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Copper in PDB 3gdc: Crystal Structure of Multicopper Oxidase

Enzymatic activity of Crystal Structure of Multicopper Oxidase

All present enzymatic activity of Crystal Structure of Multicopper Oxidase:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Multicopper Oxidase, PDB code: 3gdc was solved by I.S.Macpherson, W.C.Lee, T.I.Liang, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 128.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.956, 50.705, 134.667, 90.00, 107.86, 90.00
R / Rfree (%) 19.1 / 22.5

Other elements in 3gdc:

The structure of Crystal Structure of Multicopper Oxidase also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Copper Binding Sites:

Pages:

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

Binding sites:

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

Copper binding site 1 out of 12 in 3gdc

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Copper binding site 1 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:24.5
occ:1.00
ND1 A:HIS99 2.1 15.4 1.0
ND1 A:HIS152 2.2 18.7 1.0
SG A:CYS144 2.2 16.9 1.0
CE1 A:HIS99 3.0 17.1 1.0
CE1 A:HIS152 3.1 19.4 1.0
CG A:HIS99 3.1 17.9 1.0
CG A:HIS152 3.1 18.7 1.0
CD1 A:LEU157 3.2 15.0 1.0
CB A:CYS144 3.3 15.5 1.0
CB A:HIS99 3.5 17.1 1.0
CB A:HIS152 3.5 19.9 1.0
CA A:HIS99 3.5 17.8 1.0
O A:PRO98 3.7 19.0 1.0
CB A:GLN146 3.7 20.5 1.0
NE2 A:HIS99 4.1 17.1 1.0
NE2 A:HIS152 4.2 18.6 1.0
CD2 A:HIS99 4.2 16.8 1.0
CD2 A:HIS152 4.2 17.5 1.0
CA A:HIS152 4.3 20.2 1.0
O A:HIS152 4.4 21.6 1.0
N A:THR100 4.4 16.3 1.0
C A:PRO98 4.5 19.6 1.0
N A:HIS99 4.5 18.4 1.0
CG A:GLN146 4.6 21.6 1.0
C A:HIS99 4.6 17.2 1.0
CE3 A:TRP68 4.6 17.6 1.0
N A:GLN146 4.7 19.7 1.0
CA A:CYS144 4.7 15.9 1.0
CG A:LEU157 4.7 12.8 1.0
CZ3 A:TRP68 4.7 19.1 1.0
C A:HIS152 4.7 20.3 1.0
CA A:GLN146 4.8 20.9 1.0

Copper binding site 2 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 2 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:22.0
occ:0.60
NE2 A:HIS104 2.0 19.5 1.0
NE2 A:HIS143 2.1 15.5 1.0
NE2 C:HIS282 2.1 21.7 1.0
CE1 A:HIS104 2.9 20.3 1.0
O A:HOH439 2.9 27.6 1.0
CD2 A:HIS143 3.0 14.9 1.0
CE1 C:HIS282 3.1 22.4 1.0
CE1 A:HIS143 3.1 15.5 1.0
CD2 C:HIS282 3.1 21.3 1.0
CD2 A:HIS104 3.1 19.3 1.0
CU C:CU302 4.0 17.8 0.4
ND1 A:HIS104 4.1 19.7 1.0
CG A:HIS143 4.2 14.1 1.0
ND1 C:HIS282 4.2 20.9 1.0
ND1 A:HIS143 4.2 13.8 1.0
CG A:HIS104 4.2 19.1 1.0
CG C:HIS282 4.2 20.8 1.0
NE2 C:HIS233 4.3 20.2 1.0
CD2 A:HIS102 4.3 17.9 1.0
CD2 C:HIS233 4.5 19.1 1.0
NE2 A:HIS102 4.7 19.8 1.0
CD1 A:LEU141 4.8 15.7 1.0
CE1 C:HIS233 4.8 20.0 1.0

