Copper in PDB 3bkt: Copper-Bound C-Terminal Domain of Nikr

The structure of Copper-Bound C-Terminal Domain of Nikr, PDB code: 3bkt was solved by C.M.Phillips, E.R.Schreiter, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.17 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.949, 78.442, 81.460, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.7

The binding sites of Copper atom in the Copper-Bound C-Terminal Domain of Nikr (pdb code 3bkt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Copper-Bound C-Terminal Domain of Nikr, PDB code: 3bkt:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Copper-Bound C-Terminal Domain of Nikr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper-Bound C-Terminal Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu2 b:24.5 occ:1.00 NE2 C:HIS76 2.0 19.1 1.0 NE2 A:HIS87 2.0 20.8 1.0 SG A:CYS95 2.4 23.9 1.0 ND1 A:HIS89 2.4 20.3 1.0 CE1 C:HIS76 2.9 17.6 1.0 CE1 A:HIS87 2.9 19.3 1.0 CD2 C:HIS76 3.0 19.0 1.0 CD2 A:HIS87 3.1 19.5 1.0 CE1 A:HIS89 3.2 22.8 1.0 CB A:CYS95 3.3 16.6 1.0 CG A:HIS89 3.5 17.9 1.0 CA A:HIS89 3.8 17.4 1.0 CA A:CYS95 3.9 15.5 1.0 CB A:HIS89 3.9 18.1 1.0 CG2 C:VAL72 3.9 27.1 1.0 ND1 C:HIS76 4.0 17.8 1.0 ND1 A:HIS87 4.1 16.6 1.0 CG C:HIS76 4.1 18.4 1.0 CG A:HIS87 4.2 16.3 1.0 N A:HIS89 4.3 15.6 1.0 O A:VAL88 4.4 14.8 1.0 NE2 A:HIS89 4.4 22.0 1.0 O A:ASP94 4.5 15.1 1.0 CD2 A:HIS89 4.6 20.6 1.0 N A:CYS95 4.6 14.9 1.0 C A:VAL88 4.6 14.2 1.0 CB A:HIS62 4.7 25.2 1.0 C A:ASP94 4.8 16.0 1.0

Copper binding site 2 out of 4 in the Copper-Bound C-Terminal Domain of Nikr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper-Bound C-Terminal Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu4 b:26.9 occ:1.00 NE2 D:HIS76 2.0 22.9 1.0 NE2 B:HIS87 2.1 21.7 1.0 ND1 B:HIS89 2.2 26.7 1.0 SG B:CYS95 2.4 25.5 1.0 CD2 D:HIS76 2.9 24.1 1.0 CE1 D:HIS76 3.0 23.7 1.0 CE1 B:HIS89 3.0 27.3 1.0 CE1 B:HIS87 3.0 20.6 1.0 CD2 B:HIS87 3.1 20.3 1.0 CB B:CYS95 3.3 17.4 1.0 CG1 D:VAL72 3.3 26.5 1.0 CG B:HIS89 3.4 24.2 1.0 CA B:CYS95 3.8 17.0 1.0 CB B:HIS89 3.9 22.0 1.0 CA B:HIS89 3.9 21.0 1.0 ND1 D:HIS76 4.1 23.7 1.0 CG D:HIS76 4.1 23.7 1.0 ND1 B:HIS87 4.1 19.0 1.0 NE2 B:HIS89 4.2 28.4 1.0 CG B:HIS87 4.2 16.9 1.0 CD2 B:HIS89 4.4 26.6 1.0 N B:HIS89 4.4 18.8 1.0 O B:VAL88 4.4 15.9 1.0 N B:CYS95 4.5 16.3 1.0 O B:ASP94 4.5 16.8 1.0 C B:VAL88 4.7 16.5 1.0 CB D:VAL72 4.8 25.8 1.0 C B:ASP94 4.8 18.0 1.0 CB B:HIS62 4.9 26.4 1.0

