Copper in PDB 1kdi: Reduced Form of Plastocyanin From Dryopteris Crassirhizoma

The structure of Reduced Form of Plastocyanin From Dryopteris Crassirhizoma, PDB code: 1kdi was solved by T.Inoue, M.Gotowda, K.Hamada, T.Kohzuma, F.Yoshizaki, Y.Sugimura, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	73.194, 73.194, 31.238, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 22.6

The binding sites of Copper atom in the Reduced Form of Plastocyanin From Dryopteris Crassirhizoma (pdb code 1kdi). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Reduced Form of Plastocyanin From Dryopteris Crassirhizoma, PDB code: 1kdi:

Copper binding site 1 out of 1 in the Reduced Form of Plastocyanin From Dryopteris Crassirhizoma


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Reduced Form of Plastocyanin From Dryopteris Crassirhizoma within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu103 b:19.5 occ:1.00 ND1 A:HIS37 1.9 13.8 1.0 ND1 A:HIS90 2.1 17.1 1.0 SG A:CYS87 2.2 15.7 1.0 SD A:MET95 2.9 15.4 1.0 CG A:HIS37 3.0 14.6 1.0 CE1 A:HIS37 3.0 14.9 1.0 CE1 A:HIS90 3.0 12.1 1.0 CG A:HIS90 3.1 14.4 1.0 CB A:CYS87 3.2 17.2 1.0 CB A:HIS37 3.3 13.6 1.0 CB A:HIS90 3.5 17.4 1.0 CE A:MET95 3.7 13.6 1.0 CA A:HIS37 3.8 12.8 1.0 NE2 A:HIS37 4.1 17.2 1.0 O A:GLY36 4.1 12.5 1.0 CD2 A:HIS37 4.1 14.0 1.0 NE2 A:HIS90 4.2 11.5 1.0 N A:HIS90 4.2 17.4 1.0 CG A:MET95 4.2 14.6 1.0 CD2 A:HIS90 4.3 9.8 1.0 CA A:HIS90 4.4 17.0 1.0 CA A:CYS87 4.7 16.1 1.0 CB A:PRO89 4.7 15.4 1.0 N A:ASN38 4.7 16.0 1.0 CB A:MET95 4.8 16.9 1.0 CD A:PRO89 4.8 13.7 1.0 C A:HIS37 4.8 10.5 1.0 N A:HIS37 4.8 13.4 1.0 CG A:PRO89 4.9 16.5 1.0 C A:GLY36 4.9 12.3 1.0

T.Kohzuma, T.Inoue, F.Yoshizaki, Y.Sasakawa, K.Onodera, S.Nagatomo, T.Kitagawa, S.Uzawa, Y.Isobe, Y.Sugimura, M.Gotowda, Y.Kai. The Structure and Unusual pH Dependence of Plastocyanin From the Fern Dryopteris Crassirhizoma. the Protonation of An Active Site Histidine Is Hindered By Pi-Pi Interactions. J.Biol.Chem. V. 274 11817 1999.
ISSN: ISSN 0021-9258
PubMed: 10206999
DOI: 10.1074/JBC.274.17.11817