Copper in PDB 7vw2: Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions

The structure of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions, PDB code: 7vw2 was solved by J.Yang, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.61 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.446, 74.412, 50.786, 90, 96.18, 90
R / Rfree (%)	24.5 / 28.2

The binding sites of Copper atom in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions (pdb code 7vw2). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions, PDB code: 7vw2:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:18.5 occ:0.49 NE2 A:HIS47 2.0 12.7 1.0 CD2 A:HIS47 3.0 18.8 1.0 CE1 A:HIS47 3.0 16.8 1.0 CU B:CU201 3.7 15.8 0.5 SD A:MET51 3.8 41.0 1.0 O B:HOH315 3.9 13.2 1.0 ND1 A:HIS47 4.1 13.5 1.0 CG A:HIS47 4.1 17.3 1.0 NE2 B:HIS47 4.1 12.2 1.0 CD2 B:HIS47 4.2 18.4 1.0 CG A:MET51 4.8 17.4 1.0 CE A:MET51 4.9 42.6 1.0 CE1 B:HIS47 4.9 16.2 1.0 CU A:CU202 5.0 22.2 0.4 O B:HOH316 5.0 22.5 1.0

Copper binding site 2 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:22.2 occ:0.44 O A:HOH318 2.4 14.8 1.0 SD A:MET51 2.4 41.0 1.0 CG A:MET51 3.1 17.4 1.0 CB A:MET51 3.5 16.1 1.0 CE A:MET51 3.7 42.6 1.0 CE B:MET43 4.6 20.9 1.0 CA A:MET51 4.6 17.8 1.0 CU A:CU201 5.0 18.5 0.5

Copper binding site 3 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:50.2 occ:1.00 SD A:MET40 2.2 37.6 1.0 O B:HOH319 2.3 22.8 1.0 O B:HOH322 2.5 12.0 1.0 O B:HOH320 3.2 11.7 1.0 CE A:MET40 3.2 41.1 1.0 CG A:MET40 3.4 15.8 1.0 O A:HOH317 3.5 16.7 1.0 CB A:MET40 3.8 13.9 1.0 CG1 B:VAL54 4.3 30.5 1.0

Copper binding site 4 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu204 b:154.4 occ:1.00 O B:HOH318 2.3 27.7 1.0 SD B:MET77 2.3 36.7 1.0 SD A:MET50 2.4 34.9 1.0 CG B:MET77 3.0 29.8 1.0 CE A:MET50 3.4 29.9 1.0 CG A:MET50 3.5 20.1 1.0 CE B:MET77 3.7 42.2 1.0 O B:HOH310 4.0 21.9 1.0 CA A:GLY66 4.3 21.5 1.0 O A:GLY66 4.3 21.2 1.0 CB B:MET77 4.4 15.8 1.0 C A:GLY66 4.5 32.0 1.0 CE B:MET46 4.6 33.1 1.0 CB A:MET50 4.8 20.9 1.0 O B:GLY73 5.0 15.0 1.0

Copper binding site 5 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:15.8 occ:0.48 NE2 B:HIS47 2.0 12.2 1.0 O B:HOH316 2.7 22.5 1.0 CD2 B:HIS47 2.7 18.4 1.0 CE1 B:HIS47 3.1 16.2 1.0 SD B:MET51 3.6 20.9 1.0 CU A:CU201 3.7 18.5 0.5 NE2 A:HIS47 4.0 12.7 1.0 CG B:HIS47 4.0 20.2 1.0 CD2 A:HIS47 4.1 18.8 1.0 ND1 B:HIS47 4.1 16.8 1.0 CE B:MET51 4.6 12.5 1.0 CG B:MET51 4.8 16.1 1.0 CU B:CU202 4.8 24.7 0.5 CE1 A:HIS47 4.8 16.8 1.0

Copper binding site 6 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:24.7 occ:0.50 O B:HOH320 2.3 11.7 1.0 SD B:MET51 2.4 20.9 1.0 CG B:MET51 3.2 16.1 1.0 CE B:MET51 3.6 12.5 1.0 CB B:MET51 3.6 18.0 1.0 O B:HOH319 4.5 22.8 1.0 CA B:MET51 4.8 19.5 1.0 CU B:CU201 4.8 15.8 0.5 CE A:MET43 4.9 41.4 1.0 O B:HOH322 5.0 12.0 1.0

Copper binding site 7 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu203 b:79.4 occ:1.00 O B:HOH321 2.2 23.2 1.0 SD B:MET40 2.3 68.7 1.0 O B:HOH323 2.5 21.4 1.0 O B:HOH317 2.8 30.7 1.0 CB B:MET40 3.6 21.1 1.0 CG B:MET40 3.6 47.7 1.0 CE B:MET40 3.8 45.5 1.0 O A:HOH310 4.5 41.1 1.0

Copper binding site 8 out of 8 in the Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of A Dimeric Periplasmic Protein Bound with Cupric Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu204 b:37.8 occ:1.00 SD A:MET77 2.3 25.8 1.0 O A:HOH315 2.4 11.5 1.0 NE2 B:HIS70 2.5 30.7 1.0 SD B:MET50 2.5 19.3 1.0 CG A:MET77 2.7 33.6 1.0 CD2 B:HIS70 3.1 22.8 1.0 CE B:MET50 3.2 28.4 1.0 CG B:MET50 3.5 23.6 1.0 CE1 B:HIS70 3.7 27.4 1.0 CE A:MET77 3.8 41.3 1.0 O A:HOH313 3.9 11.2 1.0 CB A:MET77 4.2 13.4 1.0 CE A:MET46 4.3 28.9 1.0 CG B:HIS70 4.3 33.0 1.0 O B:GLY66 4.4 12.7 1.0 O A:GLY73 4.5 12.2 1.0 ND1 B:HIS70 4.6 37.8 1.0 CA B:GLY66 4.6 12.3 1.0 C B:GLY66 4.8 14.4 1.0 CB B:MET50 4.9 11.8 1.0 SD A:MET46 4.9 17.5 1.0 C A:GLY73 5.0 21.8 1.0

J.Yang, M.Gao, J.Wang, C.He, X.Wang, L.Liu. Structural Basis of Copper Binding By A Dimeric Periplasmic Protein Forming A Six-Helical Bundle. J.Inorg.Biochem. V. 229 11728 2022.
ISSN: ISSN 0162-0134
PubMed: 35066349
DOI: 10.1016/J.JINORGBIO.2022.111728