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Copper in PDB 7rab: Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice

Enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice

All present enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice, PDB code: 7rab was solved by M.M.Georgiadis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.06 / 1.92
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 224.241, 224.241, 224.241, 90, 90, 90
R / Rfree (%) 27 / 29.8

Other elements in 7rab:

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice (pdb code 7rab). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice, PDB code: 7rab:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in 7rab

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Copper binding site 1 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:27.0
occ:0.23
 ND1 A:HIS139 1.9 23.3 1.0
ND1 A:HIS192 2.0 24.3 1.0
SG A:CYS184 2.3 24.4 1.0
CE1 A:HIS139 2.9 24.3 1.0
CG A:HIS139 2.9 25.4 1.0
CG A:HIS192 3.0 25.9 1.0
CE1 A:HIS192 3.0 23.8 1.0
CD1 A:LEU197 3.1 17.9 1.0
CB A:HIS139 3.3 22.9 1.0
CB A:HIS192 3.3 22.2 1.0
CA A:HIS139 3.4 21.4 1.0
O A:PRO138 3.5 24.9 1.0
CB A:CYS184 3.5 23.4 1.0
CB A:ALA186 3.9 27.4 1.0
NE2 A:HIS139 4.0 24.3 1.0
CD2 A:HIS139 4.0 26.6 1.0
NE2 A:HIS192 4.0 30.1 1.0
CD2 A:HIS192 4.0 26.6 1.0
C A:PRO138 4.3 23.7 1.0
N A:HIS139 4.3 18.7 1.0
N A:THR140 4.4 20.9 1.0
C A:HIS139 4.5 24.6 1.0
CA A:HIS192 4.5 22.3 1.0
CE3 A:TRP108 4.6 22.6 1.0
CG A:LEU197 4.6 24.2 1.0
CZ3 A:TRP108 4.8 27.7 1.0
CA A:CYS184 4.9 20.0 1.0

Copper binding site 2 out of 16 in 7rab

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Copper binding site 2 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:64.7
occ:0.46
 NE2 A:HIS144 1.9 26.9 1.0
NE2 A:HIS183 2.1 28.4 1.0
CE1 A:HIS144 2.7 28.3 1.0
CD2 A:HIS183 2.8 24.8 1.0
CD2 A:HIS144 3.1 25.5 1.0
CE1 A:HIS183 3.2 24.1 1.0
ND1 A:HIS144 3.9 28.1 1.0
CG A:HIS183 4.1 23.0 1.0
CG A:HIS144 4.1 26.5 1.0
CD2 A:HIS142 4.2 25.2 1.0
ND1 A:HIS183 4.2 24.4 1.0
NE2 A:HIS142 4.5 25.6 1.0
CA A:GLY320 4.6 23.1 1.0
CD1 A:LEU181 4.7 22.8 1.0

Copper binding site 3 out of 16 in 7rab

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Copper binding site 3 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:27.4
occ:0.22
 ND1 B:HIS139 1.8 25.8 1.0
ND1 B:HIS192 2.1 27.7 1.0
SG B:CYS184 2.3 27.1 1.0
CG B:HIS139 2.8 27.9 1.0
CE1 B:HIS139 2.8 26.3 1.0
CG B:HIS192 3.0 22.8 1.0
CE1 B:HIS192 3.1 28.0 1.0
CD1 B:LEU197 3.2 24.7 1.0
CB B:HIS139 3.2 27.2 1.0
CB B:HIS192 3.3 23.9 1.0
CA B:HIS139 3.3 28.5 1.0
O B:PRO138 3.4 27.7 1.0
CB B:CYS184 3.5 25.2 1.0
CB B:ALA186 3.8 29.5 1.0
NE2 B:HIS139 3.9 28.6 1.0
CD2 B:HIS139 4.0 26.4 1.0
CD2 B:HIS192 4.1 26.1 1.0
NE2 B:HIS192 4.1 32.8 1.0
C B:PRO138 4.2 29.4 1.0
N B:HIS139 4.2 23.6 1.0
N B:THR140 4.4 27.8 1.0
C B:HIS139 4.4 29.9 1.0
CA B:HIS192 4.5 25.9 1.0
CE3 B:TRP108 4.5 25.8 1.0
CG B:LEU197 4.6 21.9 1.0
CZ3 B:TRP108 4.8 27.4 1.0
CA B:CYS184 4.9 23.4 1.0

