Copper in PDB 9cck: Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus

All present enzymatic activity of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus:
1.7.2.1;

The structure of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus, PDB code: 9cck was solved by R.W.Voland, K.M.Lancaster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.56 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	173.292, 92.976, 204.483, 90, 95.79, 90
R / Rfree (%)	19.9 / 22.6

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 - 50; Page 6, Binding sites: 51 - 56;

Binding sites:

The binding sites of Copper atom in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus (pdb code 9cck). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 56 binding sites of Copper where determined in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus, PDB code: 9cck:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:31.9 occ:1.00 NE2 A:HIS75 2.2 19.7 1.0 NE2 A:HIS110 2.3 25.6 1.0 O A:HOH862 2.3 21.5 1.0 NE2 B:HIS250 2.4 31.6 1.0 CE1 A:HIS75 3.0 20.9 1.0 CD2 B:HIS250 3.1 25.7 1.0 O A:HOH844 3.1 42.4 1.0 CD2 A:HIS110 3.1 20.4 1.0 CD2 A:HIS75 3.2 21.6 1.0 CE1 A:HIS110 3.3 25.9 1.0 CE1 B:HIS250 3.5 27.5 1.0 CU A:CU502 3.8 29.6 1.0 CD2 A:HIS73 4.0 21.0 1.0 ND1 A:HIS75 4.2 23.2 1.0 NE2 B:HIS201 4.3 24.6 1.0 CG B:HIS250 4.3 24.1 1.0 CG A:HIS75 4.3 25.1 1.0 CG A:HIS110 4.3 22.0 1.0 CD2 B:HIS201 4.4 19.7 1.0 ND1 A:HIS110 4.4 23.5 1.0 NE2 A:HIS73 4.5 19.9 1.0 ND1 B:HIS250 4.5 26.6 1.0 SD A:MET108 4.7 24.9 1.0 CG A:MET108 4.8 21.1 1.0 CE1 B:HIS201 4.9 24.1 1.0 CA A:GLY230 4.9 21.0 1.0 CU B:CU501 4.9 25.9 1.0

Copper binding site 2 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:29.6 occ:1.00 NE2 B:HIS201 2.0 24.6 1.0 NE2 A:HIS73 2.0 19.9 1.0 O A:HOH862 2.9 21.5 1.0 CD2 B:HIS201 2.9 19.7 1.0 CD2 A:HIS73 3.0 21.0 1.0 CE1 B:HIS201 3.0 24.1 1.0 O B:HOH859 3.0 26.4 1.0 CE1 A:HIS73 3.0 21.3 1.0 CD2 A:HIS75 3.3 21.6 1.0 CD2 B:HIS203 3.3 20.9 1.0 NE2 A:HIS75 3.4 19.7 1.0 NE2 B:HIS203 3.7 22.1 1.0 CU A:CU501 3.8 31.9 1.0 CG B:HIS203 3.9 22.6 1.0 ND1 B:HIS201 4.1 21.6 1.0 CG B:HIS201 4.1 19.9 1.0 ND1 A:HIS73 4.1 20.7 1.0 CG A:HIS73 4.1 21.1 1.0 CG A:HIS75 4.1 25.1 1.0 CA B:HIS203 4.2 22.0 1.0 CE1 A:HIS75 4.2 20.9 1.0 CU B:CU501 4.3 25.9 1.0 CE1 B:HIS203 4.3 23.6 1.0 ND1 B:HIS203 4.4 22.6 1.0 O A:HOH795 4.4 27.2 1.0 CB B:HIS203 4.5 22.2 1.0 ND1 A:HIS75 4.6 23.2 1.0 O B:VAL202 4.6 25.1 1.0 N B:HIS203 4.7 20.9 1.0 CA A:HIS75 4.8 23.6 1.0 O A:PHE74 4.8 24.8 1.0 C B:VAL202 4.9 22.8 1.0 O A:HOH844 4.9 42.4 1.0