Copper binding site 3 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 3 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:19.6
occ:0.40
NE2 B:HIS102 1.9 21.1 1.0
NE2 A:HIS233 1.9 20.6 1.0
CD2 B:HIS102 2.8 21.4 1.0
CD2 A:HIS233 2.8 19.5 1.0
CE1 B:HIS102 2.9 20.3 1.0
CE1 A:HIS233 2.9 21.0 1.0
O A:HOH440 3.0 38.0 1.0
O A:HOH352 3.3 26.1 1.0
CD2 A:HIS235 3.3 18.0 1.0
NE2 B:HIS104 3.6 21.4 1.0
NE2 A:HIS235 3.7 19.1 1.0
CD2 B:HIS104 3.9 20.7 1.0
CG A:HIS235 3.9 18.1 1.0
CE1 B:HIS104 3.9 22.1 1.0
CG B:HIS102 3.9 19.6 1.0
CG A:HIS233 4.0 17.6 1.0
CU B:CU303 4.0 23.5 0.6
ND1 B:HIS102 4.0 20.4 1.0
ND1 A:HIS233 4.0 20.2 1.0
CA A:HIS235 4.1 17.3 1.0
ND1 B:HIS104 4.3 21.9 1.0
CG B:HIS104 4.3 22.1 1.0
CE1 A:HIS235 4.3 19.4 1.0
CU A:CU304 4.3 28.5 0.5
ND1 A:HIS235 4.4 18.8 1.0
CB A:HIS235 4.5 18.0 1.0
O B:PHE103 4.6 20.4 1.0
N A:HIS235 4.6 17.4 1.0
O A:ILE234 4.6 17.4 1.0
C A:ILE234 4.8 17.1 1.0
NE2 B:HIS143 5.0 17.6 1.0

Copper binding site 4 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 4 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu304

b:28.5
occ:0.50
NE2 A:HIS280 1.9 23.0 1.0
NE2 A:HIS235 1.9 19.1 1.0
NE2 B:HIS145 2.1 24.6 1.0
O A:HOH440 2.7 38.0 1.0
CE1 A:HIS280 2.8 24.2 1.0
CE1 A:HIS235 2.8 19.4 1.0
CD2 B:HIS145 2.9 26.1 1.0
CD2 A:HIS280 2.9 23.2 1.0
CD2 A:HIS235 3.1 18.0 1.0
CE1 B:HIS145 3.1 25.5 1.0
ND1 A:HIS280 3.9 23.1 1.0
SD A:MET278 3.9 25.1 1.0
ND1 A:HIS235 4.0 18.8 1.0
CG A:HIS280 4.0 20.5 1.0
CG B:HIS145 4.1 23.8 1.0
CG A:HIS235 4.1 18.1 1.0
ND1 B:HIS145 4.2 26.7 1.0
CU A:CU302 4.3 19.6 0.4
CD2 A:HIS233 4.4 19.5 1.0
NE2 B:HIS102 4.6 21.1 1.0
CG A:MET278 4.6 22.1 1.0
CD2 B:HIS102 4.7 21.4 1.0
CB A:MET278 4.8 20.2 1.0
NE2 A:HIS233 4.9 20.6 1.0

Copper binding site 5 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 5 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:30.3
occ:1.00
ND1 B:HIS152 2.1 22.3 1.0
ND1 B:HIS99 2.1 19.8 1.0
SG B:CYS144 2.2 19.3 1.0
CE1 B:HIS152 3.0 22.4 1.0
CE1 B:HIS99 3.0 23.6 1.0
CG B:HIS152 3.1 24.3 1.0
CG B:HIS99 3.1 22.1 1.0
CB B:CYS144 3.2 19.7 1.0
CD1 B:LEU157 3.3 19.2 1.0
CB B:HIS152 3.4 24.3 1.0
CB B:HIS99 3.5 21.6 1.0
CA B:HIS99 3.6 21.9 1.0
O B:PRO98 3.6 23.1 1.0
CB B:GLN146 3.7 25.7 1.0
NE2 B:HIS152 4.1 24.4 1.0
CD2 B:HIS152 4.2 23.1 1.0
NE2 B:HIS99 4.2 23.0 1.0
CA B:HIS152 4.2 24.9 1.0
CD2 B:HIS99 4.2 22.6 1.0
O B:HIS152 4.4 26.1 1.0
C B:PRO98 4.5 23.7 1.0
N B:THR100 4.5 20.5 1.0
N B:HIS99 4.5 23.0 1.0
CG B:GLN146 4.5 26.2 1.0
C B:HIS99 4.6 21.6 1.0
CE3 B:TRP68 4.6 23.7 1.0
CA B:CYS144 4.6 20.0 1.0
N B:GLN146 4.6 24.6 1.0
CG B:LEU157 4.7 18.3 1.0
C B:HIS152 4.7 25.0 1.0
CZ3 B:TRP68 4.7 24.3 1.0
CA B:GLN146 4.8 25.9 1.0

