Copper in PDB 9f8x: Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase

All present enzymatic activity of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase:
1.7.2.4;

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x was solved by O.Einsle, A.Pomowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.50 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	65.26, 69.375, 153.188, 81.38, 77.92, 88.61
R / Rfree (%)	13 / 15.2

The structure of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase also contains other interesting chemical elements:

Calcium	(Ca)	8 atoms
Sodium	(Na)	3 atoms
Chlorine	(Cl)	4 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 Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase (pdb code 9f8x). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase, PDB code: 9f8x:
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 Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu701 b:19.8 occ:1.00 CU1 A:CUA701 0.0 19.8 1.0 SG A:CYS614 2.2 13.4 1.0 SG A:CYS618 2.3 14.6 1.0 SD A:MET625 2.3 16.2 1.0 CU2 A:CUA701 2.4 22.1 1.0 CB A:CYS614 3.1 14.4 1.0 CE A:MET625 3.2 18.7 1.0 CB A:CYS618 3.5 14.7 1.0 CG A:MET625 3.7 15.2 1.0 O A:TRP616 3.8 15.3 1.0 CB A:MET625 4.0 14.7 1.0 ND1 A:HIS622 4.2 13.9 1.0 CB A:ALA548 4.5 17.0 1.0 CB A:HIS579 4.5 14.7 1.0 CG A:HIS579 4.5 15.7 1.0 CD2 A:HIS579 4.5 16.7 1.0 CA A:CYS614 4.5 12.9 1.0 CA A:HIS579 4.6 13.1 1.0 CA A:CYS618 4.7 14.5 1.0 N A:CYS618 4.9 15.7 1.0 N A:GLY580 4.9 14.1 1.0 CA A:ALA548 5.0 15.5 1.0 CE1 A:HIS622 5.0 16.7 1.0 C A:CYS614 5.0 11.7 1.0

Copper binding site 2 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu701 b:22.1 occ:1.00 CU2 A:CUA701 0.0 22.1 1.0 ND1 A:HIS622 1.9 13.9 1.0 SG A:CYS618 2.3 14.6 1.0 CU1 A:CUA701 2.4 19.8 1.0 O A:TRP616 2.5 15.3 1.0 SG A:CYS614 2.8 13.4 1.0 CE1 A:HIS622 2.9 16.7 1.0 CG A:HIS622 3.0 15.6 1.0 N A:CYS618 3.3 15.7 1.0 CB A:CYS618 3.3 14.7 1.0 CB A:HIS622 3.4 15.7 1.0 C A:TRP616 3.5 14.9 1.0 CB A:CYS614 3.8 14.4 1.0 CA A:CYS618 3.8 14.5 1.0 CA A:HIS622 3.8 14.4 1.0 CA A:PHE617 3.9 14.1 1.0 C A:PHE617 3.9 14.9 1.0 NE2 A:HIS622 4.0 18.9 1.0 CD2 A:HIS622 4.0 17.9 1.0 N A:PHE617 4.1 14.9 1.0 O A:HIS622 4.3 14.4 1.0 O A:CYS614 4.4 12.7 1.0 SD A:MET625 4.4 16.2 1.0 N A:TRP616 4.4 14.1 1.0 C A:HIS622 4.5 14.1 1.0 CA A:TRP616 4.6 14.8 1.0 C A:CYS614 4.6 11.7 1.0 C A:CYS618 4.7 16.8 1.0 N A:HIS619 4.7 14.8 1.0 CB A:MET625 4.8 14.7 1.0 CA A:CYS614 4.8 12.9 1.0 O A:HOH862 4.9 19.4 1.0 N A:HIS622 5.0 15.2 1.0