Copper binding site 3 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:25.5 occ:1.00 ND1 A:HIS119 2.1 23.6 1.0 ND1 A:HIS70 2.1 21.2 1.0 SG A:CYS111 2.2 24.6 1.0 SD A:MET124 2.6 26.2 1.0 CE1 A:HIS119 2.9 26.0 1.0 CE1 A:HIS70 2.9 21.7 1.0 CG A:HIS119 3.1 20.8 1.0 CB A:CYS111 3.1 23.3 1.0 CG A:HIS70 3.1 22.8 1.0 CB A:HIS119 3.5 22.3 1.0 CE A:MET124 3.5 21.7 1.0 CB A:HIS70 3.6 22.7 1.0 CA A:HIS70 3.8 21.5 1.0 O A:ALA69 3.9 23.8 1.0 CG A:MET124 4.0 23.9 1.0 NE2 A:HIS119 4.1 23.9 1.0 CB A:ALA113 4.1 21.1 1.0 NE2 A:HIS70 4.1 20.2 1.0 CD2 A:HIS119 4.1 23.0 1.0 CD2 A:HIS70 4.2 20.6 1.0 CA A:CYS111 4.6 21.9 1.0 CB A:MET124 4.6 21.0 1.0 CA A:HIS119 4.7 21.1 1.0 N A:THR71 4.7 21.7 1.0 C A:ALA69 4.8 24.2 1.0 N A:HIS70 4.8 22.8 1.0 C A:HIS70 4.8 23.2 1.0 CE3 A:TRP39 4.8 25.4 1.0 N A:ALA113 4.9 22.5 1.0

Copper binding site 4 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu504 b:28.4 occ:1.00 ND1 A:HIS399 2.1 32.5 1.0 ND1 A:HIS362 2.1 28.0 1.0 SG A:CYS396 2.1 27.2 1.0 SD A:MET402 2.8 28.6 1.0 CE1 A:HIS399 3.0 31.4 1.0 CE1 A:HIS362 3.0 30.1 1.0 CG A:HIS399 3.1 31.6 1.0 CG A:HIS362 3.1 27.5 1.0 CB A:CYS396 3.2 28.9 1.0 CE A:MET402 3.4 29.7 1.0 CB A:HIS399 3.4 28.7 1.0 CB A:HIS362 3.5 24.7 1.0 CA A:HIS362 3.7 26.2 1.0 N A:HIS399 4.0 27.2 1.0 NE2 A:HIS399 4.1 33.2 1.0 O A:VAL361 4.1 28.8 1.0 NE2 A:HIS362 4.2 26.4 1.0 CD2 A:HIS399 4.2 29.4 1.0 CD2 A:HIS362 4.2 27.4 1.0 CB A:LEU398 4.3 28.8 1.0 CG A:MET402 4.3 26.4 1.0 N A:THR363 4.3 27.7 1.0 CA A:HIS399 4.3 27.3 1.0 C A:HIS362 4.6 25.2 1.0 CA A:CYS396 4.6 27.4 1.0 C A:LEU398 4.7 28.8 1.0 N A:HIS362 4.7 30.5 1.0 O A:HIS399 4.8 29.1 1.0 C A:VAL361 4.9 33.8 1.0 CA A:LEU398 4.9 27.4 1.0 CB A:MET402 4.9 26.8 1.0

Copper binding site 5 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu505 b:25.8 occ:1.00 NE2 A:HIS248 2.0 23.5 1.0 NE2 A:HIS203 2.1 21.9 1.0 NE2 C:HIS112 2.1 23.3 1.0 O C:HOH734 2.5 15.7 1.0 CE1 A:HIS248 2.9 23.1 1.0 CE1 A:HIS203 3.0 22.8 1.0 CE1 C:HIS112 3.0 26.2 1.0 CD2 A:HIS248 3.0 23.6 1.0 CD2 C:HIS112 3.1 23.5 1.0 CD2 A:HIS203 3.1 21.5 1.0 ND1 A:HIS248 4.0 23.9 1.0 CU A:CU506 4.1 29.7 1.0 CG A:HIS248 4.1 21.6 1.0 ND1 A:HIS203 4.1 23.2 1.0 ND1 C:HIS112 4.2 24.9 1.0 CG C:HIS112 4.2 23.6 1.0 CG A:HIS203 4.2 21.0 1.0 CD2 A:HIS201 4.3 22.6 1.0 NE2 C:HIS73 4.4 21.6 1.0 CD2 C:HIS73 4.4 19.2 1.0 CD1 A:LEU246 4.6 26.3 1.0 CU C:CU402 4.8 30.9 1.0 NE2 A:HIS201 4.9 20.4 1.0 CB A:LEU246 5.0 25.9 1.0

