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Potassium in PDB 1zz1: Crystal Structure of A Hdac-Like Protein with Saha Bound

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein with Saha Bound, PDB code: 1zz1 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) 38.38 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.606, 94.716, 123.924, 90.00, 104.75, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 1zz1:

The structure of Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound (pdb code 1zz1). 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 Saha Bound, PDB code: 1zz1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 1 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2450

b:15.9
occ:1.00
 O A:ASP180 2.5 13.7 1.0
O A:LEU202 2.6 13.3 1.0
O A:HIS182 2.6 13.2 1.0
OG A:SER201 2.7 16.5 1.0
OD2 A:ASP178 2.7 16.6 1.0
O A:ASP178 3.1 14.3 1.0
CG A:ASP178 3.1 15.2 1.0
OD1 A:ASP178 3.5 15.0 1.0
C A:ASP180 3.6 13.0 1.0
C A:LEU202 3.7 14.0 1.0
C A:ASP178 3.7 13.9 1.0
C A:HIS182 3.7 13.4 1.0
CB A:SER201 3.8 15.7 1.0
N A:LEU202 3.9 14.5 1.0
N A:ASP180 4.0 13.2 1.0
CB A:ASP178 4.0 14.2 1.0
CB A:HIS203 4.1 16.1 1.0
CA A:SER201 4.1 15.3 1.0
N A:GLY184 4.2 15.4 1.0
CA A:ASP180 4.3 13.0 1.0
C A:SER201 4.3 15.2 1.0
ND1 A:HIS203 4.3 18.5 1.0
C A:TRP179 4.3 13.4 1.0
N A:TRP179 4.3 13.9 1.0
CA A:HIS183 4.3 15.4 1.0
CA A:TRP179 4.4 14.0 1.0
N A:HIS182 4.4 13.1 1.0
CB A:ASP180 4.4 13.7 1.0
CE1 A:HIS142 4.4 13.3 1.0
N A:HIS183 4.5 13.6 1.0
CA A:LEU202 4.5 14.7 1.0
ND1 A:HIS142 4.5 15.6 1.0
CA A:ASP178 4.5 14.7 1.0
O A:HOH2469 4.5 13.8 1.0
N A:HIS203 4.5 13.8 1.0
CA A:HIS203 4.5 14.2 1.0
C A:HIS183 4.6 14.6 1.0
C A:VAL181 4.7 12.2 1.0
CG A:HIS203 4.7 15.7 1.0
N A:VAL181 4.7 12.4 1.0
CA A:HIS182 4.7 12.8 1.0
OD1 A:ASP180 4.9 13.8 1.0

Potassium binding site 2 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 2 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2449

b:32.0
occ:1.00
 O A:HOH2501 2.4 25.2 1.0
O A:VAL197 2.6 19.2 1.0
O A:TRP191 2.6 21.8 1.0
O A:ASP194 2.8 23.6 1.0
O A:TYR226 2.9 20.9 1.0
CB A:TRP191 3.5 21.0 1.0
C A:TRP191 3.5 21.2 1.0
C A:VAL197 3.8 18.8 1.0
C A:TYR226 3.8 21.1 1.0
C A:ASP194 3.9 22.9 1.0
OG1 A:THR199 3.9 18.8 1.0
CB A:TYR226 4.0 23.1 1.0
CA A:TRP191 4.1 21.0 1.0
N A:THR199 4.5 17.8 1.0
N A:TRP192 4.5 21.3 1.0
CG2 A:THR199 4.5 19.3 1.0
N A:ASP194 4.5 24.2 1.0
CA A:TYR226 4.6 21.4 1.0
CA A:LEU198 4.6 17.8 1.0
N A:LEU198 4.6 18.6 1.0
N A:ASN227 4.6 20.3 1.0
CA A:ASP194 4.7 23.3 1.0
O A:GLY223 4.7 24.3 1.0
CB A:THR199 4.8 17.4 1.0
CA A:VAL197 4.8 19.5 1.0
CG A:TRP191 4.8 23.1 1.0
O A:TRP192 4.8 22.5 1.0
CA A:TRP192 4.8 22.0 1.0
N A:PRO195 4.8 22.7 1.0
C A:TRP192 4.9 22.1 1.0
N A:VAL197 4.9 19.4 1.0
CA A:PRO195 4.9 21.8 1.0
C A:LEU198 4.9 18.2 1.0
CB A:ASP194 5.0 23.9 1.0
CB A:VAL197 5.0 19.6 1.0

