Manganese 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:

Potassium

(K)

6 atoms

The binding sites of Manganese 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 Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Aad-2 in Complex with Mn(II) and N-Oxalylglycine, PDB code: 5bke:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 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 Manganese with other atoms in the Mn 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:Mn401 b:16.0 occ:1.00 NE2 A:HIS115 2.1 16.0 1.0 O1 A:OGA402 2.1 23.6 1.0 NE2 A:HIS264 2.1 20.8 1.0 O A:HOH557 2.2 24.6 1.0 OD1 A:ASP117 2.2 17.4 1.0 O2' A:OGA402 2.2 23.9 1.0 C1 A:OGA402 2.8 24.7 1.0 C2 A:OGA402 2.9 24.5 1.0 CE1 A:HIS115 3.0 16.0 1.0 CD2 A:HIS264 3.1 20.3 1.0 CD2 A:HIS115 3.1 15.9 1.0 CE1 A:HIS264 3.1 20.3 1.0 CG A:ASP117 3.1 18.2 1.0 OD2 A:ASP117 3.4 17.9 1.0 NH1 A:ARG279 3.9 22.5 1.0 O2 A:OGA402 4.0 25.7 1.0 ND1 A:HIS115 4.1 15.8 1.0 OD1 A:ASN111 4.1 24.1 1.0 N1 A:OGA402 4.2 24.7 1.0 CG A:HIS115 4.2 16.6 1.0 ND1 A:HIS264 4.2 20.0 1.0 CG A:HIS264 4.2 20.5 1.0 CZ2 A:TRP257 4.3 17.0 1.0 CG A:ASN111 4.5 25.1 1.0 CB A:ASP117 4.5 17.8 1.0 K A:K403 4.8 38.6 1.0 ND2 A:ASN111 4.9 25.1 1.0 CA A:ASP117 4.9 17.9 1.0

Manganese binding site 2 out of 7 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 Manganese with other atoms in the Mn 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:Mn401 b:16.8 occ:1.00 O B:HOH559 2.0 20.2 1.0 O1 B:OGA402 2.0 23.3 1.0 OD1 B:ASP117 2.1 18.4 1.0 NE2 B:HIS264 2.1 14.8 1.0 NE2 B:HIS115 2.1 15.8 1.0 O2' B:OGA402 2.2 25.2 1.0 C1 B:OGA402 2.8 24.4 1.0 C2 B:OGA402 2.9 25.7 1.0 CE1 B:HIS264 2.9 15.1 1.0 CG B:ASP117 3.0 19.1 1.0 CD2 B:HIS115 3.1 15.9 1.0 CE1 B:HIS115 3.1 15.8 1.0 CD2 B:HIS264 3.2 15.1 1.0 OD2 B:ASP117 3.3 18.6 1.0 NH1 B:ARG279 3.8 24.5 1.0 O2 B:OGA402 4.0 24.5 1.0 ND1 B:HIS264 4.1 14.9 1.0 N1 B:OGA402 4.2 26.3 1.0 CG B:HIS264 4.2 15.3 1.0 ND1 B:HIS115 4.2 15.8 1.0 OD1 B:ASN111 4.2 23.9 1.0 CG B:HIS115 4.2 16.0 1.0 CZ2 B:TRP257 4.4 14.4 1.0 CB B:ASP117 4.4 18.4 1.0 CG B:ASN111 4.5 23.8 1.0 ND2 B:ASN111 4.8 23.5 1.0 CA B:ASP117 4.9 18.5 1.0 K B:K403 4.9 48.3 1.0

