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Zinc in PDB 3ecn: Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx

Enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx

All present enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx, PDB code: 3ecn was solved by H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.325, 101.601, 76.573, 90.00, 119.90, 90.00
R / Rfree (%) 22.1 / 25.6

Other elements in 3ecn:

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx (pdb code 3ecn). 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 PDE8A Catalytic Domain in Complex with Ibmx, PDB code: 3ecn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ecn

Go back to Zinc Binding Sites List in 3ecn
Zinc binding site 1 out of 2 in the Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx


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 PDE8A Catalytic Domain in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:40.7
occ:1.00
OD2 A:ASP597 2.2 37.2 1.0
OD1 A:ASP726 2.2 30.6 1.0
NE2 A:HIS560 2.3 30.3 1.0
NE2 A:HIS596 2.3 35.8 1.0
O A:HOH821 2.4 36.5 1.0
O A:HOH820 2.5 29.8 1.0
CD2 A:HIS596 3.1 33.5 1.0
CG A:ASP726 3.2 35.8 1.0
CD2 A:HIS560 3.2 32.5 1.0
CG A:ASP597 3.3 34.5 1.0
CE1 A:HIS560 3.3 30.3 1.0
OD2 A:ASP726 3.4 31.6 1.0
CE1 A:HIS596 3.4 38.4 1.0
OD1 A:ASP597 3.8 33.6 1.0
O A:HOH822 4.0 34.9 1.0
O A:HOH842 4.1 42.3 1.0
MG A:MG2 4.2 37.9 1.0
O A:HOH883 4.2 55.2 1.0
NE2 A:HIS556 4.3 32.1 1.0
CD2 A:HIS556 4.3 30.3 1.0
CG A:HIS596 4.3 36.1 1.0
CG A:HIS560 4.4 31.5 1.0
ND1 A:HIS560 4.4 30.9 1.0
ND1 A:HIS596 4.4 36.5 1.0
CB A:ASP597 4.4 34.0 1.0
CB A:ASP726 4.5 32.2 1.0
CG2 A:VAL564 4.6 28.6 1.0
O A:ASP726 4.7 33.6 1.0
CA A:ASP726 4.9 32.7 1.0
O A:HOH823 4.9 35.4 1.0

Zinc binding site 2 out of 2 in 3ecn

Go back to Zinc Binding Sites List in 3ecn
Zinc binding site 2 out of 2 in the Crystal Structure of PDE8A Catalytic Domain in Complex with Ibmx


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 PDE8A Catalytic Domain in Complex with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:39.6
occ:1.00
OD2 B:ASP597 2.2 36.2 1.0
OD1 B:ASP726 2.2 32.1 1.0
NE2 B:HIS560 2.3 29.0 1.0
NE2 B:HIS596 2.3 33.7 1.0
O B:HOH12 2.5 34.0 1.0
O B:HOH11 2.6 29.7 1.0
CD2 B:HIS596 3.1 32.2 1.0
CG B:ASP726 3.2 36.5 1.0
CD2 B:HIS560 3.2 31.0 1.0
CG B:ASP597 3.2 35.9 1.0
CE1 B:HIS560 3.3 30.3 1.0
CE1 B:HIS596 3.4 34.6 1.0
OD2 B:ASP726 3.4 31.7 1.0
O B:HOH13 3.8 38.2 1.0
O B:HOH127 3.8 53.5 1.0
OD1 B:ASP597 3.8 33.1 1.0
O B:HOH133 4.1 48.5 1.0
MG B:MG2 4.2 38.9 1.0
NE2 B:HIS556 4.2 30.7 1.0
CD2 B:HIS556 4.3 31.4 1.0
CG B:HIS596 4.3 35.9 1.0
CG B:HIS560 4.4 29.9 1.0
ND1 B:HIS560 4.4 29.8 1.0
CB B:ASP597 4.4 35.4 1.0
ND1 B:HIS596 4.4 34.5 1.0
CB B:ASP726 4.5 34.3 1.0
CG2 B:VAL564 4.6 28.6 1.0
O B:ASP726 4.6 35.5 1.0
CA B:ASP726 4.9 34.3 1.0
O B:HOH14 5.0 38.0 1.0

Reference:

H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke. Kinetic and Structural Studies of Phosphodiesterase-8A and Implication on the Inhibitor Selectivity Biochemistry V. 47 12760 2008.
ISSN: ISSN 0006-2960
PubMed: 18983167
DOI: 10.1021/BI801487X
Page generated: Wed Dec 16 04:15:38 2020

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