Copper binding site 4 out of 16 in 7rab

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Copper binding site 4 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:75.2
occ:0.51
 NE2 B:HIS144 1.9 31.6 1.0
NE2 B:HIS183 2.0 27.6 1.0
NE2 G:HIS342 2.3 29.8 1.0
CD2 B:HIS183 2.7 23.8 1.0
CE1 B:HIS144 2.9 27.8 1.0
CD2 B:HIS144 3.0 25.2 1.0
CE1 G:HIS342 3.0 30.2 1.0
CE1 B:HIS183 3.2 23.9 1.0
CD2 G:HIS342 3.4 25.2 1.0
CG B:HIS183 4.0 25.3 1.0
ND1 B:HIS144 4.0 30.2 1.0
CG B:HIS144 4.1 27.3 1.0
ND1 B:HIS183 4.2 26.5 1.0
ND1 G:HIS342 4.2 26.4 1.0
CD2 B:HIS142 4.3 28.7 1.0
NE2 G:HIS290 4.3 26.2 1.0
CD2 G:HIS290 4.4 26.8 1.0
CD1 B:LEU181 4.4 21.4 1.0
CG G:HIS342 4.4 27.0 1.0
CA B:GLY320 4.5 25.5 1.0
NE2 B:HIS142 4.7 32.0 1.0
CG B:LEU181 4.9 25.8 1.0
CE1 G:HIS290 4.9 26.6 1.0

Copper binding site 5 out of 16 in 7rab

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Copper binding site 5 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:29.9
occ:0.22
 ND1 C:HIS139 1.8 25.4 1.0
ND1 C:HIS192 2.1 24.4 1.0
SG C:CYS184 2.3 26.8 1.0
CE1 C:HIS139 2.8 27.9 1.0
CG C:HIS139 2.9 30.8 1.0
CG C:HIS192 2.9 22.7 1.0
CE1 C:HIS192 3.0 27.5 1.0
CD1 C:LEU197 3.1 27.1 1.0
CB C:HIS192 3.3 22.4 1.0
CB C:HIS139 3.3 29.3 1.0
CA C:HIS139 3.4 27.7 1.0
O C:PRO138 3.4 26.2 1.0
CB C:CYS184 3.5 26.1 1.0
CB C:ALA186 3.7 29.1 1.0
NE2 C:HIS139 3.9 29.5 1.0
CD2 C:HIS139 4.0 24.8 1.0
CD2 C:HIS192 4.0 24.2 1.0
NE2 C:HIS192 4.1 30.3 1.0
C C:PRO138 4.2 31.7 1.0
N C:HIS139 4.3 24.9 1.0
N C:THR140 4.4 26.0 1.0
CA C:HIS192 4.5 23.6 1.0
C C:HIS139 4.5 30.6 1.0
CE3 C:TRP108 4.5 23.0 1.0
CG C:LEU197 4.6 21.9 1.0
CZ3 C:TRP108 4.8 26.0 1.0
CA C:CYS184 4.9 23.5 1.0