Copper binding site 6 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 6 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu303

b:23.5
occ:0.60
NE2 B:HIS104 2.0 21.4 1.0
NE2 B:HIS143 2.1 17.6 1.0
NE2 A:HIS282 2.1 24.3 1.0
CE1 B:HIS104 2.8 22.1 1.0
O A:HOH440 2.9 38.0 1.0
CD2 B:HIS143 3.0 18.8 1.0
CE1 A:HIS282 3.1 24.3 1.0
CD2 A:HIS282 3.1 23.9 1.0
CD2 B:HIS104 3.1 20.7 1.0
CE1 B:HIS143 3.1 20.2 1.0
ND1 B:HIS104 4.0 21.9 1.0
CU A:CU302 4.0 19.6 0.4
CG B:HIS104 4.2 22.1 1.0
CG B:HIS143 4.2 18.3 1.0
ND1 A:HIS282 4.2 23.9 1.0
ND1 B:HIS143 4.2 16.7 1.0
CG A:HIS282 4.2 22.2 1.0
NE2 A:HIS233 4.3 20.6 1.0
CD2 B:HIS102 4.3 21.4 1.0
CD2 A:HIS233 4.5 19.5 1.0
NE2 B:HIS102 4.7 21.1 1.0
CE1 A:HIS233 4.9 21.0 1.0
CD1 B:LEU141 4.9 18.0 1.0

Copper binding site 7 out of 12 in 3gdc

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Copper binding site 7 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:31.5
occ:0.40
NE2 C:HIS102 1.8 30.1 1.0
NE2 B:HIS233 1.9 26.7 1.0
CE1 C:HIS102 2.8 30.4 1.0
CD2 C:HIS102 2.8 28.4 1.0
CE1 B:HIS233 2.8 26.7 1.0
CD2 B:HIS233 2.9 25.8 1.0
O B:HOH417 3.2 35.7 1.0
O C:HOH397 3.3 36.7 1.0
CD2 B:HIS235 3.5 25.6 1.0
NE2 C:HIS104 3.6 29.5 1.0
NE2 B:HIS235 3.8 26.5 1.0
CD2 C:HIS104 3.9 29.1 1.0
ND1 C:HIS102 3.9 29.2 1.0
ND1 B:HIS233 4.0 26.8 1.0
CG C:HIS102 4.0 28.1 1.0
CG B:HIS235 4.0 25.6 1.0
CE1 C:HIS104 4.0 28.6 1.0
CG B:HIS233 4.0 25.1 1.0
CU C:CU303 4.1 31.3 0.6
CA B:HIS235 4.1 25.6 1.0
CG C:HIS104 4.3 28.3 1.0
CE1 B:HIS235 4.4 26.6 1.0
ND1 C:HIS104 4.4 28.1 1.0
CU B:CU304 4.4 34.2 0.5
ND1 B:HIS235 4.5 26.3 1.0
CB B:HIS235 4.6 25.6 1.0
O C:PHE103 4.6 28.7 1.0
N B:HIS235 4.6 25.6 1.0
O B:ILE234 4.7 25.7 1.0
C B:ILE234 4.9 25.8 1.0
NE2 C:HIS143 4.9 24.8 1.0
O B:HOH403 5.0 34.8 1.0

Copper binding site 8 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 8 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu304

b:34.2
occ:0.50
NE2 B:HIS235 2.0 26.5 1.0
NE2 B:HIS280 2.0 30.4 1.0
NE2 C:HIS145 2.0 31.2 1.0
O C:HOH397 2.6 36.7 1.0
CE1 B:HIS280 2.8 29.3 1.0
CE1 B:HIS235 2.9 26.6 1.0
CD2 C:HIS145 2.9 30.7 1.0
CE1 C:HIS145 3.1 31.5 1.0
CD2 B:HIS235 3.1 25.6 1.0
CD2 B:HIS280 3.1 28.0 1.0
ND1 B:HIS280 4.0 28.6 1.0
SD B:MET278 4.1 32.7 1.0
CG C:HIS145 4.1 29.5 1.0
ND1 B:HIS235 4.1 26.3 1.0
ND1 C:HIS145 4.1 31.6 1.0
CG B:HIS280 4.1 26.7 1.0
CG B:HIS235 4.2 25.6 1.0
CD2 B:HIS233 4.4 25.8 1.0
CU B:CU302 4.4 31.5 0.4
NE2 C:HIS102 4.6 30.1 1.0
CG B:MET278 4.7 30.0 1.0
CD2 C:HIS102 4.7 28.4 1.0
CD2 C:LEU149 4.8 35.6 1.0
CB B:MET278 4.9 28.6 1.0
NE2 B:HIS233 4.9 26.7 1.0

