Nickel in PDB 4npp: The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms

The structure of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms, PDB code: 4npp was solved by L.Sauguet, A Shahsavar, F.Poitevin, C.Huon, A.Menny, A.Nemecz, A.Haouz, J.P.Changeux, P.J.Corringer, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.16 / 3.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.554, 127.618, 185.807, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 24.8

The binding sites of Nickel atom in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms (pdb code 4npp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms, PDB code: 4npp:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:0.3 occ:1.00 OD1 A:ASP86 2.6 0.5 1.0 OD1 A:ASP88 2.9 0.0 1.0 O A:ALA87 3.3 94.9 1.0 CG A:ASP88 3.4 0.4 1.0 OD2 A:ASP88 3.4 0.1 1.0 CG A:ASP86 3.8 0.2 1.0 C A:ALA87 3.9 85.0 1.0 N A:ALA87 4.1 84.7 1.0 OD2 A:ASP86 4.3 0.7 1.0 C A:ASP86 4.5 91.8 1.0 N A:ASP88 4.6 82.1 1.0 CA A:ALA87 4.6 83.9 1.0 CB A:ASP88 4.6 90.9 1.0 CA A:ASP88 4.8 83.0 1.0 CA A:ASP86 4.8 93.1 1.0 CB A:ASP86 4.9 93.4 1.0

Nickel binding site 2 out of 5 in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:0.7 occ:1.00 OD1 B:ASP86 2.6 1.0 1.0 OD1 B:ASP88 2.9 0.8 1.0 O B:ALA87 3.3 0.8 1.0 CG B:ASP88 3.4 0.9 1.0 OD2 B:ASP88 3.4 0.4 1.0 CG B:ASP86 3.7 0.2 1.0 C B:ALA87 3.9 87.7 1.0 N B:ALA87 4.1 81.0 1.0 OD2 B:ASP86 4.3 0.6 1.0 C B:ASP86 4.5 95.7 1.0 N B:ASP88 4.5 79.8 1.0 CA B:ALA87 4.5 87.1 1.0 CB B:ASP88 4.6 0.7 1.0 CA B:ASP86 4.8 0.5 1.0 CA B:ASP88 4.8 99.7 1.0 CB B:ASP86 4.8 0.1 1.0

Nickel binding site 3 out of 5 in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:0.6 occ:1.00 OD1 C:ASP86 2.6 0.5 1.0 OD1 C:ASP88 3.0 0.0 1.0 O C:ALA87 3.4 0.8 1.0 OD2 C:ASP88 3.5 0.9 1.0 CG C:ASP88 3.5 0.4 1.0 CG C:ASP86 3.7 0.5 1.0 C C:ALA87 4.0 95.1 1.0 N C:ALA87 4.2 88.0 1.0 OD2 C:ASP86 4.3 0.6 1.0 C C:ASP86 4.5 92.1 1.0 N C:ASP88 4.6 0.3 1.0 CA C:ALA87 4.6 89.2 1.0 CB C:ASP88 4.7 0.3 1.0 CA C:ASP86 4.8 0.7 1.0 CB C:ASP86 4.8 0.3 1.0 CA C:ASP88 4.9 0.3 1.0

Nickel binding site 4 out of 5 in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:0.4 occ:1.00 OD1 D:ASP88 2.6 0.1 1.0 OD1 D:ASP86 2.9 0.7 1.0 CG D:ASP88 3.2 0.4 1.0 OD2 D:ASP88 3.2 0.7 1.0 O D:ALA87 3.4 0.2 1.0 CG D:ASP86 4.0 0.4 1.0 C D:ALA87 4.0 84.4 1.0 N D:ALA87 4.4 88.3 1.0 OD2 D:ASP86 4.5 0.6 1.0 CB D:ASP88 4.5 99.2 1.0 N D:ASP88 4.6 88.9 1.0 CA D:ASP88 4.7 87.5 1.0 CA D:ALA87 4.8 78.1 1.0 C D:ASP86 4.8 91.7 1.0

Nickel binding site 5 out of 5 in the The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Glic-HIS10 Wild-Type Structure in Equilibrium Between the Open and Locally-Closed (Lc) Forms within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni401 b:0.4 occ:1.00 OD1 E:ASP86 2.5 0.4 1.0 OD1 E:ASP88 3.0 0.8 1.0 OD2 E:ASP88 3.4 0.5 1.0 O E:ALA87 3.4 0.5 1.0 CG E:ASP88 3.4 0.7 1.0 CG E:ASP86 3.6 0.5 1.0 C E:ALA87 4.0 87.3 1.0 OD2 E:ASP86 4.2 1.0 1.0 N E:ALA87 4.2 96.3 1.0 C E:ASP86 4.5 92.2 1.0 N E:ASP88 4.6 77.1 1.0 CA E:ALA87 4.7 94.3 1.0 CB E:ASP88 4.7 0.1 1.0 CB E:ASP86 4.7 0.4 1.0 CA E:ASP86 4.8 95.0 1.0 CA E:ASP88 4.9 86.1 1.0

L.Sauguet, A.Shahsavar, F.Poitevin, C.Huon, A.Menny, A.Nemecz, A.Haouz, J.P.Changeux, P.J.Corringer, M.Delarue. Crystal Structures of A Pentameric Ligand-Gated Ion Channel Provide A Mechanism For Activation. Proc.Natl.Acad.Sci.Usa V. 111 966 2014.
ISSN: ISSN 0027-8424
PubMed: 24367074
DOI: 10.1073/PNAS.1314997111