Atomistry » Copper » PDB 4e9v-4hd7 » 4e9v
Atomistry »
  Copper »
    PDB 4e9v-4hd7 »
      4e9v »

Copper in PDB 4e9v: Multicopper Oxidase Mglac (DATA1)

Protein crystallography data

The structure of Multicopper Oxidase Mglac (DATA1), PDB code: 4e9v 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.728, 101.130, 123.959, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / n/a

Other elements in 4e9v:

The structure of Multicopper Oxidase Mglac (DATA1) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

Pages:

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

Binding sites:

The binding sites of Copper atom in the Multicopper Oxidase Mglac (DATA1) (pdb code 4e9v). 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 (DATA1), PDB code: 4e9v:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 1 out of 12 in the Multicopper Oxidase Mglac (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 Mglac (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1401

b:11.8
occ:0.90
ND1 A:HIS1112 1.9 12.2 1.0
ND1 A:HIS1057 2.1 8.0 1.0
SG A:CYS1105 2.2 15.3 1.0
SD A:MET1118 2.7 10.9 1.0
CE1 A:HIS1112 2.8 11.7 1.0
CG A:HIS1112 2.9 14.9 1.0
CE1 A:HIS1057 3.0 8.3 1.0
CG A:HIS1057 3.1 10.4 1.0
CB A:CYS1105 3.2 14.3 1.0
CB A:HIS1112 3.4 11.1 1.0
CB A:HIS1057 3.5 10.6 1.0
CE A:MET1118 3.6 11.3 1.0
O A:VAL1107 3.8 16.6 1.0
CA A:HIS1057 3.8 14.5 1.0
O A:PRO1056 3.9 11.5 1.0
NE2 A:HIS1112 3.9 15.7 1.0
CD2 A:HIS1112 4.0 17.3 1.0
NE2 A:HIS1057 4.2 13.2 1.0
CD2 A:HIS1057 4.2 11.1 1.0
CB A:VAL1107 4.3 15.1 1.0
CG A:MET1118 4.4 7.8 1.0
CA A:CYS1105 4.6 12.3 1.0
C A:PRO1056 4.7 18.5 1.0
N A:HIS1057 4.7 12.1 1.0
C A:VAL1107 4.7 17.7 1.0
CA A:HIS1112 4.8 10.4 1.0
CB A:MET1118 4.8 5.0 1.0
N A:VAL1107 4.9 17.2 1.0
CA A:VAL1107 4.9 14.2 1.0
N A:THR1058 5.0 10.3 1.0
C A:HIS1057 5.0 13.2 1.0

Copper binding site 2 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 2 out of 12 in the Multicopper Oxidase Mglac (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 Mglac (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1402

b:16.8
occ:0.80
ND1 A:HIS1062 2.0 11.2 1.0
NE2 B:HIS2254 2.1 15.7 1.0
NE2 A:HIS1104 2.2 10.4 1.0
O A:O1403 2.4 8.4 0.7
O B:OH2403 2.7 18.1 0.7
CE1 A:HIS1062 2.8 10.2 1.0
CD2 B:HIS2254 3.0 14.2 1.0
CD2 A:HIS1104 3.1 11.4 1.0
CE1 B:HIS2254 3.1 16.0 1.0
CG A:HIS1062 3.1 15.1 1.0
CE1 A:HIS1104 3.1 7.0 1.0
CB A:HIS1062 3.5 17.1 1.0
CZ2 A:TRP1102 3.6 7.9 1.0
CU B:CU2402 3.8 18.6 0.7
CE2 A:TRP1102 4.0 7.0 1.0
NE2 A:HIS1062 4.0 11.5 1.0
CD2 A:HIS1060 4.0 13.3 1.0
NE1 A:TRP1102 4.1 7.0 1.0
CD2 A:HIS1062 4.1 9.2 1.0
CG B:HIS2254 4.2 13.4 1.0
ND1 B:HIS2254 4.2 14.2 1.0
NE2 A:HIS1060 4.2 16.0 1.0
ND1 A:HIS1104 4.2 8.5 1.0
CG A:HIS1104 4.2 11.4 1.0
CD2 B:HIS2204 4.2 7.6 1.0
NE2 B:HIS2204 4.3 14.3 1.0
CU B:CU2401 4.4 19.6 0.8
CH2 A:TRP1102 4.4 7.3 1.0
CA A:HIS1062 4.7 10.1 1.0