Copper binding site 6 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu506 b:29.7 occ:1.00 NE2 C:HIS73 2.0 21.6 1.0 NE2 A:HIS201 2.0 20.4 1.0 CD2 A:HIS201 2.8 22.6 1.0 CD2 C:HIS73 2.9 19.2 1.0 CE1 C:HIS73 3.0 20.0 1.0 O C:HOH734 3.0 15.7 1.0 CE1 A:HIS201 3.1 24.5 1.0 CD2 A:HIS203 3.2 21.5 1.0 CD2 C:HIS75 3.3 22.7 1.0 NE2 C:HIS75 3.4 22.1 1.0 O A:HOH809 3.4 26.1 1.0 NE2 A:HIS203 3.4 21.9 1.0 CU C:CU402 3.8 30.9 1.0 CG A:HIS203 3.9 21.0 1.0 CG A:HIS201 4.0 20.4 1.0 ND1 C:HIS73 4.1 20.3 1.0 CG C:HIS73 4.1 22.7 1.0 CU A:CU505 4.1 25.8 1.0 CE1 A:HIS203 4.1 22.8 1.0 CG C:HIS75 4.1 22.7 1.0 ND1 A:HIS201 4.1 22.5 1.0 CE1 C:HIS75 4.2 20.8 1.0 ND1 A:HIS203 4.3 23.2 1.0 CA A:HIS203 4.3 22.8 1.0 ND1 C:HIS75 4.5 18.7 1.0 O C:HOH649 4.6 26.0 1.0 CB A:HIS203 4.6 20.3 1.0 O A:VAL202 4.7 28.2 1.0 CA C:HIS75 4.7 24.1 1.0 O C:PHE74 4.8 26.6 1.0 N A:HIS203 4.8 21.9 1.0 CB C:HIS75 5.0 19.1 1.0 C A:VAL202 5.0 24.8 1.0

Copper binding site 7 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:25.9 occ:1.00 NE2 B:HIS248 2.0 25.4 1.0 NE2 B:HIS203 2.0 22.1 1.0 NE2 A:HIS112 2.1 22.0 1.0 O A:HOH862 2.7 21.5 1.0 O A:HOH844 2.9 42.4 1.0 CE1 B:HIS203 2.9 23.6 1.0 CD2 A:HIS112 2.9 21.5 1.0 CE1 B:HIS248 2.9 25.2 1.0 CD2 B:HIS248 3.0 21.4 1.0 CD2 B:HIS203 3.1 20.9 1.0 CE1 A:HIS112 3.2 24.6 1.0 ND1 B:HIS248 4.1 24.0 1.0 ND1 B:HIS203 4.1 22.6 1.0 CG B:HIS248 4.1 24.2 1.0 CG A:HIS112 4.1 23.5 1.0 CG B:HIS203 4.2 22.6 1.0 ND1 A:HIS112 4.2 22.7 1.0 CU A:CU502 4.3 29.6 1.0 OE2 B:GLU254 4.3 33.0 1.0 CD2 B:HIS201 4.5 19.7 1.0 CD1 B:LEU246 4.5 22.0 1.0 NE2 A:HIS73 4.5 19.9 1.0 CD2 A:HIS73 4.6 21.0 1.0 CB B:LEU246 4.8 23.0 1.0 CU A:CU501 4.9 31.9 1.0 NE2 B:HIS201 4.9 24.6 1.0

Copper binding site 8 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:27.1 occ:1.00 NE2 B:HIS75 2.2 21.2 1.0 O B:HOH917 2.2 19.9 1.0 NE2 B:HIS110 2.3 17.4 1.0 NE2 C:HIS250 2.4 24.9 1.0 CD2 C:HIS250 3.1 28.1 1.0 CE1 B:HIS75 3.1 20.0 1.0 CD2 B:HIS110 3.2 19.4 1.0 CD2 B:HIS75 3.2 20.0 1.0 CE1 B:HIS110 3.3 19.1 1.0 CE1 C:HIS250 3.6 23.3 1.0 CU B:CU503 3.8 27.1 1.0 CD2 B:HIS73 4.0 19.5 1.0 ND1 B:HIS75 4.2 19.2 1.0 NE2 C:HIS201 4.3 18.8 1.0 CG C:HIS250 4.3 22.1 1.0 CG B:HIS75 4.3 20.6 1.0 CD2 C:HIS201 4.3 20.8 1.0 CG B:HIS110 4.4 19.5 1.0 O C:HOH539 4.4 34.0 1.0 ND1 B:HIS110 4.4 17.9 1.0 NE2 B:HIS73 4.4 20.0 1.0 ND1 C:HIS250 4.5 23.7 1.0 SD B:MET108 4.6 21.3 1.0 CG B:MET108 4.9 18.3 1.0 CE1 C:HIS201 4.9 21.1 1.0 CA B:GLY230 4.9 20.2 1.0 CU C:CU401 5.0 23.1 1.0

