Copper in PDB 8sy3: Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase

The structure of Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase, PDB code: 8sy3 was solved by L.S.Mydy, R.D.Kersten, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.74 / 3.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.407, 105.407, 223.838, 90, 90, 120
R / Rfree (%)	22.8 / 26.9

The binding sites of Copper atom in the Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase (pdb code 8sy3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase, PDB code: 8sy3:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:144.6 occ:0.50 NE2 A:HIS204 2.0 114.2 1.0 NE2 A:HIS230 2.1 115.9 1.0 CE1 A:HIS204 2.5 109.0 1.0 CE1 A:HIS230 3.0 116.3 1.0 O A:GLY82 3.1 222.3 1.0 CD2 A:HIS230 3.1 100.0 1.0 CD2 A:HIS204 3.3 107.0 1.0 ND1 A:HIS204 3.8 112.5 1.0 O A:VAL83 3.9 130.8 1.0 C A:GLY82 4.1 215.3 1.0 CG A:HIS204 4.1 103.5 1.0 ND1 A:HIS230 4.2 100.5 1.0 CB A:TYR81 4.2 208.1 1.0 CG A:HIS230 4.2 93.6 1.0 N A:GLY82 4.3 248.1 1.0 CG1 A:VAL202 4.5 97.0 1.0 C A:VAL83 4.5 160.5 1.0 CD2 A:TYR81 4.6 175.6 1.0 CG A:TYR81 4.6 190.9 1.0 CA A:GLY82 4.7 221.7 1.0

Copper binding site 2 out of 2 in the Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper Complex of Peanut Usp-Type Burp Domain Peptide Cyclase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:136.6 occ:0.50 O B:HOH401 2.0 109.5 1.0 NE2 B:HIS204 2.1 119.5 1.0 NE2 B:HIS230 2.1 114.7 1.0 CE1 B:HIS204 2.8 120.8 1.0 CE1 B:HIS230 3.1 112.2 1.0 CD2 B:HIS230 3.1 106.7 1.0 CD2 B:HIS204 3.3 122.9 1.0 ND1 B:HIS204 3.9 111.7 1.0 CG B:HIS204 4.2 117.3 1.0 ND1 B:HIS230 4.2 102.6 1.0 CG B:HIS230 4.2 97.5 1.0 CG1 B:VAL202 4.6 90.8 1.0

L.S.Mydy, J.Hungerford, D.N.Chigumba, J.R.Konwerski, S.C.Jantzi, D.Wang, J.L.Smith, R.D.Kersten. An Intramolecular Macrocyclase in Plant Ribosomal Peptide Biosynthesis Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-024-01552-1