Manganese binding site 3 out of 7 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 Manganese with other atoms in the Mn 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 C:Mn401 b:21.2 occ:1.00 O1 C:OGA402 2.0 29.2 1.0 NE2 C:HIS115 2.1 17.1 1.0 OD1 C:ASP117 2.1 20.3 1.0 O2' C:OGA402 2.2 28.8 1.0 NE2 C:HIS264 2.2 22.6 1.0 C1 C:OGA402 2.8 29.9 1.0 C2 C:OGA402 2.8 28.9 1.0 CE1 C:HIS115 3.0 17.8 1.0 CD2 C:HIS115 3.1 17.5 1.0 CG C:ASP117 3.1 21.0 1.0 CE1 C:HIS264 3.1 22.6 1.0 CD2 C:HIS264 3.2 22.1 1.0 OD2 C:ASP117 3.4 21.1 1.0 NH1 C:ARG279 3.8 23.9 1.0 O2 C:OGA402 4.0 31.4 1.0 ND1 C:HIS115 4.1 17.9 1.0 N1 C:OGA402 4.1 29.8 1.0 CG C:HIS115 4.2 17.6 1.0 ND1 C:HIS264 4.3 22.4 1.0 OD1 C:ASN111 4.3 29.2 1.0 CG C:HIS264 4.3 22.8 1.0 CZ2 C:TRP257 4.3 20.2 1.0 CB C:ASP117 4.5 21.0 1.0 CG C:ASN111 4.7 28.7 1.0 CA C:ASP117 4.8 21.6 1.0 ND2 C:ASN111 4.8 28.6 1.0 O C:HOH631 4.9 29.4 1.0 C4 C:OGA402 5.0 31.2 1.0

Manganese binding site 4 out of 7 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 Manganese with other atoms in the Mn 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 D:Mn401 b:29.9 occ:1.00 O D:HOH528 1.8 39.5 1.0 OD1 D:ASP117 2.1 32.8 1.0 NE2 D:HIS264 2.2 28.0 1.0 NE2 D:HIS115 2.2 32.2 1.0 O2' D:OGA402 2.2 36.7 1.0 O2 D:OGA402 2.3 39.5 1.0 C2 D:OGA402 2.9 39.2 1.0 C1 D:OGA402 2.9 39.2 1.0 CE1 D:HIS264 3.1 29.4 1.0 CG D:ASP117 3.1 31.8 1.0 CE1 D:HIS115 3.1 32.2 1.0 CD2 D:HIS264 3.2 28.2 1.0 CD2 D:HIS115 3.2 31.4 1.0 OD2 D:ASP117 3.4 32.3 1.0 NH1 D:ARG279 3.8 39.7 1.0 OD1 D:ASN111 4.0 37.1 1.0 O1 D:OGA402 4.1 39.6 1.0 N1 D:OGA402 4.1 38.4 1.0 ND1 D:HIS264 4.2 29.1 1.0 CG D:HIS264 4.3 28.2 1.0 ND1 D:HIS115 4.3 31.6 1.0 CZ2 D:TRP257 4.3 25.9 1.0 CG D:HIS115 4.3 31.2 1.0 CG D:ASN111 4.5 35.1 1.0 CB D:ASP117 4.5 31.3 1.0 K D:K403 4.7 62.6 1.0 O D:HOH597 4.8 33.2 1.0 ND2 D:ASN111 4.8 34.9 1.0 CA D:ASP117 4.9 30.2 1.0

Manganese binding site 5 out of 7 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 Manganese with other atoms in the Mn 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 E:Mn401 b:27.2 occ:1.00 O2 E:OGA402 1.9 35.4 1.0 NE2 E:HIS264 2.1 28.2 1.0 NE2 E:HIS115 2.1 26.7 1.0 O E:HOH511 2.2 24.6 1.0 OD1 E:ASP117 2.2 31.3 1.0 O2' E:OGA402 2.4 37.9 1.0 C1 E:OGA402 2.8 38.8 1.0 CE1 E:HIS264 2.9 27.8 1.0 C2 E:OGA402 2.9 38.5 1.0 CE1 E:HIS115 3.0 27.9 1.0 CD2 E:HIS115 3.1 26.4 1.0 CG E:ASP117 3.2 30.4 1.0 CD2 E:HIS264 3.2 27.2 1.0 OD2 E:ASP117 3.4 29.3 1.0 NH1 E:ARG279 3.9 44.0 1.0 O1 E:OGA402 4.0 40.8 1.0 ND1 E:HIS264 4.0 27.8 1.0 ND1 E:HIS115 4.1 26.9 1.0 CG E:HIS115 4.2 26.7 1.0 OD1 E:ASN111 4.2 35.0 1.0 CG E:HIS264 4.2 27.1 1.0 N1 E:OGA402 4.2 39.7 1.0 CZ2 E:TRP257 4.5 30.4 1.0 CB E:ASP117 4.5 28.1 1.0 CG E:ASN111 4.6 36.7 1.0 K E:K403 4.8 69.5 1.0 CA E:ASP117 4.8 28.1 1.0 ND2 E:ASN111 5.0 36.2 1.0

