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Sodium in PDB 7cy3: Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.

Enzymatic activity of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.

All present enzymatic activity of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.:
3.1.1.74;

Protein crystallography data

The structure of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9., PDB code: 7cy3 was solved by K.Suzuki, M.Koitabashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.72 / 1.27
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 / 17.8

Other elements in 7cy3:

The structure of Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9. also contains other interesting chemical elements:

Arsenic (As) 4 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. (pdb code 7cy3). 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., PDB code: 7cy3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7cy3

Go back to Sodium Binding Sites List in 7cy3
Sodium binding site 1 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:5.2
occ:1.00
 O A:VAL54 2.3 7.5 1.0
O A:ALA51 2.3 10.7 1.0
OE1 A:GLU46 2.4 8.6 1.0
OE1 A:GLU8 2.4 6.3 1.0
O A:HOH349 2.4 18.5 1.0
OE2 A:GLU8 2.7 16.6 1.0
CD A:GLU8 2.8 7.7 1.0
C A:ALA51 3.4 9.3 1.0
CD A:GLU46 3.4 7.4 1.0
C A:VAL54 3.6 5.9 1.0
CG A:GLU46 4.0 7.4 1.0
CA A:ALA51 4.1 9.2 1.0
NZ A:LYS6 4.1 16.1 1.0
CG A:GLU8 4.3 6.5 1.0
OE2 A:GLU46 4.3 10.7 1.0
CA A:TRP55 4.4 4.8 1.0
O A:HOH405 4.4 23.0 1.0
CB A:ALA51 4.4 12.3 1.0
N A:TRP55 4.4 5.6 1.0
N A:SER52 4.4 10.8 1.0
N A:VAL54 4.5 7.0 1.0
CA A:VAL54 4.5 6.3 1.0
N A:VAL56 4.6 4.7 1.0
CA A:SER52 4.7 12.4 1.0
O A:HOH318 4.7 21.6 1.0
CE A:LYS6 4.7 13.8 1.0
O A:HOH394 4.8 19.1 1.0
CB A:VAL54 4.8 7.4 1.0
CB A:GLU8 4.8 4.4 1.0
CD1 A:TRP55 4.9 5.1 1.0
CG2 A:VAL56 4.9 6.2 1.0
C A:TRP55 5.0 4.9 1.0

Sodium binding site 2 out of 4 in 7cy3

Go back to Sodium Binding Sites List in 7cy3
Sodium binding site 2 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:10.4
occ:1.00
 OE1 A:GLU180 2.4 21.3 1.0
O A:HOH351 2.4 15.7 1.0
O A:HOH441 2.4 23.7 1.0
OD1 A:ASP179 2.4 19.9 1.0
O A:SER176 2.5 9.4 1.0
OE2 A:GLU180 2.5 21.4 1.0
OD2 A:ASP179 2.6 21.1 1.0
CD A:GLU180 2.8 17.1 1.0
CG A:ASP179 2.9 19.3 1.0
C A:SER176 3.6 7.1 1.0
O A:HOH421 4.0 26.8 1.0
OG A:SER176 4.2 9.1 1.0
CG A:GLU180 4.2 12.5 1.0
CB A:SER176 4.3 7.3 1.0
CA A:TYR177 4.3 6.5 1.0
CB A:ASP179 4.4 12.4 1.0
N A:TYR177 4.4 5.8 1.0
CA A:SER176 4.6 7.9 1.0
N A:GLU180 4.7 7.6 1.0
C A:TYR177 4.8 6.6 1.0
N A:ASP179 4.8 8.0 1.0

Sodium binding site 3 out of 4 in 7cy3

Go back to Sodium Binding Sites List in 7cy3
Sodium binding site 3 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:6.8
occ:1.00
 O B:VAL54 2.3 7.3 1.0
OE2 B:GLU46 2.3 10.2 1.0
O B:HOH500 2.3 17.0 1.0
O B:ALA51 2.4 8.8 1.0
O B:HOH559 2.4 19.9 1.0
OE1 B:GLU8 2.5 7.0 1.0
CD B:GLU8 3.2 7.1 1.0
OE2 B:GLU8 3.3 12.5 1.0
C B:ALA51 3.5 7.9 1.0
CD B:GLU46 3.5 8.7 1.0
C B:VAL54 3.5 5.0 1.0
CA B:ALA51 4.1 7.6 1.0
CG B:GLU46 4.3 7.1 1.0
CA B:TRP55 4.3 4.5 1.0
CB B:ALA51 4.3 9.2 1.0
N B:TRP55 4.4 5.2 1.0
OE1 B:GLU46 4.4 11.7 1.0
O B:HOH429 4.5 17.1 1.0
CA B:VAL54 4.5 6.2 1.0
N B:VAL54 4.5 6.0 1.0
CG B:GLU8 4.6 6.0 1.0
N B:VAL56 4.6 3.9 1.0
N B:SER52 4.6 8.8 1.0
CB B:VAL54 4.7 7.0 1.0
CD1 B:TRP55 4.7 6.2 1.0
CA B:SER52 4.8 10.1 1.0
C B:TRP55 4.9 4.3 1.0
CG2 B:VAL56 5.0 6.2 1.0

Sodium binding site 4 out of 4 in 7cy3

Go back to Sodium Binding Sites List in 7cy3
Sodium binding site 4 out of 4 in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9.


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. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:3.8
occ:1.00
 OD1 B:ASP179 2.4 6.6 1.0
O B:HOH414 2.4 9.8 1.0
O B:HOH457 2.4 16.1 1.0
OE1 B:GLU180 2.4 7.2 1.0
O B:SER176 2.4 8.3 1.0
O B:HOH540 2.5 7.3 1.0
OE2 B:GLU180 2.8 10.6 1.0
OD2 B:ASP179 2.8 9.0 1.0
CG B:ASP179 2.9 6.6 1.0
CD B:GLU180 2.9 6.3 1.0
O B:HOH401 3.4 3.2 1.0
C B:SER176 3.6 5.0 1.0
O B:HOH539 3.9 9.7 1.0
OG B:SER176 4.1 8.1 1.0
O B:HOH577 4.1 29.4 1.0
CA B:TYR177 4.2 4.1 1.0
CB B:SER176 4.3 5.7 1.0
O B:HOH511 4.3 16.1 1.0
CB B:ASP179 4.3 5.3 1.0
N B:TYR177 4.4 4.8 1.0
CG B:GLU180 4.4 6.4 1.0
CA B:SER176 4.5 4.7 1.0
N B:GLU180 4.6 5.2 1.0
N B:ASP179 4.7 5.2 1.0
C B:TYR177 4.8 5.3 1.0
O B:HOH426 4.9 13.5 1.0
CD1 B:TYR177 4.9 4.2 1.0
CA B:ASP179 5.0 5.4 1.0

Reference:

K.Suzuki, M.Koitabashi. Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9. To Be Published.
Page generated: Tue Oct 8 16:26:19 2024

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