Copper binding site 3 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:22.2 occ:1.00 CU1 A:CUK702 0.0 22.2 1.0 NE2 A:HIS378 2.1 12.8 1.0 NE2 A:HIS323 2.1 15.8 1.0 S1 A:CUK702 2.4 19.9 1.0 S2 A:CUK702 2.4 22.2 1.0 CE1 A:HIS378 2.9 13.9 1.0 CE1 A:HIS323 3.1 18.3 1.0 CU4 A:CUK702 3.1 24.3 1.0 CD2 A:HIS323 3.1 14.8 1.0 CD2 A:HIS378 3.1 14.7 1.0 CU3 A:CUK702 3.4 18.2 1.0 NE2 A:HIS429 3.7 13.3 1.0 CD2 A:HIS429 3.8 14.2 1.0 ND1 A:HIS378 4.1 13.2 1.0 ND1 A:HIS323 4.2 16.1 1.0 CG A:HIS323 4.2 15.0 1.0 CG A:HIS378 4.2 14.8 1.0 CE1 A:HIS429 4.3 14.9 1.0 CU2 A:CUK702 4.5 21.8 1.0 CE2 B:PHE617 4.6 19.9 1.0 ND2 A:ASN242 4.6 18.0 1.0 CG A:HIS429 4.6 14.3 1.0 ND1 A:HIS429 4.9 14.4 1.0 N A:HIS429 4.9 13.2 1.0

Copper binding site 4 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:21.8 occ:1.00 CU2 A:CUK702 0.0 21.8 1.0 ND1 A:HIS132 2.0 16.9 1.0 NE2 A:HIS181 2.1 17.0 1.0 S1 A:CUK702 2.2 19.9 1.0 CU4 A:CUK702 2.6 24.3 1.0 CU3 A:CUK702 2.6 18.2 1.0 CE1 A:HIS132 2.9 18.7 1.0 CE1 A:HIS181 3.1 19.1 1.0 CD2 A:HIS181 3.1 18.3 1.0 CG A:HIS132 3.2 15.5 1.0 NE2 A:HIS133 3.4 14.5 1.0 ND1 A:HIS490 3.4 17.8 1.0 CE1 A:HIS133 3.5 14.2 1.0 O B:HOH1422 3.6 26.0 1.0 CB A:HIS132 3.6 13.9 1.0 CE1 A:HIS490 3.9 19.1 1.0 NE2 A:HIS132 4.0 16.6 1.0 CG A:HIS490 4.1 15.3 1.0 ND1 A:HIS181 4.2 18.2 1.0 CD2 A:HIS132 4.2 19.5 1.0 CG A:HIS181 4.2 17.9 1.0 CB A:HIS490 4.4 15.6 1.0 CU1 A:CUK702 4.5 22.2 1.0 CD2 A:HIS133 4.5 14.2 1.0 NE2 A:HIS429 4.5 13.3 1.0 ND1 A:HIS133 4.6 13.5 1.0 NE2 A:HIS490 4.7 17.2 1.0 CD2 A:HIS490 4.8 16.7 1.0 CE B:MET623 4.9 22.6 1.0

Copper binding site 5 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:18.2 occ:1.00 CU3 A:CUK702 0.0 18.2 1.0 NE2 A:HIS429 2.0 13.3 1.0 NE2 A:HIS133 2.1 14.5 1.0 S1 A:CUK702 2.2 19.9 1.0 CU2 A:CUK702 2.6 21.8 1.0 CU4 A:CUK702 2.8 24.3 1.0 CE1 A:HIS429 2.9 14.9 1.0 CE1 A:HIS133 3.0 14.2 1.0 CD2 A:HIS133 3.1 14.2 1.0 CD2 A:HIS429 3.2 14.2 1.0 CU1 A:CUK702 3.4 22.2 1.0 NE2 A:HIS181 3.9 17.0 1.0 OD1 A:ASN242 3.9 18.6 1.0 CE1 A:HIS378 4.0 13.9 1.0 CB A:HIS490 4.0 15.6 1.0 NE2 A:HIS378 4.1 12.8 1.0 ND1 A:HIS429 4.1 14.4 1.0 ND1 A:HIS132 4.1 16.9 1.0 ND1 A:HIS133 4.2 13.5 1.0 CG A:HIS133 4.2 13.8 1.0 CG A:HIS429 4.2 14.3 1.0 O A:HOH1185 4.2 17.4 1.0 ND1 A:HIS490 4.3 17.8 1.0 CE1 A:HIS181 4.3 19.1 1.0 CB A:HIS132 4.3 13.9 1.0 S2 A:CUK702 4.3 22.2 1.0 CG A:HIS490 4.5 15.3 1.0 ND2 A:ASN242 4.6 18.0 1.0 CG A:ASN242 4.6 16.3 1.0 CG A:HIS132 4.8 15.5 1.0 NE2 A:HIS323 4.8 15.8 1.0 O A:HIS132 4.8 14.3 1.0

