Copper in PDB 7vw1: Structure of A Dimeric Periplasmic Protein Bound with Cuprous Ions

The structure of Structure of A Dimeric Periplasmic Protein Bound with Cuprous Ions, PDB code: 7vw1 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)	34.62 / 2.49
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	77.415, 77.415, 44.933, 90, 90, 90
R / Rfree (%)	20.3 / 24.8

The binding sites of Copper atom in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous Ions (pdb code 7vw1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous Ions, PDB code: 7vw1:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous 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 Cuprous Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:39.2 occ:1.00 ND1 A:HIS70 1.9 33.4 1.0 ND1 A:HIS71 1.9 37.6 1.0 CE1 A:HIS71 2.7 35.2 1.0 CE1 A:HIS70 2.8 33.4 1.0 O B:HOH313 2.9 33.5 1.0 N A:HIS71 2.9 33.0 1.0 CG A:HIS70 3.0 37.8 1.0 CG A:HIS71 3.1 34.5 1.0 CA A:HIS71 3.2 39.0 1.0 C A:HIS70 3.2 37.5 1.0 SD A:MET67 3.4 39.2 1.0 CB A:HIS70 3.4 33.2 1.0 O A:HIS70 3.5 32.1 1.0 O A:MET67 3.6 51.4 1.0 CB A:HIS71 3.6 33.9 1.0 NE2 A:HIS71 3.9 42.0 1.0 CA A:HIS70 3.9 37.0 1.0 NE2 A:HIS70 3.9 35.0 1.0 CD2 A:HIS70 4.0 32.9 1.0 CE1 B:HIS70 4.0 35.1 1.0 CD2 A:HIS71 4.1 36.0 1.0 OE1 A:GLN101 4.2 51.6 1.0 CG A:MET67 4.2 36.2 1.0 CB B:ALA74 4.4 41.7 1.0 C A:HIS71 4.5 46.1 1.0 NE2 B:HIS70 4.6 31.8 1.0 C A:MET67 4.6 44.0 1.0 CA A:MET67 4.8 42.6 1.0 N A:HIS70 4.9 33.0 1.0 ND1 B:HIS70 5.0 44.5 1.0

Copper binding site 2 out of 5 in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous 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 Cuprous Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:70.5 occ:1.00 NE2 A:HIS115 2.0 53.7 1.0 O B:HOH318 2.6 58.3 1.0 CE1 A:HIS115 2.9 64.0 1.0 CD2 A:HIS115 3.1 53.3 1.0 OD2 B:ASP87 3.3 69.7 1.0 ND1 A:HIS115 4.1 58.6 1.0 CG A:HIS115 4.2 52.1 1.0 CG B:ASP87 4.4 64.0 1.0 NE1 A:TRP111 4.6 69.0 1.0 OD1 B:ASP87 4.7 66.7 1.0

Copper binding site 3 out of 5 in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous 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 Cuprous Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:37.8 occ:1.00 ND1 B:HIS70 2.0 44.5 1.0 ND1 B:HIS71 2.0 37.5 1.0 O B:HOH313 2.7 33.5 1.0 CE1 B:HIS71 2.7 40.5 1.0 CE1 B:HIS70 2.8 35.1 1.0 N B:HIS71 2.9 34.0 1.0 CG B:HIS70 3.0 32.0 1.0 CG B:HIS71 3.1 39.7 1.0 CA B:HIS71 3.2 40.6 1.0 C B:HIS70 3.2 33.2 1.0 SD B:MET67 3.3 42.0 1.0 CB B:HIS70 3.4 32.2 1.0 O B:HIS70 3.5 33.4 1.0 O B:MET67 3.6 33.7 1.0 CB B:HIS71 3.7 45.4 1.0 CE1 A:HIS70 3.9 33.4 1.0 CA B:HIS70 3.9 35.8 1.0 NE2 B:HIS71 3.9 45.5 1.0 OE1 B:GLN101 4.0 67.2 1.0 NE2 B:HIS70 4.0 31.8 1.0 CD2 B:HIS70 4.1 31.7 1.0 CG B:MET67 4.1 33.4 1.0 CD2 B:HIS71 4.1 37.9 1.0 CB A:ALA74 4.3 32.2 1.0 NE2 A:HIS70 4.3 35.0 1.0 C B:HIS71 4.5 37.9 1.0 C B:MET67 4.6 41.4 1.0 CA B:MET67 4.8 33.1 1.0 ND1 A:HIS70 4.9 33.4 1.0 N B:HIS70 4.9 35.8 1.0 CE B:MET67 5.0 32.4 1.0

Copper binding site 4 out of 5 in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous 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 Cuprous Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:56.8 occ:1.00 NE2 B:HIS47 2.1 47.7 1.0 SD B:MET51 2.4 53.4 1.0 O B:HOH317 2.7 34.1 1.0 CG B:MET51 3.0 46.8 1.0 CE1 B:HIS47 3.0 45.0 1.0 CD2 B:HIS47 3.1 47.5 1.0 CE B:MET51 3.4 73.0 1.0 ND1 B:HIS47 4.1 47.1 1.0 CG B:HIS47 4.2 44.9 1.0 CB B:MET51 4.5 40.4 1.0 SD A:MET40 4.8 54.9 1.0

Copper binding site 5 out of 5 in the Structure of A Dimeric Periplasmic Protein Bound with Cuprous 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 Cuprous Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu203 b:84.5 occ:1.00 NE2 B:HIS31 2.3 67.9 1.0 CE1 B:HIS31 3.2 64.6 1.0 CD2 B:HIS31 3.3 60.3 1.0 O B:HOH304 3.5 44.6 1.0 ND1 B:HIS31 4.4 64.1 1.0 CG B:HIS31 4.5 57.7 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