Copper in PDB 4e9y: Multicopper Oxidase Mglac (DATA4)

The structure of Multicopper Oxidase Mglac (DATA4), PDB code: 4e9y was solved by H.Komori, K.Miyazaki, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.741, 101.174, 124.002, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / n/a

The structure of Multicopper Oxidase Mglac (DATA4) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Multicopper Oxidase Mglac (DATA4) (pdb code 4e9y). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Multicopper Oxidase Mglac (DATA4), PDB code: 4e9y:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1401 b:12.9 occ:0.90 ND1 A:HIS1112 2.0 13.9 1.0 ND1 A:HIS1057 2.1 9.1 1.0 SG A:CYS1105 2.3 16.0 1.0 SD A:MET1118 2.7 12.1 1.0 CE1 A:HIS1112 2.9 12.3 1.0 CE1 A:HIS1057 3.0 9.6 1.0 CG A:HIS1112 3.0 12.8 1.0 CG A:HIS1057 3.1 10.4 1.0 CB A:CYS1105 3.2 12.7 1.0 CB A:HIS1112 3.4 11.5 1.0 CE A:MET1118 3.5 12.9 1.0 CB A:HIS1057 3.6 13.0 1.0 O A:VAL1107 3.8 17.7 1.0 CA A:HIS1057 3.8 15.4 1.0 O A:PRO1056 3.9 11.7 1.0 NE2 A:HIS1112 4.1 17.2 1.0 CD2 A:HIS1112 4.1 17.5 1.0 NE2 A:HIS1057 4.1 10.8 1.0 CD2 A:HIS1057 4.2 10.1 1.0 CB A:VAL1107 4.3 15.5 1.0 CG A:MET1118 4.4 9.1 1.0 CA A:CYS1105 4.7 11.1 1.0 C A:PRO1056 4.7 14.4 1.0 N A:HIS1057 4.7 11.9 1.0 C A:VAL1107 4.7 16.2 1.0 N A:VAL1107 4.8 17.1 1.0 CA A:HIS1112 4.9 10.1 1.0 CB A:MET1118 4.9 8.1 1.0 N A:THR1058 4.9 10.9 1.0 CA A:VAL1107 4.9 14.7 1.0 C A:HIS1057 4.9 14.7 1.0

Copper binding site 2 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1402 b:11.3 occ:0.80 ND1 A:HIS1062 2.0 11.7 1.0 NE2 A:HIS1104 2.0 11.6 1.0 NE2 B:HIS2254 2.1 14.8 1.0 O1 B:OXY2403 2.5 10.5 0.7 CE1 A:HIS1062 2.8 9.9 1.0 O2 B:OXY2403 3.0 17.9 0.7 CD2 A:HIS1104 3.0 9.5 1.0 CE1 A:HIS1104 3.0 9.3 1.0 CD2 B:HIS2254 3.1 17.0 1.0 CG A:HIS1062 3.1 12.0 1.0 CE1 B:HIS2254 3.1 15.0 1.0 CB A:HIS1062 3.4 11.8 1.0 CZ2 A:TRP1102 3.5 7.3 1.0 CE2 A:TRP1102 3.9 8.0 1.0 CU B:CU2402 3.9 17.2 0.7 CD2 A:HIS1060 3.9 9.3 1.0 NE1 A:TRP1102 4.0 9.3 1.0 NE2 A:HIS1062 4.0 13.2 1.0 ND1 A:HIS1104 4.1 10.9 1.0 CD2 A:HIS1062 4.1 13.3 1.0 CG A:HIS1104 4.1 9.1 1.0 ND1 B:HIS2254 4.2 14.1 1.0 CG B:HIS2254 4.2 12.1 1.0 CD2 B:HIS2204 4.3 10.8 1.0 CH2 A:TRP1102 4.3 8.3 1.0 NE2 A:HIS1060 4.3 10.7 1.0 NE2 B:HIS2204 4.3 12.5 1.0 CA A:HIS1062 4.7 8.6 1.0 CD2 A:TRP1102 4.9 7.4 1.0 CU B:CU2401 4.9 13.4 0.8