Potassium binding site 3 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 3 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2550

b:9.8
occ:1.00
 O B:ASP180 2.5 8.9 1.0
O B:LEU202 2.6 8.1 1.0
O B:HIS182 2.6 9.0 1.0
OD1 B:ASP178 2.8 10.0 1.0
OG B:SER201 2.8 8.3 1.0
O B:ASP178 3.0 8.3 1.0
CG B:ASP178 3.2 9.5 1.0
OD2 B:ASP178 3.5 9.4 1.0
C B:ASP180 3.6 8.7 1.0
C B:LEU202 3.6 8.6 1.0
C B:ASP178 3.7 9.3 1.0
C B:HIS182 3.7 8.4 1.0
N B:LEU202 3.9 9.5 1.0
CB B:SER201 3.9 9.0 1.0
N B:ASP180 3.9 8.5 1.0
CB B:ASP178 4.0 7.7 1.0
CB B:HIS203 4.0 6.6 1.0
N B:GLY184 4.1 10.0 1.0
CA B:SER201 4.1 9.1 1.0
CA B:ASP180 4.2 8.5 1.0
C B:TRP179 4.3 8.2 1.0
C B:SER201 4.3 9.6 1.0
N B:TRP179 4.3 8.4 1.0
CD2 B:HIS203 4.3 4.6 1.0
CA B:TRP179 4.3 9.2 1.0
CB B:ASP180 4.4 8.3 1.0
CA B:HIS183 4.4 9.2 1.0
N B:HIS182 4.4 8.5 1.0
CE1 B:HIS142 4.4 10.3 1.0
CA B:ASP178 4.4 8.8 1.0
CA B:LEU202 4.5 9.4 1.0
ND1 B:HIS142 4.5 9.9 1.0
N B:HIS183 4.5 7.6 1.0
N B:HIS203 4.5 7.7 1.0
CA B:HIS203 4.5 7.1 1.0
C B:HIS183 4.6 9.1 1.0
CG B:HIS203 4.6 8.8 1.0
O B:HOH2555 4.6 7.8 1.0
N B:VAL181 4.6 8.1 1.0
C B:VAL181 4.6 8.1 1.0
CA B:HIS182 4.7 8.4 1.0
O B:TRP179 4.9 8.5 1.0
CA B:GLY184 4.9 9.9 1.0
OD1 B:ASP180 4.9 8.2 1.0
CA B:VAL181 4.9 8.0 1.0

Potassium binding site 4 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 4 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2549

b:22.4
occ:1.00
 O B:VAL197 2.5 13.4 1.0
O B:TRP191 2.5 12.1 1.0
O B:ASP194 2.5 13.8 1.0
O B:HOH2604 2.5 16.6 1.0
O B:TYR226 3.4 11.5 1.0
C B:TRP191 3.5 12.6 1.0
CB B:TRP191 3.5 12.1 1.0
C B:ASP194 3.5 14.5 1.0
C B:VAL197 3.7 12.2 1.0
O B:HOH2780 3.8 25.9 1.0
CB B:TYR226 4.1 11.5 1.0
CA B:TRP191 4.1 13.1 1.0
N B:ASP194 4.2 14.6 1.0
C B:TYR226 4.2 11.3 1.0
CA B:ASP194 4.3 14.6 1.0
OG1 B:THR199 4.5 13.5 1.0
N B:PRO195 4.5 13.5 1.0
N B:VAL197 4.5 12.5 1.0
N B:TRP192 4.5 13.3 1.0
CB B:ASP194 4.5 15.2 1.0
CA B:PRO195 4.6 14.1 1.0
CA B:VAL197 4.6 12.7 1.0
N B:LEU198 4.6 12.2 1.0
CA B:LEU198 4.7 12.2 1.0
O B:TRP192 4.7 12.2 1.0
N B:THR199 4.7 11.4 1.0
CA B:TYR226 4.7 11.5 1.0
C B:TRP192 4.7 13.8 1.0
CG B:TRP191 4.8 14.3 1.0
CB B:VAL197 4.8 13.5 1.0
CG2 B:THR199 4.8 11.8 1.0
CA B:TRP192 4.9 13.3 1.0
O B:GLY223 4.9 14.5 1.0
C B:PRO195 4.9 13.6 1.0

