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Calcium in PDB 5gz4: Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra)

Protein crystallography data

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra), PDB code: 5gz4 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) 29.43 / 2.55
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.679, 65.876, 89.615, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.8

Other elements in 5gz4:

The structure of Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra) 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) (pdb code 5gz4). 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), PDB code: 5gz4:

Calcium binding site 1 out of 1 in 5gz4

Go back to Calcium Binding Sites List in 5gz4
Calcium binding site 1 out of 1 in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:21.5
occ:1.00
OD1 A:ASP732 2.0 32.3 1.0
OD1 A:ASP728 2.0 31.6 1.0
OD2 A:ASP736 2.2 34.5 1.0
OD1 A:ASN730 2.2 33.9 1.0
OD1 A:ASP736 2.3 35.2 1.0
O A:HIS734 2.4 31.8 1.0
CG A:ASP736 2.5 35.3 1.0
CG A:ASP728 3.0 30.6 1.0
CG A:ASN730 3.1 35.1 1.0
CG A:ASP732 3.1 33.0 1.0
C A:HIS734 3.2 32.1 1.0
ND2 A:ASN730 3.4 35.7 1.0
N A:HIS734 3.6 31.5 1.0
OD2 A:ASP732 3.7 34.0 1.0
OD2 A:ASP728 3.8 29.7 1.0
CA A:HIS734 3.8 32.2 1.0
CB A:ASP728 3.8 30.4 1.0
CA A:ASP728 3.9 31.7 1.0
CB A:ASP736 3.9 36.5 1.0
C A:PHE735 4.1 33.9 1.0
CB A:HIS734 4.1 33.7 1.0
N A:ASP732 4.1 31.6 1.0
O A:PHE735 4.2 34.4 1.0
O A:HOH1023 4.2 39.0 1.0
N A:PHE735 4.2 31.7 1.0
N A:ASP736 4.3 35.1 1.0
CB A:ASP732 4.3 32.7 1.0
CA A:PHE735 4.4 32.5 1.0
N A:GLY733 4.4 30.6 1.0
N A:TYR731 4.5 32.9 1.0
CB A:ASN730 4.5 36.2 1.0
CA A:ASP732 4.6 31.4 1.0
CA A:ASP736 4.6 36.5 1.0
O A:PHE727 4.6 32.0 1.0
C A:ASP728 4.6 32.5 1.0
N A:ASN730 4.7 35.1 1.0
C A:ASP732 4.7 30.4 1.0
C A:GLY733 4.8 30.4 1.0
C A:ASN730 4.8 34.1 1.0
O A:HOH1043 4.8 32.4 1.0
N A:TYR729 4.9 33.8 1.0
CA A:ASN730 4.9 35.5 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) To Be Published.
Page generated: Sat Dec 12 05:27:33 2020

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