Copper in PDB 7eut: Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine

The structure of Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine, PDB code: 7eut was solved by X.D.Hou, X.Z.Liu, Z.B.Yuan, D.J.Yin, Y.J.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.62 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	42.958, 100.945, 154.506, 90, 93.72, 90
R / Rfree (%)	18.8 / 23.8

The binding sites of Copper atom in the Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine (pdb code 7eut). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine, PDB code: 7eut:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:28.2 occ:1.00 O2' A:OGA402 2.1 20.8 1.0 OD1 A:ASP172 2.1 20.6 1.0 NE2 A:HIS294 2.2 18.4 1.0 O2 A:OGA402 2.2 21.6 1.0 NE2 A:HIS170 2.2 17.8 1.0 C2 A:OGA402 2.8 21.3 1.0 C1 A:OGA402 2.8 24.0 1.0 CG A:ASP172 2.9 21.5 1.0 OD2 A:ASP172 3.0 23.7 1.0 CD2 A:HIS294 3.0 21.3 1.0 CE1 A:HIS170 3.1 16.0 1.0 CD2 A:HIS170 3.2 19.2 1.0 CE1 A:HIS294 3.3 17.6 1.0 O A:HOH502 3.9 24.7 1.0 O1 A:OGA402 4.1 21.4 1.0 N1 A:OGA402 4.1 20.2 1.0 CG A:HIS294 4.2 20.9 1.0 ND1 A:HIS170 4.2 18.4 1.0 CG A:HIS170 4.3 17.6 1.0 ND1 A:HIS294 4.3 18.7 1.0 CE A:MET280 4.3 20.3 1.0 CB A:ASP172 4.3 19.2 1.0 O A:HOH632 4.4 25.4 1.0 ND2 A:ASN203 4.6 24.2 1.0 OE1 A:GLU311 4.6 25.0 1.0 C4 A:OGA402 4.8 21.0 1.0 N A:ASP172 4.8 20.9 1.0 NH2 A:ARG140 4.8 20.9 1.0 CA A:ASP172 4.9 20.0 1.0

Copper binding site 2 out of 2 in the Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structures of 2-Oxoglutarate Dependent Dioxygenase (CTB9) in Complex with N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:28.7 occ:1.00 O2' B:OGA402 2.0 20.7 1.0 O1 B:OGA402 2.1 25.7 1.0 OD1 B:ASP172 2.1 27.9 1.0 NE2 B:HIS294 2.1 19.5 1.0 NE2 B:HIS170 2.2 23.3 1.0 O1 B:EDO403 2.5 22.6 1.0 C2 B:OGA402 2.7 22.8 1.0 C1 B:OGA402 2.7 23.7 1.0 CD2 B:HIS294 2.9 21.3 1.0 CE1 B:HIS170 2.9 21.3 1.0 CG B:ASP172 3.0 25.7 1.0 OD2 B:ASP172 3.2 27.3 1.0 CD2 B:HIS170 3.3 20.9 1.0 CE1 B:HIS294 3.3 21.1 1.0 C1 B:EDO403 3.6 32.2 1.0 O2 B:OGA402 3.9 23.6 1.0 C2 B:EDO403 4.0 24.6 1.0 N1 B:OGA402 4.1 18.9 1.0 ND1 B:HIS170 4.1 22.9 1.0 CG B:HIS294 4.1 21.7 1.0 ND1 B:HIS294 4.3 22.1 1.0 CG B:HIS170 4.3 22.3 1.0 O B:HOH501 4.3 27.4 1.0 CE B:MET280 4.4 25.6 1.0 CB B:ASP172 4.4 24.2 1.0 OE2 B:GLU311 4.5 24.3 1.0 ND2 B:ASN203 4.6 26.9 1.0 C4 B:OGA402 4.8 21.0 1.0 N B:ASP172 4.8 21.9 1.0 CA B:ASP172 4.9 25.2 1.0 O2 B:EDO403 5.0 35.4 1.0

X.Z.Liu, Z.B.Yuan, H.Su, X.D.Hou, Z.W.Deng, H.B.Xu, B.D.Guo, D.Yin, X.Sheng, Y.J.Rao. Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed By Fe(II)/Alpha-Kg-Dependent Oxygenase CTB9 Acs Catalysis V. 12 3689 2022.
ISSN: ESSN 2155-5435
DOI: DOI.ORG/10.1021/ACSCATAL.1C04627