Copper binding site 3 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 3 out of 12 in the Multicopper Oxidase Mglac (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 Mglac (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1404

b:18.4
occ:0.80
NE2 A:HIS1206 2.0 9.2 1.0
NE2 A:HIS1252 2.1 16.6 1.0
NE2 C:HIS3106 2.1 15.7 1.0
O C:O3406 2.3 7.3 0.7
O A:OH1406 2.4 19.0 0.7
CE1 A:HIS1206 2.8 9.6 1.0
CE1 A:HIS1252 3.0 17.8 1.0
CE1 C:HIS3106 3.1 16.5 1.0
CD2 C:HIS3106 3.1 12.3 1.0
CD2 A:HIS1206 3.1 5.4 1.0
CD2 A:HIS1252 3.2 18.7 1.0
CU A:CU1405 3.7 17.2 0.7
CD2 A:HIS1204 3.8 10.9 1.0
ND1 A:HIS1206 4.0 10.5 1.0
ND1 A:HIS1252 4.1 16.3 1.0
CG A:HIS1206 4.2 7.2 1.0
CD2 C:HIS3060 4.2 7.6 1.0
ND1 C:HIS3106 4.2 17.9 1.0
CG A:HIS1252 4.3 16.9 1.0
NE2 C:HIS3060 4.3 8.9 1.0
CU C:CU3405 4.3 14.5 0.8
CG C:HIS3106 4.3 18.2 1.0
NE2 A:HIS1204 4.4 8.6 1.0
CE1 C:HIS3104 4.4 6.9 1.0
CG2 A:ILE1250 4.4 11.8 1.0
CD2 A:HIS1254 4.7 12.7 1.0
NE2 A:HIS1254 4.7 13.4 1.0
NE2 C:HIS3104 4.8 7.4 1.0
CG C:HIS3060 4.9 7.3 1.0
CG A:HIS1204 5.0 7.2 1.0
CE1 C:HIS3060 5.0 11.0 1.0

Copper binding site 4 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 4 out of 12 in the Multicopper Oxidase Mglac (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 Mglac (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1405

b:17.2
occ:0.65
NE2 A:HIS1204 1.9 8.6 1.0
NE2 C:HIS3060 2.1 8.9 1.0
O C:O3406 2.1 7.3 0.7
CD2 A:HIS1204 2.7 10.9 1.0
O C:HOH3502 2.8 7.2 1.0
CE1 C:HIS3060 3.0 11.0 1.0
CE1 A:HIS1204 3.0 9.0 1.0
CD2 C:HIS3060 3.0 7.6 1.0
NE2 A:HIS1206 3.1 9.2 1.0
CD2 A:HIS1206 3.1 5.4 1.0
ND1 C:HIS3062 3.4 7.7 1.0
CG C:HIS3062 3.6 8.2 1.0
CE1 A:HIS1206 3.6 9.6 1.0
CG A:HIS1206 3.7 7.2 1.0
CU C:CU3405 3.7 14.5 0.8
CU A:CU1404 3.7 18.4 0.8
CA C:HIS3062 3.8 9.4 1.0
CB C:HIS3062 3.8 9.4 1.0
ND1 A:HIS1206 3.9 10.5 1.0
CG A:HIS1204 3.9 7.2 1.0
CE1 C:HIS3062 4.0 7.5 1.0
ND1 A:HIS1204 4.0 11.4 1.0
ND1 C:HIS3060 4.1 8.6 1.0
CG C:HIS3060 4.1 7.3 1.0
CD2 C:HIS3062 4.2 9.1 1.0
O A:OH1406 4.3 19.0 0.7
NE2 C:HIS3062 4.4 9.5 1.0
N C:GLY3063 4.5 2.3 1.0
CA A:HIS1206 4.6 6.8 1.0
CB A:HIS1206 4.6 7.1 1.0
C C:HIS3062 4.7 5.3 1.0
N C:HIS3062 4.7 7.7 1.0
NE2 C:HIS3104 4.8 7.4 1.0
O C:TRP3061 4.9 8.5 1.0

