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Zinc 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:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Snake Venom Phosphodiesterase (Pde) From Taiwan Cobra (Naja Atra Atra), PDB code: 5gz4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5gz4

Go back to Zinc Binding Sites List in 5gz4
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn901

b:30.9
occ:1.00
NE2 A:HIS309 1.9 36.7 1.0
OD1 A:ASP305 2.0 34.1 1.0
NE2 A:HIS462 2.0 33.4 1.0
O A:HOH1025 2.7 30.7 1.0
CG A:ASP305 2.8 35.4 1.0
CD2 A:HIS309 2.8 36.8 1.0
OD2 A:ASP305 2.9 37.6 1.0
CE1 A:HIS462 2.9 33.0 1.0
CE1 A:HIS309 2.9 35.5 1.0
CD2 A:HIS462 3.1 31.7 1.0
CG A:HIS309 4.0 35.7 1.0
ND1 A:HIS309 4.0 35.0 1.0
CE1 A:HIS353 4.0 33.8 1.0
ND1 A:HIS462 4.1 30.4 1.0
NE2 A:HIS353 4.1 34.5 1.0
CG A:HIS462 4.2 30.5 1.0
CB A:ASP305 4.2 34.5 1.0
OG1 A:THR185 4.2 35.6 1.0
O A:HOH1443 4.4 35.3 1.0
O A:HOH1174 4.5 27.3 1.0
ZN A:ZN902 4.5 31.7 1.0
CE A:MET355 4.6 32.5 1.0
OD1 A:ASP147 4.6 36.7 1.0
O A:ASP305 4.7 34.2 1.0
CA A:ASP305 5.0 33.6 1.0
C A:ASP305 5.0 34.7 1.0

Zinc binding site 2 out of 2 in 5gz4

Go back to Zinc Binding Sites List in 5gz4
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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:Zn902

b:31.7
occ:1.00
OD1 A:ASP147 1.9 36.7 1.0
NE2 A:HIS353 2.0 34.5 1.0
OD2 A:ASP352 2.1 33.9 1.0
OD2 A:ASP147 2.4 36.9 1.0
OG1 A:THR185 2.4 35.6 1.0
CG A:ASP147 2.4 37.4 1.0
CD2 A:HIS353 2.5 32.0 1.0
CG A:ASP352 2.9 32.0 1.0
OD1 A:ASP352 3.0 32.3 1.0
CE1 A:HIS353 3.1 33.8 1.0
CB A:THR185 3.2 35.0 1.0
CA A:THR185 3.3 32.8 1.0
CG2 A:THR185 3.5 34.6 1.0
CG A:HIS353 3.8 30.5 1.0
CB A:ASP147 3.8 38.0 1.0
N A:THR185 3.9 32.8 1.0
ND1 A:HIS353 4.0 31.5 1.0
O A:HOH1025 4.1 30.7 1.0
N A:GLY148 4.2 31.9 1.0
CE1 A:HIS462 4.3 33.0 1.0
CB A:ASP352 4.3 29.6 1.0
CA A:ASP147 4.4 32.0 1.0
OD1 A:ASP305 4.4 34.1 1.0
C A:LYS184 4.5 32.3 1.0
CE1 A:HIS189 4.5 34.6 1.0
NE2 A:HIS462 4.5 33.4 1.0
ZN A:ZN901 4.5 30.9 1.0
C A:ASP147 4.5 32.6 1.0
CG A:ASP305 4.6 35.4 1.0
C A:THR185 4.6 32.2 1.0
O A:LYS184 4.7 30.7 1.0
ND1 A:HIS189 4.8 34.0 1.0
O A:THR185 4.9 31.0 1.0
OD2 A:ASP305 4.9 37.6 1.0
CA A:GLY148 4.9 31.5 1.0
ND1 A:HIS462 4.9 30.4 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) To Be Published.
Page generated: Wed Dec 16 06:19:52 2020

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