Copper binding site 6 out of 16 in 7rab

Go back to Copper Binding Sites List in 7rab
Copper binding site 6 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:71.5
occ:0.50
 NE2 C:HIS144 1.9 33.1 1.0
NE2 C:HIS183 2.0 27.4 1.0
NE2 H:HIS342 2.5 31.4 1.0
CD2 C:HIS183 2.5 26.3 1.0
CD2 C:HIS144 2.8 27.2 1.0
CE1 C:HIS144 2.9 29.8 1.0
CE1 C:HIS183 3.2 24.9 1.0
CE1 H:HIS342 3.2 29.9 1.0
CD2 H:HIS342 3.6 25.7 1.0
CG C:HIS183 3.8 25.7 1.0
ND1 C:HIS144 4.0 32.3 1.0
CG C:HIS144 4.0 26.0 1.0
ND1 C:HIS183 4.1 26.1 1.0
CD1 C:LEU181 4.2 22.1 1.0
CD2 C:HIS142 4.2 26.0 1.0
ND1 H:HIS342 4.5 27.2 1.0
NE2 H:HIS290 4.5 28.8 1.0
CA C:GLY320 4.6 24.9 1.0
NE2 C:HIS142 4.6 31.6 1.0
CG C:LEU181 4.6 28.5 1.0
CG H:HIS342 4.7 26.7 1.0
CD2 H:HIS290 4.7 27.4 1.0
CD2 C:LEU181 4.9 31.4 1.0

Copper binding site 7 out of 16 in 7rab

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Copper binding site 7 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:54.7
occ:0.34
 ND1 D:HIS139 1.9 27.1 1.0
ND1 D:HIS192 2.1 25.2 1.0
SG D:CYS184 2.3 24.3 1.0
CE1 D:HIS139 2.9 24.9 1.0
CG D:HIS139 2.9 30.0 1.0
CG D:HIS192 2.9 25.5 1.0
CE1 D:HIS192 3.0 22.4 1.0
CD1 D:LEU197 3.1 21.6 1.0
CB D:HIS192 3.3 22.7 1.0
CB D:HIS139 3.3 22.8 1.0
CB D:CYS184 3.4 23.6 1.0
CA D:HIS139 3.4 18.8 1.0
O D:PRO138 3.5 23.9 1.0
CB D:ALA186 3.8 28.5 1.0
NE2 D:HIS139 4.0 24.6 1.0
CD2 D:HIS192 4.0 25.8 1.0
NE2 D:HIS192 4.0 27.3 1.0
CD2 D:HIS139 4.0 28.2 1.0
C D:PRO138 4.3 27.0 1.0
N D:HIS139 4.4 18.1 1.0
N D:THR140 4.4 20.9 1.0
CA D:HIS192 4.4 22.9 1.0
C D:HIS139 4.5 26.1 1.0
CE3 D:TRP108 4.5 22.7 1.0
CG D:LEU197 4.6 25.2 1.0
CA D:CYS184 4.8 20.9 1.0
CZ3 D:TRP108 4.8 26.5 1.0
CB D:LEU197 5.0 20.7 1.0

Copper binding site 8 out of 16 in 7rab

Go back to Copper Binding Sites List in 7rab
Copper binding site 8 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu402

b:71.8
occ:0.50
 NE2 D:HIS144 1.9 28.6 1.0
NE2 D:HIS183 2.1 26.8 1.0
NE2 B:HIS342 2.2 31.9 1.0
CE1 D:HIS144 2.8 28.4 1.0
CD2 D:HIS183 2.9 27.4 1.0
CE1 B:HIS342 3.0 23.8 1.0
CD2 D:HIS144 3.1 27.2 1.0
CE1 D:HIS183 3.2 28.4 1.0
CD2 B:HIS342 3.3 25.2 1.0
O D:HOH530 3.9 36.9 1.0
ND1 D:HIS144 4.0 30.2 1.0
CD2 D:HIS142 4.1 23.9 1.0
NE2 B:HIS290 4.1 24.3 1.0
CG D:HIS183 4.1 24.0 1.0
CG D:HIS144 4.1 26.2 1.0
ND1 B:HIS342 4.2 23.2 1.0
CD2 B:HIS290 4.2 26.7 1.0
ND1 D:HIS183 4.2 26.2 1.0
CG B:HIS342 4.3 23.8 1.0
NE2 D:HIS142 4.3 27.1 1.0
CD1 D:LEU181 4.7 25.0 1.0
CE1 B:HIS290 4.7 23.1 1.0
CA D:GLY320 4.7 21.1 1.0
CG B:HIS290 4.9 23.1 1.0

