Copper in PDB 4ef3: Multicopper Oxidase Cueo (Citrate Buffer)

The structure of Multicopper Oxidase Cueo (Citrate Buffer), PDB code: 4ef3 was solved by H.Komori, K.Kataoka, T.Sakurai, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.60 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.282, 91.239, 59.589, 90.00, 112.87, 90.00
R / Rfree (%)	15.2 / 18.4

The binding sites of Copper atom in the Multicopper Oxidase Cueo (Citrate Buffer) (pdb code 4ef3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Multicopper Oxidase Cueo (Citrate Buffer), PDB code: 4ef3:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Multicopper Oxidase Cueo (Citrate Buffer)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Multicopper Oxidase Cueo (Citrate Buffer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1001 b:12.2 occ:1.00 ND1 A:HIS443 2.1 11.7 1.0 ND1 A:HIS505 2.1 9.8 1.0 SG A:CYS500 2.2 10.6 1.0 CE1 A:HIS443 3.1 11.7 1.0 SD A:MET510 3.1 12.7 1.0 CG A:HIS505 3.1 10.8 1.0 CE1 A:HIS505 3.1 10.7 1.0 CG A:HIS443 3.1 12.2 1.0 CB A:CYS500 3.2 9.6 1.0 CB A:HIS505 3.4 10.3 1.0 CB A:HIS443 3.5 12.7 1.0 CA A:HIS443 3.8 12.1 1.0 O A:LEU442 3.8 13.8 1.0 CE A:MET510 3.9 12.0 1.0 CB A:LEU502 4.2 8.1 1.0 NE2 A:HIS443 4.2 13.6 1.0 NE2 A:HIS505 4.2 11.1 1.0 CD2 A:HIS505 4.2 10.4 1.0 CD2 A:HIS443 4.3 13.1 1.0 C A:LEU442 4.5 13.3 1.0 N A:HIS443 4.5 12.7 1.0 CG A:MET510 4.6 11.6 1.0 CA A:CYS500 4.6 9.1 1.0 CD1 A:LEU502 4.8 9.5 1.0 O A:LEU502 4.9 8.6 1.0 CA A:HIS505 4.9 10.7 1.0 C A:HIS443 4.9 11.5 1.0 CB A:MET510 5.0 11.1 1.0

Copper binding site 2 out of 4 in the Multicopper Oxidase Cueo (Citrate Buffer)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Multicopper Oxidase Cueo (Citrate Buffer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1002 b:12.5 occ:1.00 O A:OH1005 1.8 12.2 1.0 ND1 A:HIS103 2.1 7.9 1.0 NE2 A:HIS501 2.2 8.8 1.0 O A:O1006 2.2 28.5 1.0 NE2 A:HIS141 2.2 11.5 1.0 CE1 A:HIS103 2.9 7.8 1.0 CE1 A:HIS141 3.0 10.3 1.0 CD2 A:HIS501 3.0 8.6 1.0 CG A:HIS103 3.2 8.0 1.0 CE1 A:HIS501 3.3 9.5 1.0 CD2 A:HIS141 3.4 10.5 1.0 CU A:CU1003 3.5 13.3 1.0 CB A:HIS103 3.6 8.8 1.0 CU A:CU1004 3.8 15.0 1.0 CD2 A:HIS446 3.9 9.0 1.0 O A:HOH1101 3.9 15.7 1.0 CD2 A:HIS101 4.0 11.8 1.0 NE2 A:HIS446 4.1 10.3 1.0 NE2 A:HIS103 4.1 6.6 1.0 CD2 A:HIS103 4.2 7.7 1.0 ND1 A:HIS141 4.2 10.5 1.0 CG A:HIS501 4.2 7.6 1.0 CZ2 A:TRP139 4.3 6.7 1.0 ND1 A:HIS501 4.4 7.8 1.0 NE2 A:HIS101 4.4 11.4 1.0 CG A:HIS141 4.4 9.2 1.0 CE1 A:HIS499 4.5 10.5 1.0 NE2 A:HIS499 4.5 9.9 1.0 CE2 A:TRP139 4.7 6.9 1.0 NE1 A:TRP139 4.7 7.3 1.0 CA A:HIS103 4.8 9.5 1.0 NE2 A:HIS143 4.8 12.9 1.0 CG A:HIS446 4.8 9.0 1.0 CE1 A:HIS446 5.0 9.2 1.0

