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Calcium in PDB 5gz5: Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp

Protein crystallography data

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp, PDB code: 5gz5 was solved by C.C.Lin, B.S.Wu, W.G.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.88 / 2.09
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.207, 65.612, 88.675, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.9

Other elements in 5gz5:

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp (pdb code 5gz5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp, PDB code: 5gz5:

Calcium binding site 1 out of 1 in 5gz5

Go back to Calcium Binding Sites List in 5gz5
Calcium binding site 1 out of 1 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1015

b:11.3
occ:1.00
OD1 A:ASP728 1.9 26.1 1.0
OD1 A:ASP736 2.1 32.7 1.0
OD1 A:ASP732 2.1 24.6 1.0
O A:HIS734 2.2 18.4 1.0
OD1 A:ASN730 2.3 22.6 1.0
OD2 A:ASP736 2.5 36.8 1.0
CG A:ASP736 2.6 28.1 1.0
CG A:ASP732 3.0 25.4 1.0
CG A:ASP728 3.1 23.4 1.0
CG A:ASN730 3.3 23.4 1.0
C A:HIS734 3.4 18.0 1.0
OD2 A:ASP732 3.4 21.9 1.0
ND2 A:ASN730 3.6 23.2 1.0
N A:HIS734 3.8 21.5 1.0
O A:HOH1306 3.8 28.9 1.0
OD2 A:ASP728 3.8 17.9 1.0
N A:ASP732 3.8 19.5 1.0
CB A:ASP736 4.0 22.3 1.0
CA A:HIS734 4.1 20.6 1.0
CA A:ASP728 4.1 18.8 1.0
CB A:ASP728 4.1 17.9 1.0
O A:PHE735 4.1 25.2 1.0
C A:PHE735 4.1 25.9 1.0
CB A:ASP732 4.2 27.1 1.0
CB A:HIS734 4.4 22.7 1.0
CA A:ASP732 4.4 21.1 1.0
N A:ASP736 4.4 20.6 1.0
N A:PHE735 4.4 24.0 1.0
N A:GLY733 4.4 18.5 1.0
N A:TYR731 4.4 20.2 1.0
C A:ASP728 4.5 22.5 1.0
N A:ASN730 4.5 28.9 1.0
CA A:PHE735 4.6 25.6 1.0
CB A:ASN730 4.6 28.4 1.0
C A:ASN730 4.6 26.8 1.0
C A:ASP732 4.6 23.9 1.0
CA A:ASP736 4.6 21.7 1.0
O A:PHE727 4.8 22.9 1.0
CA A:ASN730 4.8 31.1 1.0
C A:TYR731 4.9 22.9 1.0
C A:GLY733 4.9 22.8 1.0
N A:TYR729 4.9 22.6 1.0
O A:ASP728 4.9 22.8 1.0
CA A:TYR731 4.9 22.4 1.0

Reference:

C.C.Lin, B.S.Wu, W.G.Wu. Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) in Complex with Amp To Be Published.
Page generated: Sat Dec 12 05:27:34 2020

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