Copper binding site 9 out of 16 in 7rab

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Copper binding site 9 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:28.9
occ:0.23
 ND1 E:HIS139 2.0 24.1 1.0
ND1 E:HIS192 2.1 24.7 1.0
SG E:CYS184 2.2 25.1 1.0
CG E:HIS139 2.9 25.5 1.0
CG E:HIS192 3.0 26.4 1.0
CE1 E:HIS139 3.0 25.1 1.0
CE1 E:HIS192 3.1 22.9 1.0
CD1 E:LEU197 3.1 20.6 1.0
CB E:HIS139 3.2 23.3 1.0
CB E:HIS192 3.3 24.8 1.0
CB E:CYS184 3.3 25.4 1.0
CA E:HIS139 3.4 20.6 1.0
O E:PRO138 3.5 24.3 1.0
CB E:ALA186 3.9 26.5 1.0
CD2 E:HIS192 4.1 26.0 1.0
CD2 E:HIS139 4.1 27.7 1.0
NE2 E:HIS139 4.1 21.6 1.0
NE2 E:HIS192 4.1 24.7 1.0
C E:PRO138 4.3 26.1 1.0
N E:HIS139 4.3 19.6 1.0
N E:THR140 4.3 24.3 1.0
C E:HIS139 4.4 25.3 1.0
CA E:HIS192 4.4 24.7 1.0
CG E:LEU197 4.6 26.2 1.0
CE3 E:TRP108 4.6 25.2 1.0
CA E:CYS184 4.7 22.3 1.0
CZ3 E:TRP108 4.8 26.0 1.0
CB E:LEU197 5.0 21.9 1.0

Copper binding site 10 out of 16 in 7rab

Go back to Copper Binding Sites List in 7rab
Copper binding site 10 out of 16 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice


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 A Dodecameric Multicopper Oxidase From M. Hydrothermalis in A Cubic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:64.5
occ:0.37
 NE2 E:HIS144 1.9 31.1 1.0
NE2 E:HIS183 2.1 27.5 1.0
NE2 C:HIS342 2.1 29.3 1.0
CE1 E:HIS144 2.8 30.5 1.0
CE1 C:HIS342 3.0 26.0 1.0
CD2 E:HIS183 3.0 29.3 1.0
CD2 E:HIS144 3.1 28.4 1.0
CE1 E:HIS183 3.1 29.0 1.0
CD2 C:HIS342 3.2 25.6 1.0
NE2 C:HIS290 3.8 27.8 1.0
CD2 E:HIS142 3.9 23.8 1.0
ND1 E:HIS144 4.0 33.3 1.0
CD2 C:HIS290 4.0 27.2 1.0
ND1 C:HIS342 4.1 23.7 1.0
CG E:HIS144 4.1 29.2 1.0
NE2 E:HIS142 4.2 27.3 1.0
CG E:HIS183 4.2 23.0 1.0
ND1 E:HIS183 4.2 28.1 1.0
CG C:HIS342 4.3 26.4 1.0
CE1 C:HIS290 4.5 25.3 1.0
CG C:HIS290 4.7 23.3 1.0
CA E:GLY320 4.8 23.6 1.0
CD1 E:LEU181 4.9 28.2 1.0
ND1 C:HIS290 5.0 23.3 1.0

Reference:

J.L.Paavola, U.Battistin, C.M.Ogata, M.M.Georgiadis. Crystal Structures of A Dodecameric Multicopper Oxidase From Marinithermus Hydrothermalis. Acta Crystallogr D Struct V. 77 1336 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 34605435
DOI: 10.1107/S205979832100944X
Page generated: Wed Jul 31 09:02:38 2024

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