Potassium in PDB 5bke: Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine

The structure of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 5bke was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	266.432, 55.494, 183.663, 90.00, 118.97, 90.00
R / Rfree (%)	18.8 / 23.3

The structure of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine also contains other interesting chemical elements:

Manganese

(Mn)

7 atoms

The binding sites of Potassium atom in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine (pdb code 5bke). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 5bke:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:38.6 occ:1.00 O A:HOH708 2.5 44.8 1.0 O A:HOH790 3.0 59.0 1.0 O A:HOH557 3.5 24.6 1.0 NE2 A:HIS215 3.6 21.9 1.0 N A:SER118 3.7 18.2 1.0 OD1 A:ASP117 3.8 17.4 1.0 O A:HOH677 3.8 32.2 1.0 CE2 A:PHE120 3.9 22.3 1.0 CA A:ASP117 4.0 17.9 1.0 CD2 A:HIS115 4.2 15.9 1.0 CE1 A:HIS215 4.2 21.8 1.0 C A:ASP117 4.4 17.6 1.0 CB A:ASP117 4.4 17.8 1.0 CG A:ASP117 4.5 18.2 1.0 NH1 A:ARG279 4.6 22.5 1.0 CA A:SER118 4.6 20.3 1.0 NE2 A:HIS115 4.6 16.0 1.0 CD2 A:HIS215 4.6 21.7 1.0 CZ A:PHE120 4.7 22.9 1.0 CD2 A:PHE120 4.8 22.6 1.0 MN A:MN401 4.8 16.0 1.0 O A:SER116 4.9 16.4 1.0 OD1 A:ASN111 4.9 24.1 1.0 O A:HOH742 4.9 48.5 1.0 N A:ASP117 5.0 17.2 1.0

Potassium binding site 2 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:K403 b:48.3 occ:1.00 O B:HOH688 2.6 29.9 1.0 O B:HOH743 3.0 46.6 1.0 NE2 B:HIS215 3.6 19.9 1.0 O B:HOH559 3.6 20.2 1.0 N B:SER118 3.7 18.3 1.0 O B:HOH675 3.7 28.3 1.0 CE2 B:PHE120 3.8 25.2 1.0 OD1 B:ASP117 3.9 18.4 1.0 CA B:ASP117 4.1 18.5 1.0 CE1 B:HIS215 4.2 20.5 1.0 CD2 B:HIS115 4.3 15.9 1.0 C B:ASP117 4.4 18.1 1.0 CB B:ASP117 4.5 18.4 1.0 CD2 B:PHE120 4.6 25.1 1.0 CA B:SER118 4.6 20.2 1.0 CG B:ASP117 4.6 19.1 1.0 NH1 B:ARG279 4.6 24.5 1.0 CD2 B:HIS215 4.7 19.4 1.0 CZ B:PHE120 4.7 26.0 1.0 NE2 B:HIS115 4.7 15.8 1.0 O B:SER116 4.9 18.2 1.0 MN B:MN401 4.9 16.8 1.0 OD1 B:ASN111 5.0 23.9 1.0

Potassium binding site 3 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:K403 b:62.6 occ:1.00 O D:HOH572 2.7 48.2 1.0 O D:HOH654 2.8 51.2 1.0 O D:HOH646 3.4 61.2 1.0 O D:HOH528 3.6 39.5 1.0 N D:SER118 3.8 30.8 1.0 OD1 D:ASP117 3.8 32.8 1.0 O D:HOH597 3.8 33.2 1.0 NE2 D:HIS215 3.9 26.8 1.0 CE2 D:PHE120 4.1 36.2 1.0 CA D:ASP117 4.1 30.2 1.0 NH1 D:ARG279 4.2 39.7 1.0 CE1 D:HIS215 4.4 27.5 1.0 CD2 D:HIS115 4.4 31.4 1.0 CG D:ASP117 4.5 31.8 1.0 C D:ASP117 4.5 30.4 1.0 CB D:ASP117 4.5 31.3 1.0 NE2 D:HIS115 4.7 32.2 1.0 CA D:SER118 4.7 32.5 1.0 CZ D:PHE120 4.7 37.2 1.0 MN D:MN401 4.7 29.9 1.0 NH2 D:ARG279 4.8 39.1 1.0 OD1 D:ASN111 4.9 37.1 1.0 OG D:SER118 4.9 33.6 1.0 CD2 D:HIS215 5.0 27.3 1.0 CZ D:ARG279 5.0 40.0 1.0

