Zinc in PDB 5ts5: Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox

The structure of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox, PDB code: 5ts5 was solved by P.R.Feliciano, M.C.Nonato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.640, 123.920, 105.080, 90.00, 96.03, 90.00
R / Rfree (%)	18 / 23

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox (pdb code 5ts5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox, PDB code: 5ts5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


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 L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:50.4 occ:1.00 O B:HOH850 2.1 20.4 1.0 OD2 B:ASP201 2.2 30.1 1.0 ND1 A:HIS314 2.4 30.4 1.0 CE1 A:HIS440 2.6 29.7 1.0 NE2 A:HIS440 2.9 30.9 1.0 CG B:ASP201 2.9 31.1 1.0 OD1 B:ASP201 3.1 24.9 1.0 CE1 A:HIS314 3.2 29.1 1.0 O A:HOH847 3.5 25.8 1.0 CG A:HIS314 3.6 22.8 1.0 O A:HOH845 3.6 30.1 1.0 ND1 A:HIS440 3.7 34.6 1.0 CB A:HIS314 4.0 24.0 1.0 CD2 A:HIS440 4.2 40.3 1.0 CE1 A:PHE441 4.2 31.0 1.0 CB B:ASP201 4.2 24.1 1.0 NE2 A:HIS314 4.4 21.5 1.0 O B:HOH635 4.6 26.9 1.0 CG A:HIS440 4.6 36.4 1.0 CD2 A:HIS314 4.6 22.6 1.0 CZ A:PHE441 4.8 20.0 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


