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Zinc in PDB 8qa7: Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.

Protein crystallography data

The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7 was solved by J.Sandmark, M.Ek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.63 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.39, 92.373, 96.19, 90, 90, 90
R / Rfree (%) 21.7 / 24

Other elements in 8qa7:

The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. (pdb code 8qa7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8qa7

Go back to Zinc Binding Sites List in 8qa7
Zinc binding site 1 out of 2 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:28.5
occ:1.00
OD2 A:ASP705 2.0 18.6 1.0
ND1 A:HIS614 2.0 18.6 1.0
OD1 A:ASP612 2.1 16.3 1.0
O3S A:EPE804 2.2 26.3 1.0
O2S A:EPE804 2.4 27.3 1.0
S A:EPE804 2.6 31.9 1.0
CG A:ASP612 2.7 17.5 1.0
OD2 A:ASP612 2.7 17.7 1.0
CE1 A:HIS614 2.9 19.3 1.0
CG A:ASP705 3.0 17.4 1.0
C10 A:EPE804 3.0 27.0 1.0
CG A:HIS614 3.2 18.0 1.0
OD1 A:ASP705 3.4 17.4 1.0
CB A:HIS614 3.6 16.9 1.0
N A:HIS614 3.9 16.4 1.0
NE2 A:HIS614 4.1 19.4 1.0
O1S A:EPE804 4.1 29.5 1.0
CB A:ASP612 4.2 16.5 1.0
NE2 A:HIS573 4.2 17.9 1.0
CD2 A:HIS614 4.2 18.5 1.0
CA A:GLY743 4.3 16.8 1.0
CB A:ASP705 4.3 16.9 1.0
OH A:TYR745 4.3 26.4 1.0
CG1 A:VAL613 4.4 16.7 1.0
N A:VAL613 4.4 15.7 1.0
CA A:HIS614 4.4 16.1 1.0
C9 A:EPE804 4.5 28.6 1.0
NE2 A:HIS574 4.6 17.1 1.0
CE2 A:TYR745 4.6 22.6 1.0
CE1 A:HIS573 4.6 16.6 1.0
N A:GLY743 4.7 16.3 1.0
C A:ASP612 4.9 16.1 1.0
CA A:ASP612 4.9 16.2 1.0
C A:VAL613 4.9 16.6 1.0
CZ A:TYR745 5.0 23.6 1.0

Zinc binding site 2 out of 2 in 8qa7

Go back to Zinc Binding Sites List in 8qa7
Zinc binding site 2 out of 2 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.


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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:28.1
occ:1.00
O1S B:EPE804 2.0 26.8 1.0
OD2 B:ASP705 2.0 21.7 1.0
ND1 B:HIS614 2.0 21.4 1.0
OD1 B:ASP612 2.1 17.9 1.0
O3S B:EPE804 2.3 26.5 1.0
S B:EPE804 2.3 30.8 1.0
CG B:ASP612 2.8 18.5 1.0
OD2 B:ASP612 2.8 19.7 1.0
CE1 B:HIS614 2.9 21.5 1.0
C10 B:EPE804 3.0 26.7 1.0
CG B:ASP705 3.0 19.8 1.0
CG B:HIS614 3.2 21.1 1.0
OD1 B:ASP705 3.4 19.4 1.0
CB B:HIS614 3.6 18.9 1.0
C9 B:EPE804 3.6 28.9 1.0
O2S B:EPE804 3.8 29.8 1.0
N B:HIS614 4.0 18.7 1.0
NE2 B:HIS614 4.0 21.9 1.0
CD2 B:HIS614 4.2 21.2 1.0
NE2 B:HIS573 4.2 18.2 1.0
CB B:ASP612 4.3 18.3 1.0
CB B:ASP705 4.3 19.1 1.0
CA B:GLY743 4.3 16.8 1.0
OH B:TYR745 4.3 27.8 1.0
CG1 B:VAL613 4.4 18.8 1.0
CA B:HIS614 4.4 19.0 1.0
N B:VAL613 4.4 18.6 1.0
CE2 B:TYR745 4.6 24.4 1.0
NE2 B:HIS574 4.7 17.9 1.0
CE1 B:HIS573 4.7 17.4 1.0
N B:GLY743 4.7 16.9 1.0
N1 B:EPE804 4.8 29.4 1.0
C B:ASP612 4.9 18.4 1.0
CZ B:TYR745 5.0 24.9 1.0
C B:VAL613 5.0 19.3 1.0
CA B:ASP612 5.0 17.6 1.0

Reference:

J.Sandmark, M.Ek. Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. To Be Published.
Page generated: Thu Oct 31 09:59:27 2024

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