Copper binding site 9 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu503 b:27.1 occ:1.00 NE2 B:HIS73 2.0 20.0 1.0 NE2 C:HIS201 2.1 18.8 1.0 CD2 C:HIS201 2.8 20.8 1.0 O B:HOH917 2.9 19.9 1.0 O C:HOH712 2.9 27.9 1.0 CD2 B:HIS73 2.9 19.5 1.0 CE1 B:HIS73 3.0 21.0 1.0 CE1 C:HIS201 3.2 21.1 1.0 CD2 C:HIS203 3.2 19.4 1.0 CD2 B:HIS75 3.3 20.0 1.0 NE2 B:HIS75 3.4 21.2 1.0 NE2 C:HIS203 3.6 20.5 1.0 CU B:CU502 3.8 27.1 1.0 CG C:HIS203 3.9 18.9 1.0 CG C:HIS201 4.1 21.4 1.0 ND1 B:HIS73 4.1 19.0 1.0 CG B:HIS73 4.1 20.4 1.0 CG B:HIS75 4.1 20.6 1.0 ND1 C:HIS201 4.2 21.9 1.0 CA C:HIS203 4.2 21.5 1.0 CE1 B:HIS75 4.3 20.0 1.0 CE1 C:HIS203 4.3 20.0 1.0 CU C:CU401 4.3 23.1 1.0 O B:HOH751 4.4 27.1 1.0 ND1 C:HIS203 4.4 20.4 1.0 CB C:HIS203 4.6 18.8 1.0 ND1 B:HIS75 4.6 19.2 1.0 N C:HIS203 4.7 20.8 1.0 O C:VAL202 4.7 23.9 1.0 CA B:HIS75 4.8 18.8 1.0 O B:PHE74 4.9 19.2 1.0 C C:VAL202 5.0 21.1 1.0 CB B:HIS75 5.0 19.7 1.0

Copper binding site 10 out of 56 in the Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Multi-Copper Oxidase with A C-Terminal Cupredoxin Domain From Nitrosopumilus Maritimus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu504 b:22.8 occ:1.00 ND1 B:HIS70 2.0 16.5 1.0 ND1 B:HIS119 2.1 17.2 1.0 SG B:CYS111 2.2 18.0 1.0 SD B:MET124 2.6 23.1 1.0 CE1 B:HIS70 2.9 18.3 1.0 CG B:HIS70 3.0 18.3 1.0 CE1 B:HIS119 3.1 18.0 1.0 CG B:HIS119 3.1 19.7 1.0 CB B:CYS111 3.1 19.7 1.0 CE B:MET124 3.2 22.3 1.0 CB B:HIS119 3.4 18.6 1.0 CB B:HIS70 3.5 18.2 1.0 CA B:HIS70 3.8 21.0 1.0 O B:ALA69 4.0 19.1 1.0 NE2 B:HIS70 4.0 18.7 1.0 CD2 B:HIS70 4.1 19.1 1.0 NE2 B:HIS119 4.1 19.7 1.0 CB B:ALA113 4.2 21.9 1.0 CD2 B:HIS119 4.2 20.8 1.0 CG B:MET124 4.2 19.9 1.0 CA B:CYS111 4.5 20.8 1.0 CA B:HIS119 4.6 20.0 1.0 N B:THR71 4.7 18.5 1.0 CB B:MET124 4.7 16.2 1.0 CE3 B:TRP39 4.8 21.7 1.0 C B:ALA69 4.8 18.9 1.0 N B:HIS70 4.8 22.2 1.0 C B:HIS70 4.8 19.3 1.0 N B:ALA113 4.9 19.7 1.0

R.W.Voland, H.Wang, H.D.Abruna, K.M.Lancaster. Nitrous Oxide Production Via Enzymatic Nitroxyl From the Nitrifying Archaeon Nitrosopumilus Maritimus. Proc.Natl.Acad.Sci.Usa V. 122 71122 2025.
ISSN: ESSN 1091-6490
PubMed: 39823305
DOI: 10.1073/PNAS.2416971122