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Arsenic 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:

Sodium (Na) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of A Biodegradable Plastic-Degrading Cutinase From Paraphoma Sp. B47-9., PDB code: 7cy3:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 7cy3

Go back to Arsenic Binding Sites List in 7cy3
Arsenic 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 Arsenic with other atoms in the As 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:As201

b:10.0
occ:1.00
 AS A:CAD201 0.0 10.0 1.0
O2 A:CAD201 1.7 10.1 1.0
O1 A:CAD201 1.8 11.3 1.0
C1 A:CAD201 1.9 10.9 1.0
C2 A:CAD201 1.9 10.3 1.0
OG A:SER106 2.7 7.2 1.0
OG A:SER28 3.5 6.8 1.0
O A:HOH302 3.6 10.3 1.0
CB A:SER106 3.8 5.7 1.0
OD1 A:ASN70 3.9 7.3 1.0
NE2 A:HIS174 3.9 8.7 1.0
CB A:SER28 4.0 6.1 1.0
N A:GLN107 4.1 4.7 1.0
ND2 A:ASN70 4.2 7.0 1.0
CG A:ASN70 4.3 5.2 1.0
N A:SER28 4.4 5.7 1.0
CG2 A:VAL170 4.5 9.5 1.0
CE1 A:HIS174 4.7 7.3 1.0
CA A:SER106 4.7 4.8 1.0
CD2 A:HIS174 4.8 6.9 1.0
O A:HOH338 4.8 24.6 1.0
C A:SER106 4.8 4.8 1.0
CB A:GLN107 4.8 5.1 1.0
CA A:SER28 4.8 5.7 1.0
CA A:GLN107 5.0 3.9 1.0

Arsenic binding site 2 out of 4 in 7cy3

Go back to Arsenic Binding Sites List in 7cy3
Arsenic 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 Arsenic with other atoms in the As 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:As202

b:0.5
occ:1.00
 AS A:CAD202 0.0 0.5 1.0
O2 A:CAD202 1.8 0.0 1.0
O A:HOH301 1.9 18.3 1.0
O1 A:CAD202 2.0 0.5 1.0
C2 A:CAD202 2.0 0.7 1.0
C1 A:CAD202 2.0 68.3 1.0
O A:HOH303 2.5 14.2 1.0
O A:VAL155 4.1 5.2 1.0
O A:CYS157 4.5 10.2 1.0
O A:HOH448 4.6 20.9 1.0
N A:CYS157 4.6 6.5 1.0
CA A:TYR156 4.9 4.7 1.0
O A:HOH467 4.9 22.3 1.0
O A:HOH449 5.0 20.4 1.0

Arsenic binding site 3 out of 4 in 7cy3

Go back to Arsenic Binding Sites List in 7cy3
Arsenic 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 Arsenic with other atoms in the As 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:As301

b:17.3
occ:1.00
 AS B:CAD301 0.0 17.3 1.0
O2 B:CAD301 1.7 24.1 1.0
O1 B:CAD301 1.9 24.7 1.0
C2 B:CAD301 1.9 13.2 1.0
C1 B:CAD301 2.0 19.2 1.0
O B:HOH406 3.7 21.3 1.0
O B:HOH573 3.9 19.4 1.0
O B:VAL155 4.6 5.5 1.0
O B:HOH518 4.6 19.6 1.0
CD1 B:TYR156 4.7 6.7 1.0
CE1 B:TYR156 4.7 6.3 1.0

Arsenic binding site 4 out of 4 in 7cy3

Go back to Arsenic Binding Sites List in 7cy3
Arsenic 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 Arsenic with other atoms in the As 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:As302

b:12.9
occ:1.00
 AS B:CAD302 0.0 12.9 1.0
O2 B:CAD302 1.7 10.5 1.0
C2 B:CAD302 1.8 11.1 1.0
O1 B:CAD302 1.9 21.7 1.0
C1 B:CAD302 1.9 10.9 1.0
OG B:SER106 2.7 7.8 1.0
OG B:SER28 3.5 8.3 1.0
CB B:SER106 3.7 5.3 1.0
CB B:SER28 3.8 9.8 1.0
O B:HOH578 4.0 17.8 1.0
OD1 B:ASN70 4.1 7.6 1.0
N B:GLN107 4.2 5.1 1.0
NE2 B:HIS174 4.2 7.1 1.0
N B:SER28 4.2 7.5 1.0
ND2 B:ASN70 4.3 7.9 1.0
CG B:ASN70 4.5 6.5 1.0
O B:HOH456 4.6 28.4 1.0
CA B:SER28 4.6 8.7 1.0
CG2 B:VAL170 4.7 9.4 1.0
CA B:SER106 4.7 4.3 1.0
C B:SER106 4.9 4.8 1.0
CD2 B:HIS174 4.9 7.3 1.0
CB B:GLN107 4.9 5.7 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: Wed Jul 10 13:39:58 2024

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