Copper in PDB 4ner: Multicopper Oxidase Cueo (DATA1)

The structure of Multicopper Oxidase Cueo (DATA1), PDB code: 4ner 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)	10.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.398, 90.721, 53.370, 90.00, 102.72, 90.00
R / Rfree (%)	16.8 / n/a

The binding sites of Copper atom in the Multicopper Oxidase Cueo (DATA1) (pdb code 4ner). 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 (DATA1), PDB code: 4ner:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Multicopper Oxidase Cueo (DATA1)


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 (DATA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1001 b:11.5 occ:1.00 ND1 A:HIS505 2.0 6.9 1.0 ND1 A:HIS443 2.1 10.3 1.0 SG A:CYS500 2.1 10.5 1.0 CE1 A:HIS505 2.9 10.5 1.0 CG A:HIS505 3.0 5.7 1.0 CE1 A:HIS443 3.0 10.9 1.0 CG A:HIS443 3.1 9.2 1.0 SD A:MET510 3.1 12.1 1.0 CB A:CYS500 3.2 7.9 1.0 CB A:HIS505 3.3 7.4 1.0 CB A:HIS443 3.4 9.6 1.0 O A:LEU442 3.5 10.4 1.0 CA A:HIS443 3.7 8.9 1.0 CE A:MET510 3.9 12.4 1.0 NE2 A:HIS505 4.1 9.1 1.0 CD2 A:HIS505 4.1 7.5 1.0 NE2 A:HIS443 4.1 12.7 1.0 CB A:LEU502 4.2 5.3 1.0 CD2 A:HIS443 4.2 11.8 1.0 C A:LEU442 4.3 10.3 1.0 N A:HIS443 4.4 7.9 1.0 CA A:CYS500 4.6 9.0 1.0 CG A:MET510 4.6 10.3 1.0 CD1 A:LEU502 4.8 5.8 1.0 CA A:HIS505 4.8 9.5 1.0 C A:HIS443 4.9 9.0 1.0 O A:LEU502 4.9 9.7 1.0 CB A:MET510 5.0 10.2 1.0 CG A:LEU502 5.0 5.7 1.0

Copper binding site 2 out of 4 in the Multicopper Oxidase Cueo (DATA1)


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 (DATA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1002 b:10.7 occ:0.90 O A:OH1005 2.0 6.5 0.9 NE2 A:HIS501 2.1 8.4 1.0 ND1 A:HIS103 2.1 10.6 1.0 NE2 A:HIS141 2.2 10.5 1.0 O A:O1006 2.2 15.8 0.9 CE1 A:HIS103 2.8 8.6 1.0 CD2 A:HIS501 3.0 9.1 1.0 CE1 A:HIS141 3.0 9.9 1.0 CE1 A:HIS501 3.2 9.4 1.0 CG A:HIS103 3.3 8.5 1.0 CD2 A:HIS141 3.3 9.4 1.0 CU A:CU1003 3.4 10.8 0.9 CB A:HIS103 3.7 8.2 1.0 CD2 A:HIS446 3.8 12.9 1.0 CU A:CU1004 3.8 9.4 0.8 NE2 A:HIS446 4.0 14.5 1.0 NE2 A:HIS103 4.0 9.6 1.0 O A:HOH2001 4.0 15.2 1.0 CD2 A:HIS101 4.1 10.2 1.0 CG A:HIS501 4.2 5.2 1.0 ND1 A:HIS141 4.2 10.9 1.0 CD2 A:HIS103 4.2 7.1 1.0 ND1 A:HIS501 4.2 8.0 1.0 CG A:HIS141 4.4 10.0 1.0 CZ2 A:TRP139 4.4 5.3 1.0 NE2 A:HIS101 4.4 11.1 1.0 CE1 A:HIS499 4.5 13.2 1.0 NE2 A:HIS499 4.5 11.8 1.0 NE2 A:HIS143 4.7 9.3 1.0 CG A:HIS446 4.7 8.6 1.0 CE2 A:TRP139 4.8 8.3 1.0 CA A:HIS103 4.8 6.2 1.0 NE1 A:TRP139 4.8 7.4 1.0 NE2 A:HIS448 4.9 7.7 1.0 CE1 A:HIS446 4.9 11.3 1.0

Copper binding site 3 out of 4 in the Multicopper Oxidase Cueo (DATA1)