Potassium binding site 5 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 5 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K2650

b:10.4
occ:1.00
 O C:ASP180 2.5 8.2 1.0
O C:HIS182 2.6 9.0 1.0
O C:LEU202 2.6 8.1 1.0
OD2 C:ASP178 2.7 10.3 1.0
OG C:SER201 2.7 9.8 1.0
O C:ASP178 3.1 7.9 1.0
CG C:ASP178 3.1 8.5 1.0
OD1 C:ASP178 3.5 10.5 1.0
C C:ASP180 3.6 7.5 1.0
C C:LEU202 3.7 8.4 1.0
C C:HIS182 3.7 9.2 1.0
C C:ASP178 3.7 8.8 1.0
CB C:SER201 3.9 7.4 1.0
N C:LEU202 3.9 8.7 1.0
N C:ASP180 4.0 7.5 1.0
CB C:ASP178 4.0 7.6 1.0
N C:GLY184 4.0 9.2 1.0
CB C:HIS203 4.1 8.6 1.0
CA C:SER201 4.1 7.4 1.0
CA C:ASP180 4.2 7.7 1.0
CA C:HIS183 4.3 9.8 1.0
CD2 C:HIS203 4.3 7.5 1.0
C C:TRP179 4.3 8.0 1.0
C C:SER201 4.3 9.1 1.0
CB C:ASP180 4.3 8.5 1.0
N C:TRP179 4.3 7.5 1.0
CA C:TRP179 4.4 8.8 1.0
N C:HIS182 4.4 7.4 1.0
N C:HIS183 4.4 9.0 1.0
CA C:LEU202 4.5 8.9 1.0
ND1 C:HIS142 4.5 8.4 1.0
CE1 C:HIS142 4.5 8.6 1.0
C C:HIS183 4.5 9.1 1.0
CA C:ASP178 4.5 7.8 1.0
N C:HIS203 4.6 8.6 1.0
CG C:HIS203 4.6 9.8 1.0
CA C:HIS203 4.6 8.2 1.0
O C:HOH2653 4.6 8.6 1.0
N C:VAL181 4.7 7.3 1.0
C C:VAL181 4.7 8.5 1.0
CA C:HIS182 4.7 8.2 1.0
OD1 C:ASP180 4.9 8.4 1.0
CA C:GLY184 4.9 9.0 1.0
CA C:VAL181 5.0 7.2 1.0

Potassium binding site 6 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 6 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K2649

b:18.8
occ:1.00
 O C:HOH2767 2.3 21.3 1.0
O C:TRP191 2.5 12.4 1.0
O C:VAL197 2.6 12.9 1.0
O C:ASP194 2.8 13.1 1.0
O C:HOH2774 3.0 19.7 1.0
O C:TYR226 3.1 13.9 1.0
C C:TRP191 3.4 13.1 1.0
CB C:TRP191 3.5 12.9 1.0
C C:VAL197 3.8 12.1 1.0
C C:ASP194 3.9 14.7 1.0
C C:TYR226 3.9 14.4 1.0
CB C:TYR226 4.0 14.6 1.0
OG1 C:THR199 4.1 11.5 1.0
CA C:TRP191 4.1 12.4 1.0
N C:ASP194 4.3 15.7 1.0
N C:TRP192 4.4 13.3 1.0
CA C:TYR226 4.5 13.9 1.0
N C:THR199 4.5 9.8 1.0
CA C:ASP194 4.6 14.6 1.0
N C:ASN227 4.6 13.1 1.0
O C:TRP192 4.6 15.8 1.0
CG2 C:THR199 4.6 10.1 1.0
CA C:LEU198 4.6 10.6 1.0
N C:LEU198 4.7 11.4 1.0
C C:TRP192 4.7 14.7 1.0
CA C:TRP192 4.7 14.6 1.0
O C:GLY223 4.8 17.3 1.0
CA C:VAL197 4.8 12.6 1.0
N C:PRO195 4.8 14.1 1.0
CB C:ASP194 4.8 14.2 1.0
CG C:TRP191 4.8 11.7 1.0
N C:VAL197 4.9 12.6 1.0
CA C:PRO195 4.9 13.5 1.0
CB C:THR199 4.9 10.0 1.0
C C:LEU198 5.0 10.7 1.0
CA C:ASN227 5.0 12.3 1.0