Copper binding site 5 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 5 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2401

b:19.6
occ:0.80
NE2 B:HIS2206 2.0 10.2 1.0
NE2 A:HIS1106 2.2 18.5 1.0
NE2 B:HIS2252 2.2 18.1 1.0
O B:OH2403 2.3 18.1 0.7
O A:O1403 2.4 8.4 0.7
CE1 B:HIS2206 2.9 9.9 1.0
CE1 B:HIS2252 3.0 17.1 1.0
CD2 B:HIS2206 3.1 10.3 1.0
CE1 A:HIS1106 3.2 23.6 1.0
CD2 A:HIS1106 3.2 17.8 1.0
CD2 B:HIS2252 3.3 15.4 1.0
CU B:CU2402 3.8 18.6 0.7
CD2 B:HIS2204 3.8 7.6 1.0
ND1 B:HIS2206 4.0 10.2 1.0
CD2 A:HIS1060 4.1 13.3 1.0
NE2 A:HIS1060 4.1 16.0 1.0
CG B:HIS2206 4.2 9.6 1.0
ND1 B:HIS2252 4.2 17.4 1.0
ND1 A:HIS1106 4.3 19.2 1.0
NE2 B:HIS2204 4.3 14.3 1.0
CG A:HIS1106 4.3 17.4 1.0
CG2 B:ILE2250 4.4 11.1 1.0
CU A:CU1402 4.4 16.8 0.8
CG B:HIS2252 4.4 11.6 1.0
CE1 A:HIS1104 4.5 7.0 1.0
CD2 B:HIS2254 4.6 14.2 1.0
NE2 B:HIS2254 4.7 15.7 1.0
NE2 A:HIS1104 4.8 10.4 1.0
CG A:HIS1060 4.8 16.0 1.0
CE1 A:HIS1060 4.9 10.1 1.0

Copper binding site 6 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 6 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2402

b:18.6
occ:0.65
NE2 B:HIS2204 2.0 14.3 1.0
NE2 A:HIS1060 2.0 16.0 1.0
O A:O1403 2.1 8.4 0.7
O A:HOH5001 2.7 6.2 1.0
CE1 A:HIS1060 2.8 10.1 1.0
CD2 B:HIS2204 2.9 7.6 1.0
CE1 B:HIS2204 3.0 9.2 1.0
CD2 A:HIS1060 3.1 13.3 1.0
NE2 B:HIS2206 3.1 10.2 1.0
CD2 B:HIS2206 3.2 10.3 1.0
ND1 A:HIS1062 3.4 11.2 1.0
CG A:HIS1062 3.6 15.1 1.0
CE1 B:HIS2206 3.7 9.9 1.0
CA A:HIS1062 3.7 10.1 1.0
CU B:CU2401 3.8 19.6 0.8
CG B:HIS2206 3.8 9.6 1.0
CU A:CU1402 3.8 16.8 0.8
CB A:HIS1062 3.8 17.1 1.0
ND1 A:HIS1060 3.9 9.6 1.0
CE1 A:HIS1062 4.0 10.2 1.0
CG B:HIS2204 4.0 9.2 1.0
ND1 B:HIS2206 4.0 10.2 1.0
ND1 B:HIS2204 4.1 9.2 1.0
CG A:HIS1060 4.1 16.0 1.0
CD2 A:HIS1062 4.2 9.2 1.0
O B:OH2403 4.3 18.1 0.7
NE2 A:HIS1062 4.4 11.5 1.0
N A:GLY1063 4.6 9.8 1.0
N A:HIS1062 4.6 10.0 1.0
CA B:HIS2206 4.6 8.7 1.0
C A:HIS1062 4.7 10.4 1.0
CB B:HIS2206 4.7 10.2 1.0
O A:TRP1061 4.9 7.3 1.0
NE2 A:HIS1104 4.9 10.4 1.0
O B:HOH2501 4.9 16.0 1.0

