Sodium in PDB 7cy9: Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).

Enzymatic activity of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).

All present enzymatic activity of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).:
3.1.1.74;

Protein crystallography data

The structure of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate)., PDB code: 7cy9 was solved by K.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.69 / 1.36
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 34.886, 43.517, 51.724, 103.78, 92.42, 101.49
R / Rfree (%) 12.4 / 16.9

Other elements in 7cy9:

The structure of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). also contains other interesting chemical elements:

Arsenic (As) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). (pdb code 7cy9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate)., PDB code: 7cy9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7cy9

Go back to Sodium Binding Sites List in 7cy9
Sodium binding site 1 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:5.0
occ:1.00
 O A:HOH326 2.3 18.2 1.0
OD1 A:ASP179 2.4 7.3 1.0
O A:HOH321 2.4 10.6 1.0
OE1 A:GLU180 2.4 8.1 1.0
O A:SER176 2.4 10.2 1.0
O A:HOH429 2.5 8.5 1.0
OE2 A:GLU180 2.8 11.1 1.0
OD2 A:ASP179 2.8 9.9 1.0
CG A:ASP179 2.9 7.4 1.0
CD A:GLU180 2.9 7.9 1.0
O A:HOH301 3.5 6.7 1.0
C A:SER176 3.6 6.1 1.0
O A:HOH465 4.0 26.6 1.0
OG A:SER176 4.1 9.0 1.0
CA A:TYR177 4.2 5.4 1.0
CB A:SER176 4.3 7.4 1.0
O A:HOH405 4.3 17.7 1.0
CB A:ASP179 4.3 6.1 1.0
N A:TYR177 4.3 6.0 1.0
CG A:GLU180 4.4 8.2 1.0
CA A:SER176 4.5 6.1 1.0
O A:HOH469 4.6 35.8 1.0
N A:GLU180 4.6 6.9 1.0
N A:ASP179 4.8 6.4 1.0
C A:TYR177 4.8 6.6 1.0
CD1 A:TYR177 4.9 5.2 1.0
O A:HOH332 4.9 16.0 1.0

Sodium binding site 2 out of 4 in 7cy9

Go back to Sodium Binding Sites List in 7cy9
Sodium binding site 2 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:7.7
occ:1.00
 O A:VAL54 2.3 8.1 1.0
O A:HOH435 2.3 31.5 1.0
OE2 A:GLU46 2.4 11.1 1.0
O A:HOH371 2.4 21.5 1.0
O A:ALA51 2.4 9.6 1.0
OE1 A:GLU8 2.5 7.9 1.0
CD A:GLU8 3.2 7.8 1.0
OE2 A:GLU8 3.3 13.6 1.0
C A:ALA51 3.5 9.6 1.0
C A:VAL54 3.5 6.2 1.0
CD A:GLU46 3.5 9.9 1.0
O A:HOH325 3.8 22.4 1.0
CA A:ALA51 4.1 7.8 1.0
CG A:GLU46 4.3 8.7 1.0
CA A:TRP55 4.3 6.1 1.0
CB A:ALA51 4.3 10.6 1.0
N A:TRP55 4.4 5.8 1.0
OE1 A:GLU46 4.4 12.3 1.0
O A:HOH316 4.4 19.2 1.0
CA A:VAL54 4.4 7.2 1.0
N A:VAL54 4.5 7.0 1.0
CG A:GLU8 4.6 9.4 1.0
N A:SER52 4.6 9.9 1.0
N A:VAL56 4.6 6.0 1.0
CB A:VAL54 4.7 8.3 1.0
CD1 A:TRP55 4.7 7.7 1.0
CA A:SER52 4.9 11.4 1.0
C A:TRP55 4.9 6.2 1.0

Sodium binding site 3 out of 4 in 7cy9

Go back to Sodium Binding Sites List in 7cy9
Sodium binding site 3 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:11.6
occ:1.00
 OD1 B:ASP179 2.2 40.9 1.0
O B:HOH432 2.3 28.7 1.0
O B:HOH433 2.4 30.3 1.0
O B:HOH349 2.5 17.5 1.0
OE2 B:GLU180 2.5 31.1 1.0
O B:SER176 2.5 10.7 1.0
OD2 B:ASP179 2.6 28.3 1.0
CG B:ASP179 2.8 23.7 1.0
CD B:GLU180 3.5 20.6 1.0
C B:SER176 3.6 7.7 1.0
O B:HOH310 4.1 28.2 1.0
OG B:SER176 4.3 10.0 1.0
O B:HOH443 4.3 27.6 1.0
CB B:ASP179 4.3 15.7 1.0
CG B:GLU180 4.3 15.5 1.0
OE1 B:GLU180 4.3 22.6 1.0
CB B:SER176 4.3 7.5 1.0
CA B:TYR177 4.4 7.1 1.0
N B:TYR177 4.4 7.0 1.0
CA B:SER176 4.6 7.2 1.0
N B:GLU180 4.7 8.3 1.0
C B:TYR177 4.8 7.5 1.0
N B:ASP179 4.9 8.6 1.0

Sodium binding site 4 out of 4 in 7cy9

Go back to Sodium Binding Sites List in 7cy9
Sodium binding site 4 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9 Solved By Getting the Phase From Anomalous Scattering of Uncovalently Coordinated Arsenic (Cacodylate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:6.1
occ:1.00
 O B:ALA51 2.3 11.9 1.0
O B:VAL54 2.3 8.0 1.0
OE2 B:GLU46 2.4 9.6 1.0
OE1 B:GLU8 2.4 8.3 1.0
O B:HOH348 2.4 22.6 1.0
OE2 B:GLU8 2.6 19.1 1.0
CD B:GLU8 2.8 9.8 1.0
C B:ALA51 3.4 10.5 1.0
CD B:GLU46 3.4 8.2 1.0
C B:VAL54 3.6 7.0 1.0
CG B:GLU46 4.0 8.4 1.0
NZ B:LYS6 4.1 15.8 1.0
CA B:ALA51 4.1 10.3 1.0
CG B:GLU8 4.3 8.3 1.0
CA B:TRP55 4.4 5.5 1.0
OE1 B:GLU46 4.4 12.1 1.0
O B:HOH415 4.4 22.2 1.0
CB B:ALA51 4.4 15.4 1.0
N B:TRP55 4.4 5.9 1.0
N B:SER52 4.5 11.2 1.0
CA B:VAL54 4.5 7.2 1.0
N B:VAL54 4.5 8.0 1.0
N B:VAL56 4.6 6.2 1.0
CA B:SER52 4.7 13.1 1.0
O B:HOH372 4.7 19.6 1.0
CE B:LYS6 4.8 16.4 1.0
CB B:VAL54 4.8 8.2 1.0
CB B:GLU8 4.8 6.4 1.0
CD1 B:TRP55 4.9 6.1 1.0
CG2 B:VAL56 4.9 6.7 1.0
C B:TRP55 5.0 6.0 1.0

Reference:

K.Suzuki, K.Suzuki. N/A N/A.
Page generated: Tue Dec 15 17:48:51 2020

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