Copper in PDB 7rac: Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice

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

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

Resolution Low / High (Å)	61.04 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	169.304, 176.193, 176.952, 90, 90, 90
R / Rfree (%)	13.9 / 17.7

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

Calcium

(Ca)

17 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice (pdb code 7rac). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice, PDB code: 7rac:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:22.9 occ:0.43 NE2 A:HIS144 2.0 16.6 1.0 NE2 A:HIS183 2.1 19.7 1.0 NE2 B:HIS342 2.1 22.3 1.0 CE1 A:HIS144 2.7 16.1 1.0 CD2 A:HIS183 2.9 15.1 1.0 CE1 B:HIS342 2.9 17.0 1.0 CE1 A:HIS183 3.2 19.2 1.0 CD2 B:HIS342 3.2 13.9 1.0 CD2 A:HIS144 3.2 14.7 1.0 O A:HOH618 3.3 24.6 1.0 NE2 B:HIS290 3.9 20.3 1.0 ND1 A:HIS144 4.0 22.9 1.0 CD2 A:HIS142 4.0 16.2 1.0 CD2 B:HIS290 4.0 17.9 1.0 ND1 B:HIS342 4.1 16.6 1.0 CG A:HIS183 4.1 18.2 1.0 ND1 A:HIS183 4.2 21.1 1.0 CG A:HIS144 4.2 15.3 1.0 CG B:HIS342 4.2 20.1 1.0 NE2 A:HIS142 4.3 18.9 1.0 CE1 B:HIS290 4.7 17.3 1.0 CA A:GLY320 4.8 12.6 1.0 CG B:HIS290 4.8 18.7 1.0 CD1 A:LEU181 4.9 11.5 1.0

Copper binding site 2 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:11.5 occ:0.17 ND1 A:HIS139 1.8 17.3 1.0 ND1 A:HIS192 2.0 18.2 1.0 SG A:CYS184 2.3 17.4 1.0 CE1 A:HIS139 2.8 16.0 1.0 CG A:HIS192 2.9 17.4 1.0 CG A:HIS139 2.9 12.0 1.0 CE1 A:HIS192 3.1 16.2 1.0 CD1 A:LEU197 3.1 10.7 1.0 CB A:HIS192 3.2 15.3 1.0 CB A:HIS139 3.3 11.3 1.0 O A:PRO138 3.4 20.1 1.0 CA A:HIS139 3.4 19.3 1.0 CB A:CYS184 3.5 12.2 1.0 NE2 A:HIS139 3.9 15.0 1.0 CB A:ALA186 3.9 16.0 1.0 CD2 A:HIS139 4.0 12.3 1.0 CD2 A:HIS192 4.0 15.4 1.0 NE2 A:HIS192 4.1 17.8 1.0 C A:PRO138 4.2 19.6 1.0 N A:HIS139 4.3 16.3 1.0 CA A:HIS192 4.4 17.9 1.0 N A:THR140 4.5 11.4 1.0 CE3 A:TRP108 4.5 14.3 1.0 C A:HIS139 4.5 13.2 1.0 CG A:LEU197 4.6 18.3 1.0 CZ3 A:TRP108 4.8 14.7 1.0 CA A:CYS184 4.9 11.4 1.0

Copper binding site 3 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:22.6 occ:0.43 NE2 B:HIS144 2.0 20.4 1.0 NE2 B:HIS183 2.0 19.9 1.0 NE2 C:HIS342 2.1 26.2 1.0 CE1 B:HIS144 2.7 18.5 1.0 CD2 B:HIS183 2.8 16.3 1.0 CE1 C:HIS342 2.9 18.1 1.0 CE1 B:HIS183 3.1 20.1 1.0 CD2 B:HIS144 3.2 18.4 1.0 CD2 C:HIS342 3.3 16.5 1.0 O B:HOH618 3.3 29.1 1.0 ND1 B:HIS144 3.9 22.9 1.0 CG B:HIS183 4.0 18.2 1.0 ND1 C:HIS342 4.1 19.4 1.0 NE2 C:HIS290 4.1 14.9 1.0 CD2 B:HIS142 4.1 21.8 1.0 CD2 C:HIS290 4.1 17.4 1.0 ND1 B:HIS183 4.1 14.1 1.0 CG B:HIS144 4.2 19.2 1.0 CG C:HIS342 4.3 17.4 1.0 NE2 B:HIS142 4.4 17.4 1.0 CA B:GLY320 4.7 13.2 1.0 CD1 B:LEU181 4.8 15.3 1.0 CE1 C:HIS290 4.8 12.9 1.0 CG C:HIS290 4.9 16.6 1.0