Copper binding site 3 out of 4 in the Multicopper Oxidase Cueo (Citrate Buffer)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Multicopper Oxidase Cueo (Citrate Buffer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1003 b:13.3 occ:1.00 O A:OH1005 2.0 12.2 1.0 NE2 A:HIS448 2.1 9.6 1.0 NE2 A:HIS499 2.2 9.9 1.0 NE2 A:HIS143 2.2 12.9 1.0 O A:O1006 2.2 28.5 1.0 CE1 A:HIS448 3.0 9.7 1.0 CE1 A:HIS499 3.1 10.5 1.0 CD2 A:HIS143 3.1 12.5 1.0 CD2 A:HIS448 3.1 8.8 1.0 CD2 A:HIS499 3.2 10.6 1.0 CE1 A:HIS143 3.2 12.4 1.0 CU A:CU1002 3.5 12.5 1.0 CU A:CU1004 3.6 15.0 1.0 CD2 A:HIS446 3.6 9.0 1.0 O A:HOH1101 3.8 15.7 1.0 CD2 A:HIS101 3.8 11.8 1.0 NE2 A:HIS101 3.9 11.4 1.0 NE2 A:HIS446 4.0 10.3 1.0 ND1 A:HIS448 4.1 9.7 1.0 ND1 A:HIS499 4.2 9.1 1.0 CG A:HIS448 4.2 10.9 1.0 CG A:HIS143 4.3 12.4 1.0 CG A:HIS499 4.3 9.2 1.0 ND1 A:HIS143 4.3 12.4 1.0 CE1 A:HIS141 4.4 10.3 1.0 NE2 A:HIS141 4.6 11.5 1.0 CG A:HIS101 4.6 10.7 1.0 CE1 A:HIS101 4.7 12.2 1.0 CD2 A:HIS501 4.7 8.6 1.0 NE2 A:HIS501 4.7 8.8 1.0 CG A:HIS446 4.8 9.0 1.0 CB A:MET497 4.9 10.6 1.0 ND1 A:HIS103 4.9 7.9 1.0 OE2 A:GLU506 5.0 16.9 1.0

Copper binding site 4 out of 4 in the Multicopper Oxidase Cueo (Citrate Buffer)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Multicopper Oxidase Cueo (Citrate Buffer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1004 b:15.0 occ:1.00 O A:O1006 1.9 28.5 1.0 NE2 A:HIS446 2.0 10.3 1.0 NE2 A:HIS101 2.1 11.4 1.0 O A:HOH1102 2.3 6.9 1.0 CD2 A:HIS446 3.0 9.0 1.0 CE1 A:HIS101 3.0 12.2 1.0 CE1 A:HIS446 3.0 9.2 1.0 CD2 A:HIS448 3.1 8.8 1.0 CD2 A:HIS101 3.1 11.8 1.0 NE2 A:HIS448 3.3 9.6 1.0 CG A:HIS103 3.5 8.0 1.0 CA A:HIS103 3.5 9.5 1.0 CU A:CU1003 3.6 13.3 1.0 ND1 A:HIS103 3.6 7.9 1.0 CG A:HIS448 3.7 10.9 1.0 CB A:HIS103 3.7 8.8 1.0 CU A:CU1002 3.8 12.5 1.0 CE1 A:HIS448 3.9 9.7 1.0 O A:OH1005 4.0 12.2 1.0 CD2 A:HIS103 4.0 7.7 1.0 ND1 A:HIS446 4.1 8.0 1.0 ND1 A:HIS101 4.1 12.2 1.0 N A:GLY104 4.1 9.5 1.0 CG A:HIS446 4.1 9.0 1.0 CE1 A:HIS103 4.1 7.8 1.0 ND1 A:HIS448 4.1 9.7 1.0 CG A:HIS101 4.2 10.7 1.0 C A:HIS103 4.3 9.5 1.0 CA A:HIS448 4.4 11.2 1.0 NE2 A:HIS103 4.4 6.6 1.0 O A:HOH1104 4.5 11.8 1.0 O A:HOH1103 4.5 10.3 1.0 CB A:HIS448 4.5 11.5 1.0 N A:HIS103 4.5 9.8 1.0 O A:TRP102 4.7 10.9 1.0 N A:HIS448 4.8 10.8 1.0 C A:TRP102 5.0 10.2 1.0

H.Komori, K.Kataoka, S.Tanaka, N.Matsuda, Y.Higuchi, T.Sakurai. Exogenous Acetate Ion Reaches the Type II Copper Centre in Cueo Through the Water-Excretion Channel and Potentially Affects the Enzymatic Activity. Acta Crystallogr.,Sect.F V. 72 558 2016.
ISSN: ISSN 1744-3091
PubMed: 27380373
DOI: 10.1107/S2053230X16009237