Copper binding site 7 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 7 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2404

b:9.3
occ:0.90
ND1 B:HIS2112 1.9 8.9 1.0
ND1 B:HIS2057 2.1 8.2 1.0
SG B:CYS2105 2.2 13.8 1.0
SD B:MET2118 2.7 10.2 1.0
CE1 B:HIS2112 2.8 10.5 1.0
CG B:HIS2112 3.0 11.2 1.0
CE1 B:HIS2057 3.0 9.0 1.0
CG B:HIS2057 3.0 7.7 1.0
CB B:CYS2105 3.2 11.8 1.0
CB B:HIS2057 3.4 5.5 1.0
CB B:HIS2112 3.4 8.4 1.0
CE B:MET2118 3.6 5.3 1.0
O B:VAL2107 3.8 16.4 1.0
CA B:HIS2057 3.8 7.8 1.0
NE2 B:HIS2112 4.0 12.0 1.0
O B:PRO2056 4.0 9.7 1.0
CD2 B:HIS2112 4.1 12.6 1.0
NE2 B:HIS2057 4.1 9.1 1.0
CD2 B:HIS2057 4.2 9.6 1.0
CG B:MET2118 4.3 8.8 1.0
CB B:VAL2107 4.4 10.1 1.0
CA B:CYS2105 4.6 6.5 1.0
N B:HIS2057 4.7 10.6 1.0
C B:VAL2107 4.8 13.7 1.0
C B:PRO2056 4.8 12.0 1.0
CB B:MET2118 4.9 3.8 1.0
CA B:HIS2112 4.9 6.2 1.0
N B:THR2058 4.9 5.8 1.0
N B:VAL2107 4.9 11.6 1.0
C B:HIS2057 5.0 12.8 1.0
CA B:VAL2107 5.0 8.6 1.0

Copper binding site 8 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 8 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2405

b:14.5
occ:0.80
ND1 B:HIS2062 1.9 9.3 1.0
NE2 B:HIS2104 2.1 7.7 1.0
NE2 C:HIS3254 2.2 18.0 1.0
O B:O2406 2.3 7.0 0.7
O C:OH3403 2.6 14.3 0.7
CE1 B:HIS2062 2.7 6.0 1.0
CE1 B:HIS2104 2.9 10.2 1.0
CG B:HIS2062 3.0 13.5 1.0
CD2 C:HIS3254 3.0 13.8 1.0
CD2 B:HIS2104 3.2 8.1 1.0
CE1 C:HIS3254 3.3 12.3 1.0
CB B:HIS2062 3.4 10.4 1.0
CZ2 B:TRP2102 3.7 7.8 1.0
CU C:CU3402 3.8 14.7 0.7
NE2 B:HIS2062 3.9 11.0 1.0
CD2 B:HIS2060 4.0 10.8 1.0
CD2 B:HIS2062 4.0 10.7 1.0
CE2 B:TRP2102 4.1 5.0 1.0
ND1 B:HIS2104 4.1 6.1 1.0
NE1 B:TRP2102 4.2 5.2 1.0
CD2 C:HIS3204 4.2 6.9 1.0
NE2 C:HIS3204 4.2 9.2 1.0
CG B:HIS2104 4.2 8.1 1.0
CG C:HIS3254 4.3 9.7 1.0
NE2 B:HIS2060 4.3 10.6 1.0
ND1 C:HIS3254 4.3 10.6 1.0
CU C:CU3401 4.3 16.4 0.8
CH2 B:TRP2102 4.5 12.1 1.0
CA B:HIS2062 4.7 6.9 1.0

