Copper in PDB 8um6: Structure of Copper Bound to Ycni W137F

The structure of Structure of Copper Bound to Ycni W137F, PDB code: 8um6 was solved by O.S.Fisher, Y.R.O.Silva, D.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.09 / 1.95
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.263, 90.263, 207.508, 90, 90, 120
R / Rfree (%)	20.3 / 23.9

The binding sites of Copper atom in the Structure of Copper Bound to Ycni W137F (pdb code 8um6). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Structure of Copper Bound to Ycni W137F, PDB code: 8um6:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Structure of Copper Bound to Ycni W137F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Copper Bound to Ycni W137F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:97.2 occ:0.69 ND1 A:HIS27 1.6 53.3 0.4 CG A:HIS27 1.6 41.2 0.4 CB A:HIS27 2.0 34.0 0.4 CD2 A:HIS27 2.5 32.5 0.6 CE1 A:HIS27 2.6 32.0 0.4 CD2 A:HIS27 2.6 43.8 0.4 O A:HOH342 2.6 44.8 1.0 CB A:HIS27 2.6 36.4 0.6 CG A:HIS27 2.8 34.5 0.6 NE2 A:HIS27 3.1 39.2 0.4 O A:HIS27 3.3 33.8 0.6 CA A:HIS27 3.4 38.1 0.4 O A:HIS27 3.4 33.8 0.4 CA A:HIS27 3.7 37.7 0.6 C A:HIS27 3.7 36.0 0.4 C A:HIS27 3.7 35.7 0.6 O A:HOH326 3.8 47.5 1.0 NE2 A:HIS27 3.9 27.7 0.6 ND1 A:HIS27 4.2 36.2 0.6 N A:HIS27 4.2 42.8 0.4 N A:HIS27 4.2 42.8 0.6 CE1 A:HIS27 4.6 32.6 0.6 N A:VAL28 4.8 29.4 1.0 CB A:SER29 4.9 26.9 1.0

Copper binding site 2 out of 4 in the Structure of Copper Bound to Ycni W137F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Copper Bound to Ycni W137F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:49.0 occ:0.31 N A:HIS27 2.1 42.8 0.6 N A:HIS27 2.2 42.8 0.4 OE2 A:GLU50 2.7 58.8 1.0 CA A:HIS27 3.2 37.7 0.6 CA A:HIS27 3.3 38.1 0.4 CD A:GLU50 3.3 55.7 1.0 CB A:HIS27 3.5 36.4 0.6 CG A:GLU50 3.7 39.0 1.0 CB A:HIS27 3.7 34.0 0.4 CD2 A:HIS27 3.8 43.8 0.4 CG A:HIS27 4.1 41.2 0.4 CE1 A:PHE137 4.1 31.1 1.0 OE1 A:GLU50 4.1 47.3 1.0 CZ A:PHE137 4.3 29.7 1.0 O A:HOH382 4.4 29.9 1.0 C A:HIS27 4.5 35.7 0.6 C A:HIS27 4.6 36.0 0.4 O A:HOH312 4.7 34.2 1.0 CB A:GLU50 4.7 32.1 1.0 CG A:HIS27 4.9 34.5 0.6 O A:HIS27 5.0 33.8 0.6

Copper binding site 3 out of 4 in the Structure of Copper Bound to Ycni W137F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Copper Bound to Ycni W137F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:131.4 occ:0.76 OE2 B:GLU50 1.6 48.4 0.4 ND1 B:HIS27 1.9 50.1 0.5 N B:HIS27 2.0 43.6 0.5 N B:HIS27 2.2 41.5 0.5 OE2 B:GLU50 2.4 46.8 0.6 CD B:GLU50 2.7 38.5 0.4 CA B:HIS27 2.9 43.8 0.5 CG B:HIS27 2.9 45.0 0.5 CA B:HIS27 2.9 43.7 0.5 CB B:HIS27 2.9 44.8 0.5 CE1 B:HIS27 2.9 50.1 0.5 CB B:HIS27 3.2 35.3 0.5 OE1 B:GLU50 3.3 39.7 0.4 ND1 B:HIS27 3.4 38.4 0.5 CD B:GLU50 3.4 36.8 0.6 CG B:HIS27 3.6 48.7 0.5 CG B:GLU50 3.9 37.9 0.4 CG B:GLU50 4.0 38.0 0.6 CD2 B:HIS27 4.0 47.6 0.5 NE2 B:HIS27 4.0 40.4 0.5 CE1 B:PHE137 4.3 26.4 1.0 C B:HIS27 4.3 39.2 0.5 C B:HIS27 4.3 39.1 0.5 O B:HOH331 4.3 43.6 1.0 OE1 B:GLU50 4.3 46.7 0.6 CZ B:PHE137 4.4 24.2 1.0 O B:HOH311 4.5 30.3 1.0 CE1 B:HIS27 4.7 35.4 0.5 O B:HIS27 4.8 41.1 0.5 O B:HOH301 4.8 42.1 1.0 O B:HIS27 4.9 41.1 0.5 CD2 B:HIS27 4.9 47.0 0.5

Copper binding site 4 out of 4 in the Structure of Copper Bound to Ycni W137F


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Copper Bound to Ycni W137F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:61.7 occ:0.24 CD2 B:HIS27 2.6 47.0 0.5 CG B:HIS27 2.7 48.7 0.5 CB B:HIS27 2.7 44.8 0.5 CB B:HIS27 2.8 35.3 0.5 CG B:HIS27 3.4 45.0 0.5 NE2 B:HIS27 3.6 34.0 0.5 CD2 B:HIS27 3.7 47.6 0.5 ND1 B:HIS27 3.7 38.4 0.5 CE1 B:HIS27 4.2 35.4 0.5 CA B:HIS27 4.2 43.8 0.5 CA B:HIS27 4.2 43.7 0.5 ND1 B:HIS27 4.4 50.1 0.5 O B:HIS27 4.5 41.1 0.5 C B:HIS27 4.6 39.2 0.5 O B:HIS27 4.6 41.1 0.5 C B:HIS27 4.6 39.1 0.5 N B:HIS27 4.7 43.6 0.5 NE2 B:HIS27 4.7 40.4 0.5

Y.R.O.Silva, D.Zheng, S.C.Peters, O.S.Fisher. Stabilization of A Cu-Binding Site By A Highly Conserved Tryptophan Residue J.Inorg.Biochem. 2024.
ISSN: ISSN 0162-0134