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 (DATA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1003 b:10.8 occ:0.90 O A:OH1005 1.9 6.5 0.9 NE2 A:HIS448 2.0 7.7 1.0 NE2 A:HIS499 2.1 11.8 1.0 NE2 A:HIS143 2.1 9.3 1.0 O A:O1006 2.2 15.8 0.9 CE1 A:HIS448 2.9 12.4 1.0 CE1 A:HIS499 3.0 13.2 1.0 CE1 A:HIS143 3.1 7.7 1.0 CD2 A:HIS448 3.1 8.8 1.0 CD2 A:HIS143 3.1 9.8 1.0 CD2 A:HIS499 3.2 12.3 1.0 CU A:CU1002 3.4 10.7 0.9 CD2 A:HIS446 3.5 12.9 1.0 CU A:CU1004 3.7 9.4 0.8 O A:HOH2001 3.8 15.2 1.0 CD2 A:HIS101 4.0 10.2 1.0 NE2 A:HIS446 4.0 14.5 1.0 NE2 A:HIS101 4.0 11.1 1.0 ND1 A:HIS448 4.1 12.5 1.0 ND1 A:HIS499 4.1 9.5 1.0 CG A:HIS448 4.2 11.7 1.0 ND1 A:HIS143 4.2 9.5 1.0 CE1 A:HIS141 4.2 9.9 1.0 CG A:HIS143 4.3 10.5 1.0 CG A:HIS499 4.3 13.9 1.0 NE2 A:HIS141 4.4 10.5 1.0 NE2 A:HIS501 4.5 8.4 1.0 CD2 A:HIS501 4.6 9.1 1.0 CG A:HIS446 4.7 8.6 1.0 CG A:HIS101 4.8 8.3 1.0 CE1 A:HIS101 4.8 12.6 1.0 OE2 A:GLU506 4.9 21.8 1.0 CB A:MET497 5.0 9.9 1.0 ND1 A:HIS103 5.0 10.6 1.0

Copper binding site 4 out of 4 in the Multicopper Oxidase Cueo (DATA1)


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 (DATA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1004 b:9.4 occ:0.75 O A:O1006 1.9 15.8 0.9 NE2 A:HIS101 2.0 11.1 1.0 NE2 A:HIS446 2.0 14.5 1.0 O A:HOH2002 2.2 7.2 0.8 CE1 A:HIS101 2.9 12.6 1.0 CE1 A:HIS446 3.0 11.3 1.0 CD2 A:HIS446 3.0 12.9 1.0 CD2 A:HIS101 3.0 10.2 1.0 CD2 A:HIS448 3.2 8.8 1.0 NE2 A:HIS448 3.3 7.7 1.0 CA A:HIS103 3.5 6.2 1.0 CG A:HIS103 3.6 8.5 1.0 CU A:CU1003 3.7 10.8 0.9 ND1 A:HIS103 3.7 10.6 1.0 CB A:HIS103 3.7 8.2 1.0 CG A:HIS448 3.7 11.7 1.0 CU A:CU1002 3.8 10.7 0.9 CE1 A:HIS448 3.8 12.4 1.0 ND1 A:HIS101 4.0 11.9 1.0 CD2 A:HIS103 4.1 7.1 1.0 ND1 A:HIS448 4.1 12.5 1.0 ND1 A:HIS446 4.1 11.7 1.0 CG A:HIS446 4.1 8.6 1.0 CG A:HIS101 4.1 8.3 1.0 N A:GLY104 4.1 10.2 1.0 CE1 A:HIS103 4.2 8.6 1.0 O A:OH1005 4.3 6.5 0.9 C A:HIS103 4.4 11.9 1.0 NE2 A:HIS103 4.4 9.6 1.0 N A:HIS103 4.4 6.2 1.0 CA A:HIS448 4.4 7.9 1.0 O A:HOH2004 4.6 18.6 1.0 CB A:HIS448 4.6 10.8 1.0 O A:TRP102 4.6 10.4 1.0 O A:HOH2003 4.6 11.0 0.4 C A:TRP102 4.8 13.1 1.0 N A:HIS448 5.0 9.3 1.0 NE2 A:HIS141 5.0 10.5 1.0

H.Komori, R.Sugiyama, K.Kataoka, K.Miyazaki, Y.Higuchi, T.Sakurai. New Insights Into the Catalytic Active-Site Structure of Multicopper Oxidases Acta Crystallogr.,Sect.D V. 70 772 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713033051