Potassium binding site 7 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 7 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2750

b:12.6
occ:1.00
 O D:ASP180 2.5 11.2 1.0
O D:HIS182 2.6 11.9 1.0
O D:LEU202 2.6 13.2 1.0
OD1 D:ASP178 2.7 13.8 1.0
OG D:SER201 2.7 13.0 1.0
O D:ASP178 3.0 11.8 1.0
CG D:ASP178 3.1 12.9 1.0
OD2 D:ASP178 3.5 11.7 1.0
C D:ASP180 3.6 10.9 1.0
C D:LEU202 3.7 12.9 1.0
C D:ASP178 3.7 11.2 1.0
C D:HIS182 3.7 12.0 1.0
N D:LEU202 3.9 12.4 1.0
CB D:SER201 3.9 11.6 1.0
N D:ASP180 3.9 10.6 1.0
CB D:ASP178 4.0 11.9 1.0
N D:GLY184 4.0 11.7 1.0
CB D:HIS203 4.1 11.4 1.0
CA D:SER201 4.1 12.2 1.0
CA D:ASP180 4.2 10.5 1.0
C D:SER201 4.2 12.6 1.0
C D:TRP179 4.3 10.2 1.0
N D:TRP179 4.3 10.9 1.0
ND1 D:HIS203 4.3 12.2 1.0
CA D:HIS183 4.3 12.3 1.0
CA D:TRP179 4.4 10.7 1.0
CB D:ASP180 4.4 10.3 1.0
N D:HIS182 4.4 11.5 1.0
CE1 D:HIS142 4.4 9.3 1.0
CA D:ASP178 4.4 11.6 1.0
ND1 D:HIS142 4.4 12.7 1.0
CA D:LEU202 4.5 12.3 1.0
N D:HIS183 4.5 11.9 1.0
N D:HIS203 4.5 11.1 1.0
C D:HIS183 4.5 11.5 1.0
O D:HOH2757 4.5 12.2 1.0
CA D:HIS203 4.6 11.4 1.0
C D:VAL181 4.7 10.9 1.0
CG D:HIS203 4.7 12.8 1.0
N D:VAL181 4.7 10.5 1.0
CA D:HIS182 4.7 11.8 1.0
CA D:GLY184 4.9 12.0 1.0
O D:TRP179 5.0 10.8 1.0
OD1 D:ASP180 5.0 10.1 1.0

Potassium binding site 8 out of 8 in 1zz1

Go back to Potassium Binding Sites List in 1zz1
Potassium binding site 8 out of 8 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2749

b:25.6
occ:1.00
 O D:HOH2822 2.2 17.1 1.0
O D:TRP191 2.5 16.0 1.0
O D:VAL197 2.5 15.7 1.0
O D:ASP194 2.6 17.2 1.0
O D:TYR226 3.3 14.7 1.0
O D:HOH2957 3.4 32.5 1.0
C D:TRP191 3.5 16.1 1.0
CB D:TRP191 3.5 16.2 1.0
C D:ASP194 3.6 17.6 1.0
C D:VAL197 3.7 14.4 1.0
CB D:TYR226 4.0 15.4 1.0
C D:TYR226 4.0 15.7 1.0
CA D:TRP191 4.1 16.0 1.0
N D:ASP194 4.3 17.1 1.0
OG1 D:THR199 4.3 15.2 1.0
CA D:ASP194 4.4 16.9 1.0
N D:TRP192 4.5 16.2 1.0
N D:PRO195 4.6 16.7 1.0
CA D:VAL197 4.6 14.8 1.0
N D:LEU198 4.6 14.1 1.0
N D:VAL197 4.6 14.8 1.0
CB D:ASP194 4.6 16.9 1.0
CA D:PRO195 4.6 16.7 1.0
CA D:LEU198 4.6 13.9 1.0
CA D:TYR226 4.6 15.4 1.0
O D:TRP192 4.6 16.3 1.0
N D:THR199 4.7 13.3 1.0
C D:TRP192 4.7 16.6 1.0
N D:ASN227 4.8 14.7 1.0
CG D:TRP191 4.8 16.1 1.0
CG2 D:THR199 4.8 16.8 1.0
CA D:TRP192 4.8 16.1 1.0
CB D:VAL197 4.9 15.3 1.0
O D:GLY223 4.9 17.0 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 05:55:45 2024

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