Copper binding site 9 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 9 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3401

b:16.4
occ:0.80
NE2 C:HIS3206 2.0 8.9 1.0
NE2 C:HIS3252 2.1 13.3 1.0
NE2 B:HIS2106 2.2 11.8 1.0
O C:OH3403 2.4 14.3 0.7
O B:O2406 2.4 7.0 0.7
CE1 C:HIS3206 2.8 10.1 1.0
CE1 C:HIS3252 2.9 12.8 1.0
CD2 B:HIS2106 3.1 8.6 1.0
CE1 B:HIS2106 3.2 11.5 1.0
CD2 C:HIS3206 3.2 9.9 1.0
CD2 C:HIS3252 3.2 13.6 1.0
CU C:CU3402 3.8 14.7 0.7
CD2 C:HIS3204 3.9 6.9 1.0
ND1 C:HIS3206 4.0 12.0 1.0
CD2 B:HIS2060 4.1 10.8 1.0
ND1 C:HIS3252 4.1 12.0 1.0
CG C:HIS3206 4.2 10.7 1.0
NE2 B:HIS2060 4.2 10.6 1.0
ND1 B:HIS2106 4.3 14.0 1.0
CG C:HIS3252 4.3 10.0 1.0
CG B:HIS2106 4.3 9.4 1.0
CU B:CU2405 4.3 14.5 0.8
CG2 C:ILE3250 4.3 8.1 1.0
NE2 C:HIS3204 4.4 9.2 1.0
CE1 B:HIS2104 4.5 10.2 1.0
CG B:HIS2060 4.8 13.4 1.0
CD2 C:HIS3254 4.8 13.8 1.0
NE2 C:HIS3254 4.9 18.0 1.0
CE1 B:HIS2060 4.9 10.5 1.0

Copper binding site 10 out of 12 in 4e9v

Go back to Copper Binding Sites List in 4e9v
Copper binding site 10 out of 12 in the Multicopper Oxidase Mglac (DATA1)


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 (DATA1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3402

b:14.7
occ:0.65
NE2 B:HIS2060 2.0 10.6 1.0
NE2 C:HIS3204 2.0 9.2 1.0
O B:O2406 2.2 7.0 0.7
O C:HOH3501 2.6 5.1 1.0
CE1 B:HIS2060 2.8 10.5 1.0
CD2 C:HIS3204 2.9 6.9 1.0
CD2 B:HIS2060 3.0 10.8 1.0
CE1 C:HIS3204 3.1 10.6 1.0
NE2 C:HIS3206 3.2 8.9 1.0
CD2 C:HIS3206 3.3 9.9 1.0
ND1 B:HIS2062 3.5 9.3 1.0
CE1 C:HIS3206 3.6 10.1 1.0
CG B:HIS2062 3.6 13.5 1.0
CG C:HIS3206 3.7 10.7 1.0
CB B:HIS2062 3.8 10.4 1.0
CA B:HIS2062 3.8 6.9 1.0
CU B:CU2405 3.8 14.5 0.8
CU C:CU3401 3.8 16.4 0.8
ND1 C:HIS3206 3.8 12.0 1.0
ND1 B:HIS2060 3.9 10.9 1.0
CG C:HIS3204 4.1 5.5 1.0
CG B:HIS2060 4.1 13.4 1.0
CE1 B:HIS2062 4.1 6.0 1.0
ND1 C:HIS3204 4.1 10.5 1.0
CD2 B:HIS2062 4.2 10.7 1.0
O C:OH3403 4.3 14.3 0.7
NE2 B:HIS2062 4.4 11.0 1.0
N B:GLY2063 4.6 7.8 1.0
CA C:HIS3206 4.6 5.3 1.0
CB C:HIS3206 4.6 5.1 1.0
C B:HIS2062 4.7 8.9 1.0
N B:HIS2062 4.7 6.5 1.0
O C:HOH3506 4.9 10.3 1.0
O B:TRP2061 4.9 6.8 1.0
NE2 B:HIS2104 4.9 7.7 1.0
N C:HIS3206 5.0 8.3 1.0

Reference:

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
Page generated: Sun Dec 13 11:14:07 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy