Nickel in PDB 1q5y: Nickel-Bound C-Terminal Regulatory Domain of Nikr

The structure of Nickel-Bound C-Terminal Regulatory Domain of Nikr, PDB code: 1q5y was solved by E.R.Schreiter, M.D.Sintchak, Y.Guo, P.T.Chivers, R.T.Sauer, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.849, 78.287, 81.386, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 22

The binding sites of Nickel atom in the Nickel-Bound C-Terminal Regulatory Domain of Nikr (pdb code 1q5y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Nickel-Bound C-Terminal Regulatory Domain of Nikr, PDB code: 1q5y:
Jump to Nickel binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nickel-Bound C-Terminal Regulatory Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni534 b:18.1 occ:1.00 NE2 C:HIS76 1.9 19.4 1.0 NE2 A:HIS87 1.9 20.1 1.0 ND1 A:HIS89 2.0 19.9 1.0 SG A:CYS95 2.2 21.5 1.0 CD2 C:HIS76 2.8 20.6 1.0 CE1 A:HIS87 2.9 21.9 1.0 CE1 C:HIS76 2.9 18.7 1.0 CD2 A:HIS87 3.0 19.3 1.0 CE1 A:HIS89 3.0 21.1 1.0 CG A:HIS89 3.1 20.4 1.0 CB A:CYS95 3.3 18.9 1.0 CB A:HIS89 3.5 19.5 1.0 CA A:HIS89 3.5 17.9 1.0 CA A:CYS95 3.9 16.2 1.0 CG2 C:VAL72 4.0 25.6 1.0 CG C:HIS76 4.0 21.0 1.0 ND1 A:HIS87 4.0 20.7 1.0 ND1 C:HIS76 4.0 20.0 1.0 N A:HIS89 4.1 17.6 1.0 CG A:HIS87 4.1 18.6 1.0 NE2 A:HIS89 4.1 20.5 1.0 CD2 A:HIS89 4.2 21.1 1.0 O A:VAL88 4.3 17.9 1.0 C A:VAL88 4.4 16.8 1.0 O A:HOH553 4.5 40.7 1.0 O A:ASP94 4.6 19.9 1.0 N A:CYS95 4.6 16.8 1.0 C A:HIS89 4.9 20.0 1.0 C A:ASP94 4.9 19.4 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nickel-Bound C-Terminal Regulatory Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni634 b:23.1 occ:1.00 NE2 A:HIS76 1.9 30.7 1.0 NE2 C:HIS87 2.0 20.7 1.0 ND1 C:HIS89 2.0 31.4 1.0 SG C:CYS95 2.2 23.0 1.0 CE1 A:HIS76 2.9 30.2 1.0 CD2 A:HIS76 2.9 30.2 1.0 CE1 C:HIS89 3.0 33.1 1.0 CE1 C:HIS87 3.0 19.9 1.0 CD2 C:HIS87 3.0 19.9 1.0 CG C:HIS89 3.1 34.0 1.0 CB C:CYS95 3.3 19.6 1.0 CB C:HIS89 3.6 32.6 1.0 CA C:HIS89 3.6 28.0 1.0 CG2 A:VAL72 3.7 40.9 1.0 CA C:CYS95 3.9 18.5 1.0 ND1 A:HIS76 4.0 30.9 1.0 CG A:HIS76 4.0 31.2 1.0 ND1 C:HIS87 4.1 20.1 1.0 NE2 C:HIS89 4.1 34.1 1.0 N C:HIS89 4.1 25.3 1.0 CG C:HIS87 4.2 19.5 1.0 CD2 C:HIS89 4.2 35.7 1.0 O C:VAL88 4.4 21.2 1.0 