Copper binding site 3 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1403 b:13.1 occ:0.80 NE2 A:HIS1206 2.0 9.6 1.0 NE2 A:HIS1252 2.0 14.0 1.0 NE2 C:HIS3106 2.1 14.4 1.0 O2 A:OXY1405 2.2 11.3 0.7 O1 A:OXY1405 2.6 10.7 0.7 CE1 A:HIS1206 2.8 11.6 1.0 CE1 A:HIS1252 3.0 15.7 1.0 CD2 A:HIS1252 3.0 16.3 1.0 CE1 C:HIS3106 3.0 17.9 1.0 CD2 C:HIS3106 3.1 11.5 1.0 CD2 A:HIS1206 3.1 7.7 1.0 CD2 A:HIS1204 3.9 11.6 1.0 ND1 A:HIS1206 4.0 9.4 1.0 CU A:CU1404 4.0 17.1 0.7 CG2 A:ILE1250 4.0 14.3 1.0 ND1 A:HIS1252 4.1 12.7 1.0 CG A:HIS1252 4.1 12.8 1.0 CG A:HIS1206 4.1 6.8 1.0 ND1 C:HIS3106 4.2 15.9 1.0 CG C:HIS3106 4.2 15.8 1.0 CD2 C:HIS3060 4.3 9.6 1.0 NE2 C:HIS3060 4.4 8.3 1.0 NE2 A:HIS1204 4.5 8.9 1.0 CE1 C:HIS3104 4.8 10.9 1.0 CU C:CU3405 4.9 11.1 0.8 CD2 A:HIS1254 4.9 15.3 1.0 CG C:HIS3060 5.0 7.6 1.0 NE2 A:HIS1254 5.0 15.3 1.0

Copper binding site 4 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1404 b:17.1 occ:0.65 NE2 A:HIS1204 1.8 8.9 1.0 NE2 C:HIS3060 1.9 8.3 1.0 O1 A:OXY1405 2.3 10.7 0.7 CD2 A:HIS1204 2.7 11.6 1.0 CE1 C:HIS3060 2.8 12.5 1.0 CE1 A:HIS1204 2.9 10.9 1.0 CD2 C:HIS3060 2.9 9.6 1.0 O C:HOH3501 3.0 11.1 1.0 NE2 A:HIS1206 3.1 9.6 1.0 CD2 A:HIS1206 3.2 7.7 1.0 ND1 C:HIS3062 3.5 10.0 1.0 O2 A:OXY1405 3.5 11.3 0.7 CG C:HIS3062 3.6 8.3 1.0 CE1 A:HIS1206 3.6 11.6 1.0 CG A:HIS1206 3.8 6.8 1.0 CA C:HIS3062 3.8 9.7 1.0 CB C:HIS3062 3.8 8.8 1.0 CU C:CU3405 3.9 11.1 0.8 ND1 C:HIS3060 3.9 10.4 1.0 CG A:HIS1204 3.9 8.9 1.0 ND1 A:HIS1206 3.9 9.4 1.0 ND1 A:HIS1204 4.0 13.0 1.0 CG C:HIS3060 4.0 7.6 1.0 CU A:CU1403 4.0 13.1 0.8 CE1 C:HIS3062 4.0 8.2 1.0 CD2 C:HIS3062 4.2 14.4 1.0 NE2 C:HIS3062 4.4 9.2 1.0 N C:GLY3063 4.5 7.8 1.0 CA A:HIS1206 4.6 6.0 1.0 CB A:HIS1206 4.7 6.5 1.0 C C:HIS3062 4.7 10.2 1.0 N C:HIS3062 4.7 8.4 1.0 NE2 C:HIS3104 4.9 8.1 1.0 O C:HOH3527 4.9 12.7 1.0 O C:TRP3061 4.9 9.2 1.0

Copper binding site 5 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2401 b:13.4 occ:0.80 NE2 B:HIS2206 2.0 11.5 1.0 NE2 B:HIS2252 2.1 18.1 1.0 O2 B:OXY2403 2.1 17.9 0.7 NE2 A:HIS1106 2.1 18.4 1.0 O1 B:OXY2403 2.5 10.5 0.7 CE1 B:HIS2206 2.8 11.9 1.0 CE1 B:HIS2252 3.0 17.8 1.0 CE1 A:HIS1106 3.1 26.1 1.0 CD2 B:HIS2252 3.1 13.1 1.0 CD2 B:HIS2206 3.1 10.4 1.0 CD2 A:HIS1106 3.2 16.6 1.0 CD2 B:HIS2204 3.9 10.8 1.0 ND1 B:HIS2206 4.0 9.6 1.0 CU B:CU2402 4.1 17.2 0.7 CG2 B:ILE2250 4.1 13.1 1.0 ND1 B:HIS2252 4.1 17.8 1.0 CG B:HIS2252 4.2 12.2 1.0 CG B:HIS2206 4.2 8.0 1.0 ND1 A:HIS1106 4.2 16.6 1.0 CG A:HIS1106 4.3 13.0 1.0 CD2 A:HIS1060 4.3 9.3 1.0 NE2 A:HIS1060 4.4 10.7 1.0 NE2 B:HIS2204 4.5 12.5 1.0 CE1 A:HIS1104 4.8 9.3 1.0 CD2 B:HIS2254 4.9 17.0 1.0 CU A:CU1402 4.9 11.3 0.8 CG A:HIS1060 4.9 10.8 1.0

