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

Protein crystallography data

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

Copper Binding Sites:

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 3bkt

Go back to Copper Binding Sites List in 3bkt
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 3bkt

Go back to Copper Binding Sites List in 3bkt
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 3bkt

Go back to Copper Binding Sites List in 3bkt
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 3bkt

Go back to Copper Binding Sites List in 3bkt
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

Reference:

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
Page generated: Sun Dec 13 11:09:11 2020

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