Copper binding site 9 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 9 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu302

b:17.8
occ:0.40
NE2 C:HIS233 1.8 20.2 1.0
NE2 A:HIS102 1.9 19.8 1.0
CD2 C:HIS233 2.8 19.1 1.0
CE1 C:HIS233 2.8 20.0 1.0
CD2 A:HIS102 2.9 17.9 1.0
CE1 A:HIS102 2.9 19.1 1.0
O A:HOH439 3.0 27.6 1.0
O C:HOH330 3.1 23.0 1.0
CD2 C:HIS235 3.3 18.0 1.0
NE2 A:HIS104 3.6 19.5 1.0
NE2 C:HIS235 3.7 20.5 1.0
CG C:HIS235 3.9 18.4 1.0
CD2 A:HIS104 3.9 19.3 1.0
ND1 C:HIS233 3.9 20.8 1.0
CG C:HIS233 3.9 17.4 1.0
ND1 A:HIS102 4.0 16.3 1.0
CG A:HIS102 4.0 17.2 1.0
CU A:CU303 4.0 22.0 0.6
CE1 A:HIS104 4.0 20.3 1.0
CA C:HIS235 4.1 18.1 1.0
CE1 C:HIS235 4.3 20.1 1.0
CU C:CU304 4.4 24.2 0.5
ND1 C:HIS235 4.4 20.0 1.0
CG A:HIS104 4.4 19.1 1.0
ND1 A:HIS104 4.5 19.7 1.0
CB C:HIS235 4.5 17.9 1.0
O A:PHE103 4.6 18.3 1.0
N C:HIS235 4.6 17.8 1.0
O C:ILE234 4.7 18.7 1.0
C C:ILE234 4.9 17.9 1.0

Copper binding site 10 out of 12 in 3gdc

Go back to Copper Binding Sites List in 3gdc
Copper binding site 10 out of 12 in the Crystal Structure of Multicopper Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Multicopper Oxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu304

b:24.2
occ:0.50
NE2 A:HIS145 1.9 22.6 1.0
NE2 C:HIS280 2.0 24.7 1.0
NE2 C:HIS235 2.0 20.5 1.0
O A:HOH439 2.8 27.6 1.0
CE1 C:HIS235 2.9 20.1 1.0
CE1 C:HIS280 2.9 24.4 1.0
CD2 A:HIS145 2.9 23.1 1.0
CE1 A:HIS145 2.9 22.6 1.0
CD2 C:HIS280 3.0 23.1 1.0
CD2 C:HIS235 3.2 18.0 1.0
SD C:MET278 3.9 26.0 1.0
ND1 C:HIS280 4.0 23.6 1.0
ND1 A:HIS145 4.0 22.3 1.0
CG A:HIS145 4.0 19.6 1.0
ND1 C:HIS235 4.0 20.0 1.0
CG C:HIS280 4.1 21.8 1.0
O C:HOH400 4.1 47.7 1.0
CG C:HIS235 4.2 18.4 1.0
CU C:CU302 4.4 17.8 0.4
CD2 C:HIS233 4.4 19.1 1.0
NE2 A:HIS102 4.7 19.8 1.0
CG C:MET278 4.8 23.3 1.0
CB C:MET278 4.8 21.2 1.0
CD2 A:HIS102 4.9 17.9 1.0
NE2 C:HIS233 4.9 20.2 1.0

Reference:

I.S.Macpherson, W.C.Lee, T.I.Liang, M.E.P.Murphy. A Trimeric Multicopper Oxidase Provides An Evolutionary Link to Nitrite Reductase To Be Published.
Page generated: Sun Dec 13 11:09:48 2020

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