Copper binding site 6 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2402 b:17.2 occ:0.65 NE2 B:HIS2204 1.8 12.5 1.0 NE2 A:HIS1060 1.9 10.7 1.0 O1 B:OXY2403 2.7 10.5 0.7 CE1 A:HIS1060 2.7 12.9 1.0 CD2 B:HIS2204 2.8 10.8 1.0 O A:HOH5001 2.8 10.8 1.0 CE1 B:HIS2204 2.9 12.6 1.0 CD2 A:HIS1060 2.9 9.3 1.0 NE2 B:HIS2206 3.2 11.5 1.0 CD2 B:HIS2206 3.3 10.4 1.0 ND1 A:HIS1062 3.5 11.7 1.0 CG A:HIS1062 3.6 12.0 1.0 CE1 B:HIS2206 3.7 11.9 1.0 CG B:HIS2206 3.8 8.0 1.0 CA A:HIS1062 3.8 8.6 1.0 O2 B:OXY2403 3.8 17.9 0.7 ND1 A:HIS1060 3.9 9.5 1.0 CB A:HIS1062 3.9 11.8 1.0 CU A:CU1402 3.9 11.3 0.8 CG B:HIS2204 3.9 9.4 1.0 ND1 B:HIS2204 3.9 8.6 1.0 CG A:HIS1060 4.0 10.8 1.0 ND1 B:HIS2206 4.0 9.6 1.0 CE1 A:HIS1062 4.0 9.9 1.0 CU B:CU2401 4.1 13.4 0.8 CD2 A:HIS1062 4.2 13.3 1.0 NE2 A:HIS1062 4.4 13.2 1.0 N A:GLY1063 4.5 10.4 1.0 CA B:HIS2206 4.7 8.0 1.0 C A:HIS1062 4.7 11.3 1.0 CB B:HIS2206 4.7 9.1 1.0 N A:HIS1062 4.7 11.1 1.0 O A:HOH5036 4.8 15.3 1.0 O A:TRP1061 4.9 10.2 1.0 NE2 A:HIS1104 5.0 11.6 1.0

Copper binding site 7 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2404 b:10.5 occ:0.90 ND1 B:HIS2112 2.0 12.4 1.0 ND1 B:HIS2057 2.1 9.6 1.0 SG B:CYS2105 2.2 12.8 1.0 SD B:MET2118 2.8 10.8 1.0 CE1 B:HIS2112 2.9 9.2 1.0 CE1 B:HIS2057 3.0 10.3 1.0 CG B:HIS2112 3.0 8.6 1.0 CG B:HIS2057 3.1 10.2 1.0 CB B:CYS2105 3.2 7.8 1.0 CB B:HIS2112 3.4 8.3 1.0 CB B:HIS2057 3.5 8.1 1.0 CE B:MET2118 3.6 9.9 1.0 CA B:HIS2057 3.8 8.6 1.0 O B:VAL2107 3.9 15.1 1.0 O B:PRO2056 4.0 10.5 1.0 NE2 B:HIS2112 4.1 12.6 1.0 CD2 B:HIS2112 4.1 11.5 1.0 NE2 B:HIS2057 4.2 11.7 1.0 CD2 B:HIS2057 4.2 12.5 1.0 CB B:VAL2107 4.3 10.3 1.0 CG B:MET2118 4.4 8.1 1.0 CA B:CYS2105 4.6 6.3 1.0 N B:HIS2057 4.7 10.6 1.0 C B:VAL2107 4.7 10.6 1.0 C B:PRO2056 4.7 10.9 1.0 N B:VAL2107 4.8 10.2 1.0 N B:THR2058 4.8 7.2 1.0 CB B:MET2118 4.9 6.2 1.0 CA B:VAL2107 4.9 10.2 1.0 CA B:HIS2112 4.9 8.5 1.0 C B:HIS2057 4.9 12.3 1.0 CG2 B:VAL2107 5.0 10.4 1.0

Copper binding site 8 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2405 b:10.4 occ:0.80 ND1 B:HIS2062 1.9 11.7 1.0 NE2 B:HIS2104 2.0 10.2 1.0 NE2 C:HIS3254 2.2 14.6 1.0 O1 C:OXY3403 2.4 9.2 0.7 CE1 B:HIS2062 2.7 5.9 1.0 O2 C:OXY3403 2.9 13.0 0.7 CE1 B:HIS2104 2.9 9.2 1.0 CG B:HIS2062 3.0 11.6 1.0 CD2 B:HIS2104 3.0 8.0 1.0 CD2 C:HIS3254 3.1 13.6 1.0 CE1 C:HIS3254 3.1 14.5 1.0 CB B:HIS2062 3.4 7.8 1.0 CZ2 B:TRP2102 3.6 8.1 1.0 CU C:CU3402 3.9 14.5 0.7 CE2 B:TRP2102 3.9 6.0 1.0 NE2 B:HIS2062 3.9 10.4 1.0 CD2 B:HIS2060 4.0 10.1 1.0 NE1 B:TRP2102 4.0 6.5 1.0 CD2 B:HIS2062 4.0 12.3 1.0 ND1 B:HIS2104 4.1 8.6 1.0 CG B:HIS2104 4.1 7.2 1.0 ND1 C:HIS3254 4.3 12.0 1.0 CD2 C:HIS3204 4.3 10.6 1.0 CG C:HIS3254 4.3 9.9 1.0 NE2 C:HIS3204 4.3 7.8 1.0 NE2 B:HIS2060 4.3 8.6 1.0 CH2 B:TRP2102 4.4 9.6 1.0 CA B:HIS2062 4.7 8.0 1.0 CU C:CU3401 4.9 12.2 0.8 CD2 B:TRP2102 4.9 6.2 1.0

