Copper in PDB 3sbr: Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate:
1.7.99.6;

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate, PDB code: 3sbr was solved by A.Pomowski, W.G.Zumft, P.M.H.Kroneck, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.00 / 2.24
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	96.577, 106.453, 130.876, 111.45, 107.22, 90.72
R / Rfree (%)	17.3 / 22.7

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Calcium	(Ca)	8 atoms
Chlorine	(Cl)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Copper atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate (pdb code 3sbr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 48 binding sites of Copper where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate, PDB code: 3sbr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu701 b:33.9 occ:1.00 CU1 A:CUA701 0.0 33.9 1.0 SG A:CYS618 2.3 26.6 1.0 SG A:CYS622 2.4 26.6 1.0 SD A:MET629 2.4 30.2 1.0 ND1 A:HIS583 2.5 24.9 1.0 CU2 A:CUA701 2.7 30.6 1.0 CE A:MET629 3.1 27.5 1.0 CB A:CYS618 3.3 25.1 1.0 CB A:CYS622 3.3 24.9 1.0 CE1 A:HIS583 3.3 25.6 1.0 CG A:HIS583 3.6 26.2 1.0 O A:TRP620 3.8 25.7 1.0 CG A:MET629 3.8 27.4 1.0 CB A:HIS583 3.9 25.8 1.0 CA A:HIS583 4.2 25.7 1.0 CB A:MET629 4.2 27.3 1.0 ND1 A:HIS626 4.4 28.9 1.0 NE2 A:HIS583 4.5 24.9 1.0 O A:SER582 4.6 26.6 1.0 CD2 A:HIS583 4.7 25.9 1.0 CA A:CYS622 4.7 25.2 1.0 CA A:CYS618 4.7 25.1 1.0 N A:CYS622 4.9 24.8 1.0 N A:GLY584 4.9 24.9 1.0 C A:TRP620 4.9 25.9 1.0

Copper binding site 2 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu701 b:30.6 occ:1.00 CU2 A:CUA701 0.0 30.6 1.0 ND1 A:HIS626 1.8 28.9 1.0 O A:TRP620 2.4 25.7 1.0 SG A:CYS618 2.4 26.6 1.0 SG A:CYS622 2.4 26.6 1.0 CU1 A:CUA701 2.7 33.9 1.0 CE1 A:HIS626 2.8 28.7 1.0 CG A:HIS626 2.9 28.9 1.0 CB A:HIS626 3.3 28.6 1.0 C A:TRP620 3.4 25.9 1.0 N A:CYS622 3.5 24.8 1.0 CB A:CYS622 3.5 24.9 1.0 CB A:CYS618 3.6 25.1 1.0 NE2 A:HIS626 3.9 28.7 1.0 CA A:PHE621 3.9 25.2 1.0 CD2 A:HIS626 4.0 29.4 1.0 CA A:HIS626 4.0 28.9 1.0 N A:PHE621 4.0 25.4 1.0 CA A:CYS622 4.1 25.2 1.0 C A:PHE621 4.1 25.1 1.0 O A:CYS618 4.1 24.6 1.0 O A:HIS626 4.2 29.2 1.0 SD A:MET629 4.3 30.2 1.0 N A:TRP620 4.3 26.0 1.0 CA A:TRP620 4.4 26.4 1.0 C A:CYS618 4.4 25.1 1.0 C A:HIS626 4.5 29.0 1.0 CB A:MET629 4.6 27.3 1.0 CA A:CYS618 4.6 25.1 1.0 O A:HOH2485 4.7 26.4 1.0 ND1 A:HIS583 4.9 24.9 1.0 C A:SER619 4.9 25.8 1.0 CG A:MET629 5.0 27.4 1.0

