Copper in PDB 7exk: An AA9 Lpmo of Ceriporiopsis Subvermispora

The structure of An AA9 Lpmo of Ceriporiopsis Subvermispora, PDB code: 7exk was solved by H.Nguyen, K.Kondo, T.Nagata, M.Katahira, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.063, 52.428, 134.625, 90, 90.55, 90
R / Rfree (%)	17.2 / 23

The structure of An AA9 Lpmo of Ceriporiopsis Subvermispora also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Copper atom in the An AA9 Lpmo of Ceriporiopsis Subvermispora (pdb code 7exk). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the An AA9 Lpmo of Ceriporiopsis Subvermispora, PDB code: 7exk:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:28.8 occ:1.00 ND1 A:HIS1 2.0 29.9 1.0 NE2 A:HIS75 2.1 31.7 1.0 N A:HIS1 2.2 22.7 1.0 OH A:TYR160 2.7 22.6 1.0 CG A:HIS1 3.0 29.6 1.0 CD2 A:HIS75 3.0 28.3 1.0 CE1 A:HIS1 3.0 29.4 1.0 CA A:HIS1 3.1 26.8 1.0 CE1 A:HIS75 3.1 30.6 1.0 CB A:HIS1 3.2 26.0 1.0 OH A:TYR74 3.7 33.5 1.0 CZ A:TYR160 3.7 26.9 1.0 OE1 A:GLN158 4.0 31.9 1.0 CD2 A:HIS1 4.1 29.1 1.0 NE2 A:HIS1 4.1 26.7 1.0 ND1 A:HIS75 4.2 29.2 1.0 CG A:HIS75 4.2 31.1 1.0 CZ A:TYR74 4.3 25.7 1.0 CE1 A:TYR160 4.4 20.7 1.0 C A:HIS1 4.5 26.4 1.0 CE2 A:TYR160 4.6 25.0 1.0 CE1 A:TYR74 4.6 31.1 1.0 NE2 A:HIS149 4.9 36.8 1.0 CD A:GLN158 5.0 32.3 1.0

Copper binding site 2 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:22.2 occ:1.00 NE2 B:HIS75 1.9 24.5 1.0 ND1 B:HIS1 2.1 23.0 1.0 N B:HIS1 2.1 20.7 1.0 OH B:TYR160 2.8 21.5 1.0 CD2 B:HIS75 2.9 23.8 1.0 CE1 B:HIS75 2.9 23.7 1.0 CG B:HIS1 3.0 20.2 1.0 CA B:HIS1 3.0 24.9 1.0 CE1 B:HIS1 3.1 23.9 1.0 CB B:HIS1 3.2 23.9 1.0 OH B:TYR74 3.5 29.9 1.0 CZ B:TYR160 3.8 25.8 1.0 OE1 B:GLN158 4.0 26.7 1.0 ND1 B:HIS75 4.0 24.9 1.0 CG B:HIS75 4.1 28.0 1.0 CD2 B:HIS1 4.2 21.8 1.0 NE2 B:HIS1 4.2 17.1 1.0 CZ B:TYR74 4.2 25.7 1.0 CE1 B:TYR160 4.5 20.7 1.0 C B:HIS1 4.5 26.3 1.0 CE1 B:TYR74 4.5 27.1 1.0 CE2 B:TYR160 4.6 21.4 1.0 NE2 B:HIS149 5.0 29.0 1.0

Copper binding site 3 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu302 b:34.8 occ:1.00 NE2 C:HIS75 2.0 34.2 1.0 N C:HIS1 2.1 29.7 1.0 ND1 C:HIS1 2.2 29.2 1.0 OH C:TYR160 2.8 32.5 1.0 CD2 C:HIS75 3.0 32.5 1.0 CA C:HIS1 3.0 30.0 1.0 CG C:HIS1 3.0 24.1 1.0 CE1 C:HIS75 3.1 34.8 1.0 CB C:HIS1 3.2 25.5 1.0 CE1 C:HIS1 3.2 27.4 1.0 OH C:TYR74 3.7 34.2 1.0 CZ C:TYR160 3.8 31.3 1.0 CG C:HIS75 4.1 32.0 1.0 ND1 C:HIS75 4.1 30.1 1.0 CD2 C:HIS1 4.2 26.1 1.0 OE1 C:GLN158 4.2 32.2 1.0 CZ C:TYR74 4.3 33.5 1.0 NE2 C:HIS1 4.3 26.1 1.0 C C:HIS1 4.4 29.7 1.0 CE1 C:TYR160 4.4 26.0 1.0 CE1 C:TYR74 4.4 32.8 1.0 CE2 C:TYR160 4.7 26.3 1.0 O C:HIS1 5.0 37.7 1.0