Copper binding site 4 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu404 b:16.2 occ:0.20 ND1 B:HIS139 2.0 17.1 1.0 ND1 B:HIS192 2.0 16.8 1.0 SG B:CYS184 2.3 14.6 1.0 CG B:HIS192 2.9 16.3 1.0 CG B:HIS139 2.9 12.4 1.0 CE1 B:HIS139 3.0 15.6 1.0 CE1 B:HIS192 3.0 20.7 1.0 CD1 B:LEU197 3.1 11.6 1.0 CB B:HIS192 3.2 14.9 1.0 CB B:HIS139 3.2 13.6 1.0 CA B:HIS139 3.4 15.3 1.0 O B:PRO138 3.4 16.4 1.0 CB B:CYS184 3.4 13.5 1.0 CB B:ALA186 3.9 16.6 1.0 CD2 B:HIS192 4.0 19.2 1.0 CD2 B:HIS139 4.0 12.2 1.0 NE2 B:HIS139 4.0 15.0 1.0 NE2 B:HIS192 4.1 21.8 1.0 C B:PRO138 4.2 18.6 1.0 N B:HIS139 4.3 16.4 1.0 CA B:HIS192 4.4 15.8 1.0 N B:THR140 4.4 13.9 1.0 C B:HIS139 4.5 18.0 1.0 CE3 B:TRP108 4.5 13.9 1.0 CG B:LEU197 4.6 13.8 1.0 CZ3 B:TRP108 4.8 16.4 1.0 CA B:CYS184 4.8 12.8 1.0

Copper binding site 5 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu403 b:22.1 occ:0.41 NE2 C:HIS144 2.0 20.6 1.0 NE2 A:HIS342 2.0 23.6 1.0 NE2 C:HIS183 2.1 24.1 1.0 CE1 C:HIS144 2.8 17.9 1.0 CE1 A:HIS342 2.8 23.2 1.0 CD2 C:HIS183 2.9 17.6 1.0 CD2 C:HIS144 3.2 18.1 1.0 CE1 C:HIS183 3.2 19.1 1.0 CD2 A:HIS342 3.2 20.3 1.0 O A:HOH622 3.4 25.2 1.0 ND1 C:HIS144 4.0 25.1 1.0 ND1 A:HIS342 4.0 23.5 1.0 NE2 A:HIS290 4.0 19.7 1.0 CD2 A:HIS290 4.1 17.9 1.0 CD2 C:HIS142 4.1 14.4 1.0 CG C:HIS183 4.1 16.6 1.0 CG C:HIS144 4.2 19.5 1.0 CG A:HIS342 4.2 17.4 1.0 ND1 C:HIS183 4.2 17.8 1.0 NE2 C:HIS142 4.4 20.5 1.0 CA C:GLY320 4.7 10.4 1.0 CE1 A:HIS290 4.7 16.3 1.0 CG A:HIS290 4.8 15.8 1.0 CD1 C:LEU181 4.8 15.0 1.0

Copper binding site 6 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu404 b:14.1 occ:0.18 ND1 C:HIS139 1.9 16.2 1.0 ND1 C:HIS192 2.1 15.8 1.0 SG C:CYS184 2.4 18.4 1.0 CE1 C:HIS139 2.8 18.6 1.0 CG C:HIS139 2.9 17.6 1.0 CG C:HIS192 2.9 20.1 1.0 CD1 C:LEU197 3.0 10.6 1.0 CE1 C:HIS192 3.0 15.5 1.0 CB C:HIS192 3.2 14.1 1.0 CB C:HIS139 3.3 13.4 1.0 CA C:HIS139 3.4 15.2 1.0 CB C:CYS184 3.5 12.2 1.0 O C:PRO138 3.5 18.9 1.0 NE2 C:HIS139 3.9 17.4 1.0 CD2 C:HIS139 3.9 17.8 1.0 CB C:ALA186 4.0 19.1 1.0 CD2 C:HIS192 4.0 20.4 1.0 NE2 C:HIS192 4.1 16.4 1.0 C C:PRO138 4.3 21.6 1.0 N C:HIS139 4.3 15.3 1.0 CA C:HIS192 4.4 16.6 1.0 CE3 C:TRP108 4.4 15.6 1.0 CG C:LEU197 4.5 14.9 1.0 N C:THR140 4.5 14.9 1.0 C C:HIS139 4.5 20.1 1.0 CZ3 C:TRP108 4.7 17.4 1.0 CA C:CYS184 4.9 15.8 1.0 CB C:LEU197 5.0 14.9 1.0

Copper binding site 7 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu403 b:23.9 occ:0.41 NE2 D:HIS183 2.0 20.9 1.0 NE2 D:HIS144 2.0 17.0 1.0 NE2 F:HIS342 2.1 26.8 1.0 CE1 D:HIS144 2.8 16.9 1.0 CE1 F:HIS342 2.8 18.2 1.0 CD2 D:HIS183 2.8 19.8 1.0 CE1 D:HIS183 3.1 18.7 1.0 CD2 D:HIS144 3.2 12.5 1.0 CD2 F:HIS342 3.3 17.9 1.0 O D:HOH588 3.5 28.7 1.0 ND1 D:HIS144 4.0 17.2 1.0 ND1 F:HIS342 4.0 16.9 1.0 CG D:HIS183 4.0 18.1 1.0 CD2 D:HIS142 4.1 19.0 1.0 NE2 F:HIS290 4.1 16.9 1.0 ND1 D:HIS183 4.1 22.4 1.0 CD2 F:HIS290 4.1 18.8 1.0 CG D:HIS144 4.2 15.6 1.0 CG F:HIS342 4.3 22.9 1.0 NE2 D:HIS142 4.4 18.0 1.0 CA D:GLY320 4.8 14.0 1.0 CD1 D:LEU181 4.8 18.6 1.0 CE1 F:HIS290 4.9 15.9 1.0 CG F:HIS290 5.0 17.7 1.0