Copper binding site 3 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:47.2 occ:0.80 CU1 A:CUK702 0.0 47.2 0.8 NE2 A:HIS326 2.3 27.2 1.0 NE2 A:HIS382 2.4 28.2 1.0 S1 A:CUK702 2.4 45.2 0.8 S2 A:CUK702 2.6 47.1 0.8 CD2 A:HIS326 3.0 26.1 1.0 CD2 A:HIS382 3.1 27.8 1.0 CE1 A:HIS326 3.4 27.2 1.0 CU4 A:CUK702 3.4 44.7 0.8 CU3 A:CUK702 3.4 42.5 0.8 CD2 A:HIS433 3.5 30.4 1.0 NE2 A:HIS433 3.6 32.1 1.0 CE1 A:HIS382 3.6 28.4 1.0 CG A:HIS326 4.3 26.4 1.0 CG A:HIS382 4.4 26.6 1.0 ND1 A:HIS326 4.4 27.4 1.0 CG A:HIS433 4.5 28.2 1.0 ND1 A:HIS382 4.6 27.2 1.0 CE1 A:HIS433 4.6 31.9 1.0 CU2 A:CUK702 4.6 46.4 0.8 OD1 A:ASN241 4.6 32.9 1.0 CE2 B:PHE621 4.7 29.4 1.0 N A:HIS433 4.8 22.9 1.0 C A:GLY432 5.0 23.1 1.0

Copper binding site 4 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:46.4 occ:0.80 CU2 A:CUK702 0.0 46.4 0.8 S1 A:CUK702 2.2 45.2 0.8 ND1 A:HIS129 2.3 29.0 1.0 NE2 A:HIS178 2.4 31.1 1.0 CU4 A:CUK702 2.8 44.7 0.8 CU3 A:CUK702 2.8 42.5 0.8 CE1 A:HIS178 3.1 30.9 1.0 CE1 A:HIS129 3.1 30.5 1.0 CG A:HIS129 3.2 27.0 1.0 CD2 A:HIS178 3.3 30.3 1.0 O B:HOH2976 3.4 24.8 1.0 NE2 A:HIS130 3.6 24.9 1.0 CB A:HIS129 3.6 26.1 1.0 CE1 A:HIS130 3.7 24.9 1.0 ND1 A:HIS494 3.8 33.4 1.0 ND1 A:HIS178 4.1 29.9 1.0 NE2 A:HIS129 4.1 30.1 1.0 CD2 A:HIS129 4.2 29.3 1.0 CG A:HIS178 4.2 28.6 1.0 CG A:HIS494 4.3 31.2 1.0 CE1 A:HIS494 4.3 34.0 1.0 CU1 A:CUK702 4.6 47.2 0.8 CB A:HIS494 4.6 28.8 1.0 CD2 A:HIS130 4.7 24.3 1.0 ND1 A:HIS130 4.8 24.6 1.0 CA A:HIS129 5.0 25.6 1.0 SD B:MET627 5.0 36.4 1.0

Copper binding site 5 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:42.5 occ:0.80 CU3 A:CUK702 0.0 42.5 0.8 NE2 A:HIS130 2.0 24.9 1.0 S1 A:CUK702 2.2 45.2 0.8 NE2 A:HIS433 2.3 32.1 1.0 CD2 A:HIS130 2.8 24.3 1.0 CU2 A:CUK702 2.8 46.4 0.8 CU4 A:CUK702 3.0 44.7 0.8 CE1 A:HIS130 3.1 24.9 1.0 CD2 A:HIS433 3.1 30.4 1.0 CU1 A:CUK702 3.4 47.2 0.8 CE1 A:HIS433 3.4 31.9 1.0 ND2 A:ASN241 3.8 32.6 1.0 NE2 A:HIS382 4.0 28.2 1.0 CG A:HIS130 4.0 24.8 1.0 ND1 A:HIS130 4.1 24.6 1.0 CB A:HIS129 4.1 26.1 1.0 CB A:HIS494 4.2 28.8 1.0 CE1 A:HIS382 4.3 28.4 1.0 CE1 A:HIS178 4.3 30.9 1.0 CG A:HIS433 4.3 28.2 1.0 OD1 A:ASN241 4.3 32.9 1.0 ND1 A:HIS129 4.4 29.0 1.0 S2 A:CUK702 4.4 47.1 0.8 ND1 A:HIS433 4.4 31.6 1.0 NE2 A:HIS178 4.4 31.1 1.0 CG A:ASN241 4.5 29.1 1.0 NE2 A:HIS326 4.6 27.2 1.0 CG A:HIS129 4.7 27.0 1.0 O A:HIS129 4.7 25.0 1.0 ND1 A:HIS494 4.8 33.4 1.0 CG A:HIS494 4.9 31.2 1.0 C A:HIS129 5.0 24.9 1.0