Copper binding site 4 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu302 b:23.8 occ:1.00 NE2 D:HIS75 2.0 25.4 1.0 ND1 D:HIS1 2.0 22.3 1.0 N D:HIS1 2.1 21.1 1.0 OH D:TYR160 2.7 21.0 1.0 CG D:HIS1 2.9 19.3 1.0 CD2 D:HIS75 3.0 22.7 1.0 CE1 D:HIS75 3.0 24.3 1.0 CA D:HIS1 3.0 25.5 1.0 CE1 D:HIS1 3.1 23.1 1.0 CB D:HIS1 3.1 27.4 1.0 OH D:TYR74 3.6 33.7 1.0 CZ D:TYR160 3.7 24.2 1.0 O D:HOH508 3.8 33.7 1.0 CD2 D:HIS1 4.1 21.1 1.0 ND1 D:HIS75 4.1 29.0 1.0 OE1 D:GLN158 4.1 28.1 1.0 CG D:HIS75 4.1 26.3 1.0 NE2 D:HIS1 4.1 25.7 1.0 CZ D:TYR74 4.3 25.9 1.0 CE1 D:TYR160 4.4 18.6 1.0 C D:HIS1 4.4 26.5 1.0 CE1 D:TYR74 4.4 30.7 1.0 CE2 D:TYR160 4.6 21.7 1.0

Copper binding site 5 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu302 b:26.2 occ:1.00 NE2 E:HIS75 2.0 28.4 1.0 N E:HIS1 2.1 22.8 1.0 ND1 E:HIS1 2.2 26.6 1.0 OH E:TYR160 2.8 23.3 1.0 CD2 E:HIS75 2.9 27.9 1.0 CE1 E:HIS75 3.0 28.4 1.0 CA E:HIS1 3.1 26.6 1.0 CG E:HIS1 3.1 23.6 1.0 CE1 E:HIS1 3.2 25.4 1.0 CB E:HIS1 3.3 21.3 1.0 OH E:TYR74 3.5 27.7 1.0 CZ E:TYR160 3.7 24.1 1.0 OE1 E:GLN158 4.0 33.1 1.0 ND1 E:HIS75 4.1 34.4 1.0 CG E:HIS75 4.1 32.3 1.0 CZ E:TYR74 4.2 27.5 1.0 CD2 E:HIS1 4.3 24.1 1.0 NE2 E:HIS1 4.3 24.7 1.0 CE1 E:TYR160 4.4 21.7 1.0 C E:HIS1 4.5 28.2 1.0 CE2 E:TYR160 4.6 22.2 1.0 CE1 E:TYR74 4.6 30.9 1.0 NE2 E:HIS149 4.7 30.7 1.0 CE1 E:HIS149 5.0 31.3 1.0 CD E:GLN158 5.0 27.9 1.0

Copper binding site 6 out of 6 in the An AA9 Lpmo of Ceriporiopsis Subvermispora


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of An AA9 Lpmo of Ceriporiopsis Subvermispora within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu302 b:20.0 occ:1.00 NE2 F:HIS75 2.0 23.1 1.0 ND1 F:HIS1 2.0 21.8 1.0 OE2 B:GLU53 2.2 37.0 1.0 N F:HIS1 2.2 17.7 1.0 OH F:TYR160 2.8 22.8 1.0 CD B:GLU53 2.9 33.3 1.0 CD2 F:HIS75 3.0 19.3 1.0 OE1 B:GLU53 3.0 35.8 1.0 CG F:HIS1 3.0 19.4 1.0 CE1 F:HIS75 3.0 24.1 1.0 CE1 F:HIS1 3.0 23.3 1.0 CA F:HIS1 3.1 20.2 1.0 CB F:HIS1 3.3 18.8 1.0 OH F:TYR74 3.7 27.0 1.0 CZ F:TYR160 3.8 21.3 1.0 OE1 F:GLN158 3.9 25.1 1.0 ND1 F:HIS75 4.1 18.0 1.0 CG F:HIS75 4.1 23.0 1.0 NE2 F:HIS1 4.1 19.8 1.0 CD2 F:HIS1 4.2 21.3 1.0 CG B:GLU53 4.3 28.7 1.0 CZ F:TYR74 4.4 25.9 1.0 CE1 F:TYR160 4.5 20.9 1.0 C F:HIS1 4.5 18.7 1.0 CE2 F:TYR160 4.6 20.8 1.0 CE1 F:TYR74 4.6 25.4 1.0 O B:HOH446 4.8 27.2 1.0 CD F:GLN158 4.8 27.9 1.0 NE2 F:HIS149 5.0 26.8 1.0

H.Nguyen, K.Kondo, Y.Yagi, Y.Iseki, N.Okuoka, T.Watanabe, B.Mikami, T.Nagata, M.Katahira. Functional and Structural Characterizations of Lytic Polysaccharide Monooxygenase, Which Cooperates Synergistically with Cellulases, From Ceriporiopsis Subvermispora. Acs Sustain Chem Eng V. 10 923 2022.
ISSN: ESSN 2168-0485
DOI: 10.1021/ACSSUSCHEMENG.1C06810