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 L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:35.8 occ:0.55 OE2 A:GLU100 2.1 24.7 1.0 CD A:GLU100 2.9 27.5 1.0 OE1 A:GLU100 3.0 23.6 1.0 O A:LYS24 4.0 21.1 1.0 CA A:LYS24 4.1 23.2 1.0 CG A:GLU100 4.2 20.7 1.0 CB A:LYS24 4.3 26.6 1.0 CG A:LYS24 4.3 34.6 1.0 NZ A:LYS104 4.3 34.3 1.0 C A:LYS24 4.5 26.5 1.0 O A:GLU100 5.0 21.1 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:54.5 occ:1.00 O A:HOH868 2.1 22.6 1.0 OD2 A:ASP201 2.3 27.4 1.0 ND1 B:HIS314 2.6 24.4 1.0 CE1 B:HIS440 2.6 29.7 1.0 NE2 B:HIS440 2.7 38.1 1.0 O B:HOH604 2.9 32.6 1.0 CG A:ASP201 3.1 26.6 1.0 OD1 A:ASP201 3.2 29.8 1.0 CE1 B:HIS314 3.3 26.3 1.0 O B:HOH669 3.6 30.3 1.0 CG B:HIS314 3.7 26.4 1.0 ND1 B:HIS440 3.9 34.2 1.0 CD2 B:HIS440 3.9 37.0 1.0 CB B:HIS314 4.1 17.0 1.0 CE1 B:PHE441 4.1 27.5 1.0 O A:HOH658 4.1 18.1 1.0 O B:HOH865 4.2 40.9 1.0 CB A:ASP201 4.4 24.1 1.0 NE2 B:HIS314 4.5 21.1 1.0 CG B:HIS440 4.5 30.8 1.0 CD2 B:HIS314 4.7 19.9 1.0 CZ B:PHE441 4.8 25.0 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:41.6 occ:0.50 ZN B:ZN502 0.0 41.6 0.5 OE2 B:GLU337 2.1 34.2 1.0 ZN B:ZN502 2.7 38.6 0.5 OD2 D:ASP267 2.8 44.1 1.0 CD B:GLU337 3.0 30.6 1.0 NZ B:LYS334 3.1 34.9 1.0 OD1 D:ASP267 3.2 41.0 1.0 OE1 B:GLU337 3.2 35.8 1.0 CG D:ASP267 3.3 40.0 1.0 ND2 B:ASN361 3.7 45.8 1.0 CE B:LYS334 3.7 35.5 1.0 O B:HOH673 3.9 24.8 1.0 CG B:GLU337 4.3 23.6 1.0 CE1 B:HIS342 4.4 33.1 1.0 ND1 B:HIS342 4.4 33.9 1.0 CB D:ASP267 4.7 30.7 1.0 CG B:ASN361 4.8 45.5 1.0 CD B:LYS334 4.9 27.1 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:38.6 occ:0.50 ZN B:ZN502 0.0 38.6 0.5 ZN B:ZN502 2.7 41.6 0.5 NZ B:LYS334 3.1 34.9 1.0 OD2 D:ASP267 3.3 44.1 1.0 CE B:LYS334 3.3 35.5 1.0 ND2 B:ASN361 3.9 45.8 1.0 OE2 B:GLU337 4.0 34.2 1.0 OE1 B:GLU337 4.1 35.8 1.0 CG D:ASP267 4.4 40.0 1.0 CD B:GLU337 4.5 30.6 1.0 O B:HOH797 4.5 28.0 1.0 CD B:LYS334 4.8 27.1 1.0 OD1 D:ASP267 4.9 41.0 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:52.4 occ:1.00 O C:HOH857 2.2 21.1 1.0 OE2 B:GLU132 2.4 25.7 1.0 OE1 B:GLU132 2.5 39.0 1.0 OE1 C:GLU141 2.7 32.0 1.0 OE2 C:GLU141 2.7 32.1 1.0 CD B:GLU132 2.7 30.7 1.0 CD C:GLU141 3.0 27.1 1.0 O B:HOH643 3.9 22.6 1.0 CG B:GLU132 4.2 27.5 1.0 CG B:ARG129 4.3 19.7 1.0 O B:HOH857 4.4 26.8 1.0 N B:ARG129 4.4 19.8 1.0 CG C:GLU141 4.5 21.5 1.0 O C:HOH778 4.6 34.1 1.0 CA B:LYS128 4.6 16.1 1.0 NZ B:LYS128 4.6 21.6 1.0 CG B:LYS128 4.7 28.3 1.0 O B:ARG127 4.7 23.2 1.0 O B:HOH693 4.9 36.6 1.0 CD1 C:ILE126 4.9 22.9 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:50.5 occ:1.00 OE2 B:GLU8 2.0 53.4 1.0 OD1 B:ASP225 2.2 45.1 1.0 O B:HOH804 2.3 35.0 1.0 O B:HOH809 2.5 33.8 1.0 CG B:ASP225 2.9 38.6 1.0 OD2 B:ASP225 3.1 40.6 1.0 CD B:GLU8 3.1 49.4 1.0 OE1 B:GLU8 3.6 48.8 1.0 O B:ASP225 3.7 36.6 1.0 CB B:ASN5 4.0 44.6 1.0 ND2 B:ASN5 4.2 39.3 1.0 CB B:ASP225 4.2 35.0 1.0 CG B:GLU8 4.4 48.6 1.0 C B:ASP225 4.5 35.3 1.0 CA B:ASP225 4.5 29.4 1.0 CG B:ASN5 4.6 39.1 1.0 CB B:GLU8 4.6 41.4 1.0 CD B:ARG4 4.8 37.5 1.0 CB B:TYR229 4.9 30.4 1.0 CA B:GLU8 4.9 48.1 1.0 CD2 B:TYR229 4.9 40.4 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:60.6 occ:1.00 OD2 D:ASP201 2.1 44.1 1.0 NE2 C:HIS440 2.2 48.2 1.0 O C:HOH851 2.2 33.0 1.0 CE1 C:HIS440 2.4 41.0 1.0 CG D:ASP201 3.1 39.2 1.0 O C:HOH757 3.2 27.1 1.0 ND1 C:HIS314 3.2 32.3 1.0 OD1 D:ASP201 3.4 38.6 1.0 CD2 C:HIS440 3.5 40.8 1.0 ND1 C:HIS440 3.6 44.5 1.0 O C:HOH866 3.8 31.7 1.0 CE1 C:HIS314 3.8 32.4 1.0 O C:HOH632 3.8 27.3 1.0 O D:HOH664 3.9 29.8 1.0 O D:HOH876 4.0 27.6 1.0 CG C:HIS440 4.2 41.3 1.0 CG C:HIS314 4.4 26.6 1.0 CB D:ASP201 4.4 28.7 1.0 CE1 C:PHE441 4.4 29.9 1.0 CB C:HIS314 4.8 21.2 1.0 CG C:LYS311 4.9 25.5 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:52.2 occ:0.61 OE2 C:GLU100 2.1 32.8 1.0 O C:HOH816 2.6 40.7 1.0 CD C:GLU100 3.0 25.5 1.0 OE1 C:GLU100 3.3 22.9 1.0 O C:LYS24 3.9 27.2 1.0 CA C:LYS24 4.1 24.7 1.0 NZ C:LYS104 4.1 24.9 1.0 CB C:LYS24 4.3 22.8 1.0 CG C:GLU100 4.3 20.8 1.0 CG C:LYS24 4.3 23.5 1.0 C C:LYS24 4.4 26.5 1.0 O C:GLU100 4.8 21.9 1.0 CB C:LYS104 4.8 24.2 1.0 CD C:ARG103 4.8 28.7 1.0 CE C:LYS104 5.0 29.1 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of L-Amino Acid Oxidase From Bothrops Atrox within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn506 b:65.3 occ:1.00 OD2 C:ASP201 2.4 43.9 1.0 O D:HOH871 2.6 24.2 1.0 ND1 D:HIS314 2.7 38.0 1.0 NE2 D:HIS440 2.8 38.2 1.0 CE1 D:HIS440 2.8 40.0 1.0 O D:HOH663 3.0 32.7 1.0 CG C:ASP201 3.2 36.0 1.0 O D:HOH748 3.2 23.3 1.0 OD1 C:ASP201 3.5 32.6 1.0 CE1 D:HIS314 3.6 32.0 1.0 CG D:HIS314 3.8 30.8 1.0 ND1 D:HIS440 4.0 40.3 1.0 CB D:HIS314 4.0 24.2 1.0 CD2 D:HIS440 4.0 47.3 1.0 CE1 D:PHE441 4.3 27.5 1.0 CB C:ASP201 4.5 27.6 1.0 CG D:HIS440 4.7 41.3 1.0 NE2 D:HIS314 4.7 28.4 1.0 CD2 D:HIS314 4.9 24.6 1.0 CA D:LYS311 4.9 17.4 1.0

P.R.Feliciano, J.K.Rustiguel, R.O.Soares, S.V.Sampaio, M.Cristina Nonato. Crystal Structure and Molecular Dynamics Studies of L-Amino Acid Oxidase From Bothrops Atrox. Toxicon V. 128 50 2017.
ISSN: ISSN 1879-3150
PubMed: 28137621
DOI: 10.1016/J.TOXICON.2017.01.017