Copper binding site 6 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:24.3 occ:1.00 CU4 A:CUK702 0.0 24.3 1.0 ND1 A:HIS490 2.1 17.8 1.0 S1 A:CUK702 2.2 19.9 1.0 S2 A:CUK702 2.5 22.2 1.0 CU2 A:CUK702 2.6 21.8 1.0 CU3 A:CUK702 2.8 18.2 1.0 CE1 A:HIS490 3.0 19.1 1.0 CU1 A:CUK702 3.1 22.2 1.0 CG A:HIS490 3.1 15.3 1.0 CB A:HIS490 3.4 15.6 1.0 O B:HOH1422 3.5 26.0 1.0 NE2 A:HIS429 3.7 13.3 1.0 CD2 A:HIS429 3.8 14.2 1.0 ND1 A:HIS132 3.8 16.9 1.0 NE2 A:HIS490 4.1 17.2 1.0 NZ A:LYS450 4.2 20.6 1.0 CD2 A:HIS490 4.2 16.7 1.0 CA A:HIS490 4.3 14.2 1.0 CE1 A:HIS132 4.4 18.7 1.0 CE2 B:PHE617 4.5 19.9 1.0 NE2 A:HIS181 4.5 17.0 1.0 NE2 A:HIS133 4.6 14.5 1.0 CD2 B:PHE617 4.6 19.4 1.0 NE2 A:HIS323 4.7 15.8 1.0 NE2 A:HIS378 4.7 12.8 1.0 CG A:HIS132 4.8 15.5 1.0 CE A:LYS450 4.8 20.0 1.0 CE1 A:HIS429 5.0 14.9 1.0

Copper binding site 7 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu701 b:20.8 occ:1.00 CU1 B:CUA701 0.0 20.8 1.0 SG B:CYS614 2.3 13.4 1.0 ND1 B:HIS579 2.3 22.7 1.0 SG B:CYS618 2.4 15.2 1.0 SD B:MET625 2.5 16.9 1.0 CU2 B:CUA701 2.5 21.3 1.0 CB B:CYS614 3.2 14.8 1.0 CE1 B:HIS579 3.2 23.1 1.0 CE B:MET625 3.3 18.2 1.0 CB B:CYS618 3.4 16.1 1.0 CG B:HIS579 3.4 20.0 1.0 O B:TRP616 3.8 16.5 1.0 CB B:HIS579 3.8 16.1 1.0 CG B:MET625 3.8 15.3 1.0 CA B:HIS579 4.1 14.1 1.0 ND1 B:HIS622 4.4 14.6 1.0 CB B:MET625 4.4 15.4 1.0 NE2 B:HIS579 4.4 20.4 1.0 CD2 B:HIS579 4.5 22.2 1.0 CA B:CYS614 4.6 14.5 1.0 N B:GLY580 4.7 13.6 1.0 CA B:CYS618 4.7 15.0 1.0 O B:THR578 4.7 14.0 1.0 N B:CYS618 4.9 14.7 1.0 C B:TRP616 5.0 15.3 1.0

Copper binding site 8 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu701 b:21.3 occ:1.00 CU2 B:CUA701 0.0 21.3 1.0 ND1 B:HIS622 2.0 14.6 1.0 SG B:CYS618 2.3 15.2 1.0 CU1 B:CUA701 2.5 20.8 1.0 O B:TRP616 2.5 16.5 1.0 SG B:CYS614 2.6 13.4 1.0 CE1 B:HIS622 2.8 17.0 1.0 CG B:HIS622 3.1 16.9 1.0 CB B:CYS618 3.3 16.1 1.0 N B:CYS618 3.4 14.7 1.0 CB B:CYS614 3.5 14.8 1.0 C B:TRP616 3.5 15.3 1.0 CB B:HIS622 3.5 17.6 1.0 CA B:CYS618 3.9 15.0 1.0 CA B:PHE617 4.0 15.1 1.0 CA B:HIS622 4.0 16.8 1.0 NE2 B:HIS622 4.0 18.6 1.0 C B:PHE617 4.0 15.5 1.0 CD2 B:HIS622 4.1 18.1 1.0 SD B:MET625 4.1 16.9 1.0 N B:PHE617 4.2 15.1 1.0 N B:TRP616 4.4 13.5 1.0 O B:HIS622 4.4 16.6 1.0 O B:CYS614 4.4 14.8 1.0 C B:CYS614 4.5 14.3 1.0 CA B:TRP616 4.5 13.1 1.0 ND1 B:HIS579 4.6 22.7 1.0 CA B:CYS614 4.6 14.5 1.0 CB B:MET625 4.7 15.4 1.0 C B:HIS622 4.7 17.7 1.0 C B:CYS618 4.8 17.0 1.0 N B:HIS619 4.9 16.9 1.0 CG B:MET625 4.9 15.3 1.0

