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Zinc in PDB 6ezu: Schistosoma Mansoni Phosphodiesterase 4A

Protein crystallography data

The structure of Schistosoma Mansoni Phosphodiesterase 4A, PDB code: 6ezu was solved by D.G.Brown, S.Schroeder, C.Gil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.44 / 2.04
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.550, 81.550, 255.870, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.3

Other elements in 6ezu:

The structure of Schistosoma Mansoni Phosphodiesterase 4A also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Schistosoma Mansoni Phosphodiesterase 4A (pdb code 6ezu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Schistosoma Mansoni Phosphodiesterase 4A, PDB code: 6ezu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ezu

Go back to Zinc Binding Sites List in 6ezu
Zinc binding site 1 out of 2 in the Schistosoma Mansoni Phosphodiesterase 4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Schistosoma Mansoni Phosphodiesterase 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:43.9
occ:1.00
O1P A:CMP703 2.0 47.3 1.0
O A:HOH802 2.1 48.1 1.0
OD1 A:ASP575 2.1 39.5 1.0
NE2 A:HIS421 2.1 38.2 1.0
NE2 A:HIS457 2.2 38.0 1.0
OD2 A:ASP458 2.2 39.9 1.0
CD2 A:HIS457 3.0 38.7 1.0
CG A:ASP575 3.0 41.2 1.0
CD2 A:HIS421 3.1 38.9 1.0
CE1 A:HIS421 3.2 40.7 1.0
CG A:ASP458 3.2 45.3 1.0
CE1 A:HIS457 3.3 40.9 1.0
P A:CMP703 3.3 63.8 1.0
OD2 A:ASP575 3.4 42.3 1.0
OD1 A:ASP458 3.6 45.0 1.0
O2P A:CMP703 3.8 54.0 1.0
MG A:MG702 3.9 40.6 1.0
O A:HOH818 4.0 44.1 1.0
O5' A:CMP703 4.2 48.7 1.0
CG A:HIS457 4.2 38.0 1.0
CG A:HIS421 4.2 38.7 1.0
ND1 A:HIS421 4.2 39.0 1.0
ND1 A:HIS457 4.3 39.5 1.0
CB A:ASP458 4.4 41.3 1.0
CD2 A:HIS417 4.4 44.5 1.0
CB A:ASP575 4.4 36.0 1.0
CG2 A:VAL425 4.7 37.8 1.0
C5' A:CMP703 4.7 55.1 1.0
NE2 A:HIS417 4.9 46.5 1.0
O A:HOH815 4.9 41.7 1.0
CA A:ASP575 5.0 37.6 1.0

Zinc binding site 2 out of 2 in 6ezu

Go back to Zinc Binding Sites List in 6ezu
Zinc binding site 2 out of 2 in the Schistosoma Mansoni Phosphodiesterase 4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Schistosoma Mansoni Phosphodiesterase 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:47.2
occ:1.00
O2P B:AMP703 2.1 55.4 1.0
NE2 B:HIS421 2.1 41.2 1.0
O B:HOH801 2.2 44.3 1.0
OD2 B:ASP458 2.2 45.8 1.0
NE2 B:HIS457 2.2 40.8 1.0
OD1 B:ASP575 2.2 43.3 1.0
CD2 B:HIS421 3.0 43.9 1.0
CD2 B:HIS457 3.1 43.4 1.0
CG B:ASP458 3.1 46.3 1.0
CG B:ASP575 3.1 45.5 1.0
CE1 B:HIS421 3.2 48.1 1.0
CE1 B:HIS457 3.2 40.9 1.0
P B:AMP703 3.3 61.0 1.0
OD2 B:ASP575 3.3 46.9 1.0
OD1 B:ASP458 3.6 46.6 1.0
O3P B:AMP703 3.7 50.7 1.0
MG B:MG702 3.9 44.1 1.0
O B:HOH809 4.0 54.2 1.0
O5' B:AMP703 4.1 49.5 1.0
CG B:HIS421 4.2 43.6 1.0
CG B:HIS457 4.3 40.6 1.0
ND1 B:HIS421 4.3 49.1 1.0
ND1 B:HIS457 4.3 40.5 1.0
CB B:ASP458 4.4 41.6 1.0
CD2 B:HIS417 4.5 44.7 1.0
CB B:ASP575 4.5 43.8 1.0
O1P B:AMP703 4.6 57.0 1.0
CG2 B:VAL425 4.7 45.5 1.0
O B:HOH806 4.9 45.5 1.0
C5' B:AMP703 4.9 53.5 1.0
NE2 B:HIS417 4.9 49.8 1.0

Reference:

D.G.Brown, S.Schroeder, C.Gil, J.Munday, H.Koning, M.Siderius, R.Leurs. The Structure of Schistosoma Mansoni Phosphodiesterase 4A in Complex with Camp To Be Published.
Page generated: Wed Dec 16 11:45:24 2020

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