4.7 13.7 1.0
CA C:TRP192 4.8 14.4 1.0
C C:TRP192 4.8 14.4 1.0
CB C:ASN227 4.8 12.9 1.0
CA C:ASN227 4.8 13.4 1.0
C C:LEU198 4.9 13.9 1.0
CA C:VAL197 4.9 14.1 1.0
CG C:TRP191 4.9 14.0 1.0
O C:GLY223 4.9 16.7 1.0
CB C:ASP194 4.9 17.2 1.0
N C:PRO195 4.9 16.6 1.0
N C:VAL197 5.0 14.5 1.0
CA C:PRO195 5.0 16.5 1.0

Potassium binding site 7 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 7 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1749

b:15.1
occ:1.00
 O D:HOH1785 2.6 18.9 1.0
O D:VAL197 2.7 13.4 1.0
O D:TRP191 2.7 14.5 1.0
O D:ASP194 2.9 18.3 1.0
O D:TYR226 2.9 14.7 1.0
O D:HOH1784 3.0 14.8 1.0
CB D:TRP191 3.6 14.5 1.0
C D:TRP191 3.6 14.4 1.0
OG1 D:THR199 3.7 14.2 1.0
C D:TYR226 3.7 15.3 1.0
C D:VAL197 3.9 14.0 1.0
C D:ASP194 4.0 17.6 1.0
CB D:TYR226 4.0 16.1 1.0
CA D:TRP191 4.2 13.6 1.0
N D:THR199 4.3 13.7 1.0
CG2 D:THR199 4.4 14.7 1.0
N D:ASN227 4.5 14.8 1.0
CA D:TYR226 4.5 15.4 1.0
N D:TRP192 4.5 15.0 1.0
N D:ASP194 4.5 17.1 1.0
CA D:LEU198 4.6 13.4 1.0
CB D:THR199 4.6 15.3 1.0
CA D:ASP194 4.7 17.7 1.0
N D:LEU198 4.7 13.8 1.0
O D:TRP192 4.7 15.9 1.0
CA D:TRP192 4.8 15.3 1.0
CB D:ASN227 4.8 14.8 1.0
CA D:ASN227 4.8 15.3 1.0
C D:TRP192 4.8 15.8 1.0
C D:LEU198 4.8 14.0 1.0
CG D:TRP191 4.8 15.2 1.0
O D:GLY223 4.9 18.5 1.0
CA D:VAL197 4.9 14.1 1.0
N D:PRO195 4.9 17.1 1.0
CB D:ASP194 5.0 17.5 1.0
CA D:PRO195 5.0 16.9 1.0

Potassium binding site 8 out of 8 in 1zz0

Go back to Potassium Binding Sites List in 1zz0
Potassium binding site 8 out of 8 in the Crystal Structure of A Hdac-Like Protein with Acetate 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 Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1750

b:15.3
occ:1.00
 O D:ASP180 2.5 10.6 1.0
O D:LEU202 2.7 13.8 1.0
O D:HIS182 2.7 12.7 1.0
OG D:SER201 2.7 13.3 1.0
OD2 D:ASP178 2.8 16.4 1.0
O D:ASP178 3.0 13.6 1.0
CG D:ASP178 3.2 16.8 1.0
OD1 D:ASP178 3.5 18.7 1.0
C D:ASP180 3.6 10.7 1.0
C D:ASP178 3.7 13.6 1.0
C D:LEU202 3.7 13.6 1.0
C D:HIS182 3.8 13.4 1.0
CB D:SER201 3.9 14.8 1.0
N D:LEU202 3.9 13.4 1.0
N D:ASP180 3.9 10.9 1.0
CB D:ASP178 4.0 14.2 1.0
CB D:HIS203 4.0 12.5 1.0
N D:GLY184 4.1 13.0 1.0
CA D:SER201 4.1 13.8 1.0
CA D:ASP180 4.2 10.7 1.0
C D:SER201 4.2 13.8 1.0
C D:TRP179 4.3 12.1 1.0
CB D:ASP180 4.3 11.3 1.0
N D:TRP179 4.3 13.7 1.0
CA D:HIS183 4.3 13.4 1.0
N D:HIS182 4.4 11.0 1.0
ND1 D:HIS203 4.4 15.4 1.0
CA D:TRP179 4.4 13.4 1.0
CA D:ASP178 4.4 14.7 1.0
CA D:LEU202 4.5 14.2 1.0
N D:HIS183 4.5 12.4 1.0
ND1 D:HIS142 4.5 14.4 1.0
CE1 D:HIS142 4.5 15.0 1.0
CA D:HIS203 4.5 12.6 1.0
C D:HIS183 4.5 12.1 1.0
N D:HIS203 4.5 12.9 1.0
O D:HOH1774 4.6 14.9 1.0
N D:VAL181 4.7 10.8 1.0
C D:VAL181 4.7 11.7 1.0
CG D:HIS203 4.7 13.4 1.0
CA D:HIS182 4.7 12.0 1.0
CA D:GLY184 4.9 12.0 1.0
OD1 D:ASP180 4.9 12.0 1.0
CA D:VAL181 5.0 10.9 1.0
O D:TRP179 5.0 12.9 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: Mon Aug 12 05:55:38 2024

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