Copper binding site 9 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu702 b:22.5 occ:1.00 CU1 B:CUK702 0.0 22.5 1.0 NE2 B:HIS323 2.1 13.7 1.0 NE2 B:HIS378 2.1 13.8 1.0 S1 B:CUK702 2.4 18.8 1.0 S2 B:CUK702 2.4 23.8 1.0 CE1 B:HIS378 3.0 14.1 1.0 CU4 B:CUK702 3.1 24.7 1.0 CE1 B:HIS323 3.1 15.4 1.0 CD2 B:HIS323 3.1 15.0 1.0 CD2 B:HIS378 3.2 13.7 1.0 CU3 B:CUK702 3.4 17.6 1.0 NE2 B:HIS429 3.6 14.9 1.0 CD2 B:HIS429 3.8 14.5 1.0 ND1 B:HIS378 4.2 13.5 1.0 CG B:HIS323 4.2 13.9 1.0 ND1 B:HIS323 4.2 15.4 1.0 CG B:HIS378 4.3 14.6 1.0 CE1 B:HIS429 4.4 14.8 1.0 CU2 B:CUK702 4.5 20.4 1.0 ND2 B:ASN242 4.6 15.8 1.0 CE2 A:PHE617 4.6 20.6 1.0 CG B:HIS429 4.6 13.8 1.0 ND1 B:HIS429 4.8 15.3 1.0 N B:HIS429 5.0 14.0 1.0

Copper binding site 10 out of 24 in the Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Low-Dose Structure of Marinobacter Nauticus Nitrous Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu702 b:20.4 occ:1.00 CU2 B:CUK702 0.0 20.4 1.0 NE2 B:HIS181 2.1 15.8 1.0 ND1 B:HIS132 2.1 16.5 1.0 S1 B:CUK702 2.2 18.8 1.0 CU4 B:CUK702 2.6 24.7 1.0 CU3 B:CUK702 2.7 17.6 1.0 CE1 B:HIS132 3.0 18.0 1.0 CE1 B:HIS181 3.0 17.2 1.0 CD2 B:HIS181 3.2 15.3 1.0 CG B:HIS132 3.2 15.5 1.0 NE2 B:HIS133 3.4 13.2 1.0 O A:HOH1358 3.4 24.1 1.0 ND1 B:HIS490 3.4 16.0 1.0 CE1 B:HIS133 3.5 14.1 1.0 CB B:HIS132 3.6 13.4 1.0 CE1 B:HIS490 3.9 17.9 1.0 CG B:HIS490 4.1 13.9 1.0 NE2 B:HIS132 4.1 17.5 1.0 ND1 B:HIS181 4.2 15.6 1.0 CD2 B:HIS132 4.2 19.0 1.0 CG B:HIS181 4.3 15.2 1.0 CB B:HIS490 4.5 14.1 1.0 CU1 B:CUK702 4.5 22.5 1.0 CD2 B:HIS133 4.5 13.6 1.0 NE2 B:HIS429 4.6 14.9 1.0 ND1 B:HIS133 4.6 13.6 1.0 NE2 B:HIS490 4.7 16.4 1.0 CD2 B:HIS490 4.8 15.3 1.0 CE A:MET623 4.9 21.7 1.0 S2 B:CUK702 4.9 23.8 1.0 OD1 B:ASN242 5.0 17.2 1.0

A.Pomowski, S.Dell'acqua, A.Wust, S.R.Pauleta, I.Moura, O.Einsle. Revisiting the Metal Sites of Nitrous Oxide Reductase in A Low-Dose Structure From Marinobacter Nauticus. J.Biol.Inorg.Chem. V. 29 279 2024.
ISSN: ESSN 1432-1327
PubMed: 38720157
DOI: 10.1007/S00775-024-02056-Y