C C:VAL88 4.5 21.1 1.0 O C:ASP94 4.6 23.7 1.0 N C:CYS95 4.6 18.8 1.0 CD2 C:HIS62 4.8 27.3 1.0 C C:ASP94 4.9 21.3 1.0 C C:HIS89 4.9 29.8 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nickel-Bound C-Terminal Regulatory Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni434 b:18.8 occ:1.00 NE2 D:HIS76 1.7 20.5 1.0 NE2 B:HIS87 1.9 19.0 1.0 ND1 B:HIS89 2.0 24.8 1.0 SG B:CYS95 2.2 23.0 1.0 CE1 D:HIS76 2.7 23.0 1.0 CD2 D:HIS76 2.8 21.7 1.0 CE1 B:HIS87 2.9 19.6 1.0 CD2 B:HIS87 2.9 20.1 1.0 CE1 B:HIS89 3.0 25.2 1.0 CG B:HIS89 3.0 24.3 1.0 CB B:CYS95 3.2 20.6 1.0 CB B:HIS89 3.5 23.4 1.0 CA B:HIS89 3.5 20.5 1.0 CG1 D:VAL72 3.6 33.9 1.0 ND1 D:HIS76 3.8 24.3 1.0 CA B:CYS95 3.9 18.2 1.0 CG D:HIS76 3.9 24.3 1.0 ND1 B:HIS87 4.0 20.2 1.0 CG B:HIS87 4.1 20.0 1.0 NE2 B:HIS89 4.1 25.6 1.0 CD2 B:HIS89 4.1 26.3 1.0 N B:HIS89 4.1 18.7 1.0 O B:VAL88 4.4 16.9 1.0 C B:VAL88 4.5 16.1 1.0 O B:ASP94 4.6 20.6 1.0 N B:CYS95 4.6 19.1 1.0 C B:HIS89 4.9 22.8 1.0 C B:ASP94 4.9 19.2 1.0 CB D:VAL72 4.9 28.3 1.0 O D:VAL72 5.0 30.4 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nickel-Bound C-Terminal Regulatory Domain of Nikr within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni734 b:16.3 occ:1.00 NE2 B:HIS76 1.9 18.4 1.0 NE2 D:HIS87 1.9 18.1 1.0 ND1 D:HIS89 2.0 18.7 1.0 SG D:CYS95 2.3 19.9 1.0 CE1 B:HIS76 2.9 18.5 1.0 CE1 D:HIS87 2.9 16.7 1.0 CE1 D:HIS89 2.9 18.6 1.0 CD2 B:HIS76 2.9 17.9 1.0 CD2 D:HIS87 3.0 17.8 1.0 CG D:HIS89 3.0 20.1 1.0 CB D:CYS95 3.3 19.2 1.0 CB D:HIS89 3.5 18.2 1.0 CA D:HIS89 3.5 17.4 1.0 CG2 B:VAL72 3.6 25.6 0.5 CG1 B:VAL72 3.7 26.8 0.5 CA D:CYS95 3.9 17.2 1.0 ND1 B:HIS76 4.0 18.9 1.0 ND1 D:HIS87 4.0 18.1 1.0 NE2 D:HIS89 4.1 20.8 1.0 CG B:HIS76 4.1 19.9 1.0 N D:HIS89 4.1 17.3 1.0 CD2 D:HIS89 4.1 20.5 1.0 CG D:HIS87 4.1 16.9 1.0 O D:VAL88 4.3 17.5 1.0 C D:VAL88 4.4 14.1 1.0 O D:ASP94 4.6 18.7 1.0 N D:CYS95 4.6 17.7 1.0 O D:HOH749 4.6 33.6 1.0 C D:ASP94 4.9 17.4 1.0 C D:HIS89 4.9 18.3 1.0 CD2 D:HIS62 4.9 24.9 1.0

E.R.Schreiter, M.D.Sintchak, Y.Guo, P.T.Chivers, R.T.Sauer, C.L.Drennan. Crystal Structure of the Nickel-Responsive Transcription Factor Nikr Nat.Struct.Biol. V. 10 794 2003.
ISSN: ISSN 1072-8368
PubMed: 12970756
DOI: 10.1038/NSB985