Potassium binding site 4 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ E:K403 b:69.5 occ:1.00 O E:HOH543 2.2 36.6 1.0 O E:HOH511 3.3 24.6 1.0 OD1 E:ASP117 3.7 31.3 1.0 N E:SER118 3.9 29.9 1.0 NH1 E:ARG279 4.0 44.0 1.0 O E:HOH596 4.2 34.1 1.0 CE2 E:PHE120 4.2 39.4 1.0 CA E:ASP117 4.3 28.1 1.0 CG E:ASP117 4.5 30.4 1.0 NE2 E:HIS215 4.5 30.5 1.0 NH2 E:ARG279 4.5 45.2 1.0 CB E:ASP117 4.6 28.1 1.0 C E:ASP117 4.7 29.1 1.0 CD2 E:HIS115 4.7 26.4 1.0 OG E:SER118 4.7 37.3 1.0 CZ E:PHE120 4.7 40.2 1.0 MN E:MN401 4.8 27.2 1.0 CZ E:ARG279 4.8 43.8 1.0 CA E:SER118 4.9 32.9 1.0 NE2 E:HIS115 4.9 26.7 1.0 OD1 E:ASN111 4.9 35.0 1.0

Potassium binding site 5 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ F:K403 b:45.8 occ:1.00 O F:HOH718 2.6 39.7 1.0 NE2 F:HIS215 3.4 20.9 1.0 O F:HOH513 3.5 17.3 1.0 N F:SER118 3.6 17.2 1.0 O F:HOH713 3.7 40.2 1.0 CA F:ASP117 4.0 17.3 1.0 OD1 F:ASP117 4.0 16.3 1.0 CE2 F:PHE120 4.0 21.0 1.0 CE1 F:HIS215 4.1 20.5 1.0 CD2 F:HIS115 4.1 14.8 1.0 C F:ASP117 4.3 17.1 1.0 CD2 F:HIS215 4.4 20.7 1.0 CB F:ASP117 4.5 17.5 1.0 CA F:SER118 4.5 19.0 1.0 NE2 F:HIS115 4.6 14.8 1.0 CG F:ASP117 4.6 17.9 1.0 NH1 F:ARG279 4.7 43.6 1.0 O F:SER116 4.8 16.5 1.0 CZ F:PHE120 4.8 22.2 1.0 MN F:MN401 4.8 17.3 1.0 CD2 F:PHE120 4.8 20.9 1.0 O F:HOH656 4.9 42.3 1.0 CE1 F:PHE107 5.0 43.3 1.0 N F:ASP117 5.0 16.9 1.0

Potassium binding site 6 out of 6 in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ G:K403 b:48.7 occ:1.00 O G:HOH681 2.6 35.2 1.0 O G:HOH551 3.3 18.0 1.0 O G:HOH695 3.5 34.1 1.0 N G:SER118 3.7 18.7 1.0 NE2 G:HIS215 3.7 21.6 1.0 OD1 G:ASP117 3.9 17.1 1.0 CE2 G:PHE120 3.9 29.9 1.0 CA G:ASP117 4.1 18.7 1.0 CE1 G:HIS215 4.3 21.1 1.0 CD2 G:HIS115 4.4 16.6 1.0 NH1 G:ARG279 4.4 31.7 1.0 C G:ASP117 4.5 18.3 1.0 CE1 G:PHE107 4.5 38.8 1.0 CG G:ASP117 4.5 18.4 1.0 CB G:ASP117 4.5 18.1 1.0 CZ G:PHE120 4.6 29.4 1.0 CA G:SER118 4.7 20.6 1.0 NE2 G:HIS115 4.8 17.1 1.0 O G:HOH508 4.8 51.6 1.0 CD2 G:HIS215 4.8 20.6 1.0 MN G:MN401 4.9 17.5 1.0 CD2 G:PHE120 4.9 29.0 1.0

J.R.Chekan, C.Ongpipattanakul, T.R.Wright, B.Zhang, J.M.Bollinger Jr., L.J.Rajakovich, C.Krebs, R.M.Cicchillo, S.K.Nair. Molecular Basis For Enantioselective Herbicide Degradation Imparted By Aryloxyalkanoate Dioxygenases in Transgenic Plants. Proc.Natl.Acad.Sci.Usa V. 116 13299 2019.
ISSN: ESSN 1091-6490
PubMed: 31209034
DOI: 10.1073/PNAS.1900711116