Copper binding site 3 out of 4 in the Copper-Bound C-Terminal Domain of Nikr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copper-Bound C-Terminal Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu1 b:23.7 occ:1.00 NE2 C:HIS87 2.1 18.8 1.0 NE2 A:HIS76 2.1 18.2 1.0 SG C:CYS95 2.5 21.4 1.0 ND1 C:HIS89 2.5 25.3 1.0 CE1 C:HIS87 2.9 18.3 1.0 CD2 A:HIS76 3.1 20.9 1.0 CE1 A:HIS76 3.1 21.1 1.0 CD2 C:HIS87 3.2 19.6 1.0 CE1 C:HIS89 3.3 26.2 1.0 CB C:CYS95 3.3 15.4 1.0 CG1 A:VAL72 3.4 20.1 0.5 CG2 A:VAL72 3.5 19.8 0.5 CG C:HIS89 3.7 22.8 1.0 CA C:CYS95 3.8 15.0 1.0 CA C:HIS89 4.1 18.8 1.0 ND1 C:HIS87 4.1 19.4 1.0 CB C:HIS89 4.1 19.9 1.0 ND1 A:HIS76 4.2 20.2 1.0 CG A:HIS76 4.2 20.1 1.0 CG C:HIS87 4.2 16.9 1.0 O C:VAL88 4.5 13.9 1.0 O C:ASP94 4.5 15.4 1.0 N C:CYS95 4.5 14.8 1.0 NE2 C:HIS89 4.5 27.5 1.0 N C:HIS89 4.5 16.9 1.0 CD2 C:HIS62 4.6 20.9 1.0 C C:VAL88 4.7 15.0 1.0 CD2 C:HIS89 4.7 26.9 1.0 C C:ASP94 4.8 15.8 1.0 CB A:VAL72 4.9 20.6 0.5 CB A:VAL72 4.9 20.5 0.5 CG C:HIS62 4.9 19.5 1.0

Copper binding site 4 out of 4 in the Copper-Bound C-Terminal Domain of Nikr


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copper-Bound C-Terminal Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu3 b:20.7 occ:1.00 NE2 B:HIS76 2.0 16.4 1.0 NE2 D:HIS87 2.0 17.4 1.0 SG D:CYS95 2.4 19.9 1.0 ND1 D:HIS89 2.5 23.3 1.0 CE1 D:HIS87 2.9 18.8 1.0 CE1 B:HIS76 2.9 18.4 1.0 CD2 B:HIS76 3.1 20.3 1.0 CD2 D:HIS87 3.1 18.8 1.0 CE1 D:HIS89 3.3 24.2 1.0 CB D:CYS95 3.3 13.8 1.0 CG2 B:VAL72 3.5 22.3 0.5 CG D:HIS89 3.6 19.1 1.0 CG1 B:VAL72 3.7 22.4 0.5 CA D:CYS95 3.8 13.8 1.0 CA D:HIS89 3.9 17.9 1.0 CB D:HIS89 4.0 18.6 1.0 ND1 D:HIS87 4.1 18.4 1.0 ND1 B:HIS76 4.1 18.8 1.0 CG B:HIS76 4.2 18.6 1.0 CG D:HIS87 4.2 15.2 1.0 O D:VAL88 4.4 13.4 1.0 NE2 D:HIS89 4.5 22.9 1.0 N D:HIS89 4.5 15.5 1.0 O D:ASP94 4.5 14.1 1.0 N D:CYS95 4.5 14.0 1.0 CD2 D:HIS89 4.6 22.7 1.0 C D:VAL88 4.6 14.3 1.0 CD2 D:HIS62 4.7 20.9 1.0 C D:ASP94 4.8 15.5 1.0

C.M.Phillips, E.R.Schreiter, Y.Guo, S.C.Wang, D.B.Zamble, C.L.Drennan. Structural Basis of the Metal Specificity For Nickel Regulatory Protein Nikr. Biochemistry V. 47 1938 2008.
ISSN: ISSN 0006-2960
PubMed: 18193897
DOI: 10.1021/BI702006H