Copper binding site 6 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu702 b:44.7 occ:0.80 CU4 A:CUK702 0.0 44.7 0.8 S1 A:CUK702 2.4 45.2 0.8 ND1 A:HIS494 2.4 33.4 1.0 S2 A:CUK702 2.5 47.1 0.8 CU2 A:CUK702 2.8 46.4 0.8 CU3 A:CUK702 3.0 42.5 0.8 CB A:HIS494 3.0 28.8 1.0 CG A:HIS494 3.1 31.2 1.0 CU1 A:CUK702 3.4 47.2 0.8 CE1 A:HIS494 3.6 34.0 1.0 O B:HOH2976 3.7 24.8 1.0 ND1 A:HIS129 3.7 29.0 1.0 CD2 A:HIS433 3.7 30.4 1.0 CA A:HIS494 4.1 28.2 1.0 NE2 A:HIS433 4.1 32.1 1.0 NZ A:LYS454 4.2 31.0 1.0 CD2 A:HIS494 4.3 33.5 1.0 CE1 A:HIS129 4.5 30.5 1.0 NE2 A:HIS494 4.5 34.6 1.0 CE2 B:PHE621 4.6 29.4 1.0 CG A:HIS129 4.6 27.0 1.0 NE2 A:HIS130 4.7 24.9 1.0 CD2 B:PHE621 4.7 29.0 1.0 C A:HIS494 4.7 27.6 1.0 CB A:HIS129 4.7 26.1 1.0 OE2 A:GLU492 4.9 35.2 1.0 CE A:LYS454 4.9 29.4 1.0

Copper binding site 7 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu701 b:37.9 occ:1.00 CU1 B:CUA701 0.0 37.9 1.0 SG B:CYS618 2.4 27.7 1.0 SG B:CYS622 2.4 34.1 1.0 SD B:MET629 2.5 32.5 1.0 ND1 B:HIS583 2.6 29.4 1.0 CU2 B:CUA701 2.7 38.8 1.0 CB B:CYS618 3.3 27.6 1.0 CE B:MET629 3.3 32.2 1.0 CB B:CYS622 3.4 32.5 1.0 CE1 B:HIS583 3.4 29.6 1.0 CG B:HIS583 3.5 29.1 1.0 CB B:HIS583 3.8 28.3 1.0 O B:TRP620 3.9 30.6 1.0 CG B:MET629 4.0 30.8 1.0 CA B:HIS583 4.1 27.6 1.0 CB B:MET629 4.4 30.8 1.0 O B:SER582 4.4 28.4 1.0 NE2 B:HIS583 4.6 31.3 1.0 ND1 B:HIS626 4.6 32.0 1.0 CD2 B:HIS583 4.6 29.9 1.0 CA B:CYS618 4.8 27.5 1.0 N B:GLY584 4.8 26.4 1.0 CA B:CYS622 4.8 32.4 1.0 N B:CYS622 5.0 32.0 1.0 CA B:ALA552 5.0 36.8 1.0

Copper binding site 8 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu701 b:38.8 occ:1.00 CU2 B:CUA701 0.0 38.8 1.0 ND1 B:HIS626 1.9 32.0 1.0 O B:TRP620 2.4 30.6 1.0 SG B:CYS622 2.5 34.1 1.0 CU1 B:CUA701 2.7 37.9 1.0 SG B:CYS618 2.8 27.7 1.0 CE1 B:HIS626 2.9 32.3 1.0 CG B:HIS626 3.0 33.1 1.0 N B:CYS622 3.4 32.0 1.0 CB B:HIS626 3.4 33.5 1.0 CB B:CYS622 3.4 32.5 1.0 C B:TRP620 3.5 30.2 1.0 CB B:CYS618 3.5 27.6 1.0 CA B:HIS626 3.9 33.9 1.0 CA B:PHE621 4.0 31.0 1.0 NE2 B:HIS626 4.0 32.9 1.0 CA B:CYS622 4.0 32.4 1.0 C B:PHE621 4.1 31.5 1.0 CD2 B:HIS626 4.1 32.8 1.0 N B:PHE621 4.1 30.6 1.0 O B:HIS626 4.2 34.0 1.0 SD B:MET629 4.4 32.5 1.0 O B:CYS618 4.4 27.4 1.0 C B:HIS626 4.4 33.8 1.0 CA B:TRP620 4.5 30.2 1.0 N B:TRP620 4.6 29.5 1.0 C B:CYS618 4.6 27.5 1.0 CB B:MET629 4.6 30.8 1.0 CA B:CYS618 4.7 27.5 1.0 C B:CYS622 4.9 32.8 1.0 N B:HIS623 4.9 32.9 1.0