Manganese binding site 6 out of 7 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 Manganese with other atoms in the Mn 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 F:Mn401 b:17.3 occ:1.00 OD1 F:ASP117 2.0 16.3 1.0 O F:HOH513 2.1 17.3 1.0 O2' F:OGA402 2.1 33.9 1.0 NE2 F:HIS115 2.2 14.8 1.0 NE2 F:HIS264 2.2 12.9 1.0 O1 F:OGA402 2.3 32.7 1.0 C2 F:OGA402 2.8 38.8 1.0 C1 F:OGA402 3.0 36.4 1.0 CE1 F:HIS264 3.0 13.1 1.0 CG F:ASP117 3.1 17.9 1.0 CD2 F:HIS115 3.1 14.8 1.0 CE1 F:HIS115 3.1 14.3 1.0 CD2 F:HIS264 3.3 13.0 1.0 OD2 F:ASP117 3.4 18.8 1.0 OD1 F:ASN111 3.8 23.8 1.0 NH1 F:ARG279 4.0 43.6 1.0 N1 F:OGA402 4.1 42.3 1.0 O2 F:OGA402 4.2 36.3 1.0 ND1 F:HIS264 4.2 13.6 1.0 ND1 F:HIS115 4.2 14.8 1.0 CG F:HIS115 4.3 15.0 1.0 CG F:HIS264 4.3 13.5 1.0 CG F:ASN111 4.4 22.9 1.0 CB F:ASP117 4.5 17.5 1.0 CZ2 F:TRP257 4.5 17.3 1.0 ND2 F:ASN111 4.8 23.1 1.0 K F:K403 4.8 45.8 1.0 CA F:ASP117 4.8 17.3 1.0

Manganese binding site 7 out of 7 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 Manganese with other atoms in the Mn binding site number 7 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:Mn401 b:17.5 occ:1.00 O2 G:OGA402 2.1 29.1 1.0 OD1 G:ASP117 2.1 17.1 1.0 NE2 G:HIS115 2.2 17.1 1.0 NE2 G:HIS264 2.2 17.4 1.0 O2' G:OGA402 2.2 33.9 1.0 O G:HOH551 2.2 18.0 1.0 C1 G:OGA402 2.8 31.7 1.0 C2 G:OGA402 2.9 33.1 1.0 CG G:ASP117 3.1 18.4 1.0 CE1 G:HIS264 3.1 17.8 1.0 CD2 G:HIS115 3.1 16.6 1.0 CE1 G:HIS115 3.1 17.2 1.0 CD2 G:HIS264 3.2 17.3 1.0 OD2 G:ASP117 3.3 18.5 1.0 OD1 G:ASN111 3.8 22.3 1.0 NH1 G:ARG279 3.9 31.7 1.0 O1 G:OGA402 4.0 32.0 1.0 N1 G:OGA402 4.2 33.3 1.0 ND1 G:HIS115 4.2 16.6 1.0 ND1 G:HIS264 4.2 17.4 1.0 CG G:HIS115 4.3 17.0 1.0 CG G:HIS264 4.3 17.1 1.0 CG G:ASN111 4.4 21.4 1.0 CZ2 G:TRP257 4.4 18.1 1.0 CB G:ASP117 4.5 18.1 1.0 ND2 G:ASN111 4.8 20.6 1.0 CA G:ASP117 4.8 18.7 1.0 K G:K403 4.9 48.7 1.0 N G:ASP117 5.0 18.8 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