Copper binding site 9 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu3401 b:12.2 occ:0.80 NE2 C:HIS3206 2.0 9.8 1.0 NE2 C:HIS3252 2.1 15.1 1.0 O2 C:OXY3403 2.1 13.0 0.7 NE2 B:HIS2106 2.1 11.6 1.0 O1 C:OXY3403 2.6 9.2 0.7 CE1 C:HIS3206 2.7 10.2 1.0 CE1 C:HIS3252 3.0 15.0 1.0 CE1 B:HIS2106 3.0 14.1 1.0 CD2 C:HIS3252 3.0 13.7 1.0 CD2 C:HIS3206 3.1 11.2 1.0 CD2 B:HIS2106 3.2 8.7 1.0 CD2 C:HIS3204 3.9 10.6 1.0 ND1 C:HIS3206 4.0 9.0 1.0 CG2 C:ILE3250 4.0 8.0 1.0 CU C:CU3402 4.0 14.5 0.7 ND1 C:HIS3252 4.1 13.0 1.0 CG C:HIS3206 4.1 9.8 1.0 CG C:HIS3252 4.2 11.3 1.0 ND1 B:HIS2106 4.2 13.6 1.0 CG B:HIS2106 4.3 8.4 1.0 CD2 B:HIS2060 4.3 10.1 1.0 NE2 B:HIS2060 4.4 8.6 1.0 NE2 C:HIS3204 4.5 7.8 1.0 CE1 B:HIS2104 4.8 9.2 1.0 CU B:CU2405 4.9 10.4 0.8 CG B:HIS2060 4.9 9.4 1.0 CD2 C:HIS3254 5.0 13.6 1.0

Copper binding site 10 out of 12 in the Multicopper Oxidase Mglac (DATA4)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Multicopper Oxidase Mglac (DATA4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu3402 b:14.5 occ:0.65 NE2 B:HIS2060 1.9 8.6 1.0 NE2 C:HIS3204 1.9 7.8 1.0 O1 C:OXY3403 2.6 9.2 0.7 CE1 B:HIS2060 2.8 10.7 1.0 CD2 C:HIS3204 2.8 10.6 1.0 O B:HOH2501 2.9 9.8 1.0 CD2 B:HIS2060 2.9 10.1 1.0 CE1 C:HIS3204 2.9 9.2 1.0 NE2 C:HIS3206 3.2 9.8 1.0 CD2 C:HIS3206 3.3 11.2 1.0 ND1 B:HIS2062 3.5 11.7 1.0 CG B:HIS2062 3.6 11.6 1.0 CE1 C:HIS3206 3.6 10.2 1.0 O2 C:OXY3403 3.7 13.0 0.7 CB B:HIS2062 3.8 7.8 1.0 CG C:HIS3206 3.8 9.8 1.0 CA B:HIS2062 3.8 8.0 1.0 ND1 B:HIS2060 3.9 9.6 1.0 CU B:CU2405 3.9 10.4 0.8 ND1 C:HIS3206 3.9 9.0 1.0 CG C:HIS3204 4.0 8.2 1.0 CG B:HIS2060 4.0 9.4 1.0 ND1 C:HIS3204 4.0 10.5 1.0 CU C:CU3401 4.0 12.2 0.8 CE1 B:HIS2062 4.1 5.9 1.0 CD2 B:HIS2062 4.2 12.3 1.0 NE2 B:HIS2062 4.4 10.4 1.0 N B:GLY2063 4.5 8.9 1.0 CA C:HIS3206 4.6 5.3 1.0 C B:HIS2062 4.7 8.5 1.0 CB C:HIS3206 4.7 6.0 1.0 N B:HIS2062 4.7 7.9 1.0 O B:HOH2519 4.8 10.8 1.0 O B:TRP2061 4.9 9.1 1.0 NE2 B:HIS2104 4.9 10.2 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: ESSN 1399-0047
PubMed: 24598746
DOI: 10.1107/S1399004713033051