Copper binding site 8 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu404 b:17.0 occ:0.25 ND1 D:HIS139 1.9 16.8 1.0 ND1 D:HIS192 2.0 18.7 1.0 SG D:CYS184 2.3 15.2 1.0 CG D:HIS192 2.8 20.9 1.0 CE1 D:HIS139 2.9 17.4 1.0 CG D:HIS139 2.9 17.1 1.0 CE1 D:HIS192 3.0 16.6 1.0 CB D:HIS192 3.1 13.9 1.0 CD1 D:LEU197 3.2 11.1 1.0 CB D:HIS139 3.3 16.3 1.0 O D:PRO138 3.4 15.3 1.0 CA D:HIS139 3.5 14.3 1.0 CB D:CYS184 3.5 13.7 1.0 CB D:ALA186 3.7 19.8 1.0 CD2 D:HIS192 3.9 18.3 1.0 NE2 D:HIS139 4.0 14.5 1.0 NE2 D:HIS192 4.0 21.8 1.0 CD2 D:HIS139 4.0 15.5 1.0 C D:PRO138 4.2 14.4 1.0 CA D:HIS192 4.3 17.7 1.0 N D:HIS139 4.3 16.8 1.0 CE3 D:TRP108 4.4 17.3 1.0 N D:THR140 4.6 19.1 1.0 C D:HIS139 4.6 17.3 1.0 CZ3 D:TRP108 4.7 16.8 1.0 CG D:LEU197 4.7 18.9 1.0 CA D:CYS184 4.9 15.4 1.0 N D:ALA186 5.0 22.8 1.0 CA D:ALA186 5.0 19.5 1.0

Copper binding site 9 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu404 b:20.9 occ:0.32 NE2 E:HIS144 2.0 20.3 1.0 NE2 J:HIS342 2.0 24.3 1.0 NE2 E:HIS183 2.1 22.6 1.0 CE1 E:HIS144 2.8 22.0 1.0 CD2 E:HIS183 2.8 17.8 1.0 CE1 J:HIS342 2.9 16.9 1.0 CD2 J:HIS342 3.1 19.8 1.0 CE1 E:HIS183 3.2 19.5 1.0 CD2 E:HIS144 3.2 23.2 1.0 O E:HOH551 3.8 31.0 1.0 ND1 E:HIS144 4.0 27.0 1.0 ND1 J:HIS342 4.0 20.9 1.0 CG E:HIS183 4.1 15.8 1.0 CD2 E:HIS142 4.1 18.6 1.0 NE2 J:HIS290 4.1 22.1 1.0 ND1 E:HIS183 4.2 19.9 1.0 CD2 J:HIS290 4.2 22.8 1.0 CG J:HIS342 4.2 20.7 1.0 CG E:HIS144 4.2 19.6 1.0 NE2 E:HIS142 4.4 18.4 1.0 CA E:GLY320 4.7 13.4 1.0 CE1 J:HIS290 4.8 19.3 1.0 CD1 E:LEU181 4.9 15.9 1.0 CG J:HIS290 4.9 25.3 1.0

Copper binding site 10 out of 24 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic 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 An Orthorhombic Lattice within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu405 b:22.5 occ:0.24 ND1 E:HIS139 1.9 18.7 1.0 ND1 E:HIS192 2.1 17.9 1.0 SG E:CYS184 2.3 16.3 1.0 CE1 E:HIS139 2.9 19.8 1.0 CG E:HIS139 2.9 20.4 1.0 CG E:HIS192 2.9 20.9 1.0 CD1 E:LEU197 3.1 15.1 1.0 CB E:HIS192 3.1 13.7 1.0 CE1 E:HIS192 3.1 19.2 1.0 CB E:HIS139 3.2 15.8 1.0 O E:PRO138 3.4 19.8 1.0 CA E:HIS139 3.4 17.7 1.0 CB E:CYS184 3.5 17.6 1.0 CB E:ALA186 3.9 19.0 1.0 NE2 E:HIS139 3.9 18.0 1.0 CD2 E:HIS139 4.0 17.5 1.0 CD2 E:HIS192 4.0 20.4 1.0 NE2 E:HIS192 4.1 18.5 1.0 C E:PRO138 4.2 19.4 1.0 N E:HIS139 4.2 18.2 1.0 CA E:HIS192 4.3 16.8 1.0 CE3 E:TRP108 4.4 14.8 1.0 C E:HIS139 4.5 23.3 1.0 N E:THR140 4.5 16.6 1.0 CG E:LEU197 4.6 14.6 1.0 CZ3 E:TRP108 4.7 17.9 1.0 CA E:CYS184 4.9 13.6 1.0

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