Copper binding site 9 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu702 b:53.3 occ:0.80 CU1 B:CUK702 0.0 53.3 0.8 S1 B:CUK702 2.4 53.1 0.8 ND1 B:HIS494 2.4 27.8 1.0 S2 B:CUK702 2.5 55.7 0.8 CB B:HIS494 2.8 25.8 1.0 CU2 B:CUK702 2.8 55.1 0.8 CG B:HIS494 2.9 27.3 1.0 CU3 B:CUK702 3.0 51.1 0.8 CU4 B:CUK702 3.4 57.6 0.8 CE1 B:HIS494 3.6 27.3 1.0 ND1 B:HIS129 3.8 24.4 1.0 CD2 B:HIS433 3.8 24.8 1.0 NE2 B:HIS433 4.0 24.4 1.0 CA B:HIS494 4.0 25.5 1.0 CD2 B:HIS494 4.1 26.5 1.0 NE2 B:HIS494 4.4 27.3 1.0 NZ B:LYS454 4.5 24.7 1.0 CB B:HIS129 4.6 21.3 1.0 CG B:HIS129 4.7 22.4 1.0 C B:HIS494 4.7 24.7 1.0 NE2 B:HIS178 4.7 26.8 1.0 CE1 B:HIS129 4.8 24.3 1.0 CE2 A:PHE621 4.8 25.8 1.0 NE2 B:HIS130 4.9 18.9 1.0 CD2 A:PHE621 4.9 25.7 1.0 CG B:HIS433 4.9 23.4 1.0 NE2 B:HIS326 5.0 26.6 1.0

Copper binding site 10 out of 48 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu702 b:55.1 occ:0.80 CU2 B:CUK702 0.0 55.1 0.8 NE2 B:HIS178 2.0 26.8 1.0 S1 B:CUK702 2.2 53.1 0.8 ND1 B:HIS129 2.5 24.4 1.0 CU3 B:CUK702 2.8 51.1 0.8 CU1 B:CUK702 2.8 53.3 0.8 CD2 B:HIS178 2.9 26.1 1.0 CE1 B:HIS178 3.0 26.9 1.0 CG B:HIS129 3.2 22.4 1.0 CE1 B:HIS129 3.3 24.3 1.0 CB B:HIS129 3.5 21.3 1.0 NE2 B:HIS130 3.6 18.9 1.0 CE1 B:HIS130 3.7 17.6 1.0 ND1 B:HIS494 3.9 27.8 1.0 CG B:HIS178 4.0 24.5 1.0 ND1 B:HIS178 4.1 27.7 1.0 CD2 B:HIS129 4.1 23.6 1.0 NE2 B:HIS129 4.1 25.7 1.0 CG B:HIS494 4.3 27.3 1.0 CE1 B:HIS494 4.4 27.3 1.0 CB B:HIS494 4.6 25.8 1.0 CU4 B:CUK702 4.6 57.6 0.8 CD2 B:HIS130 4.7 20.0 1.0 ND1 B:HIS130 4.8 19.3 1.0 CA B:HIS129 4.9 21.2 1.0 O B:HOH2307 5.0 27.6 1.0 CD2 B:HIS494 5.0 26.5 1.0

A.Pomowski, W.G.Zumft, P.M.Kroneck, O.Einsle. N2O Binding at A [4CU:2S] Copper-Sulphur Cluster in Nitrous Oxide Reductase. Nature V. 477 234 2011.
ISSN: ISSN 0028-0836
PubMed: 21841804
DOI: 10.1038/NATURE10332