Nickel in PDB 6tl7: Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121)

The structure of Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121), PDB code: 6tl7 was solved by H.Nar, D.Fiegen, G.Schnapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.32 / 1.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.490, 64.700, 101.850, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 16.2

The binding sites of Nickel atom in the Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121) (pdb code 6tl7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121), PDB code: 6tl7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:14.1 occ:0.60 N A:SER140 1.9 20.6 1.0 ND1 A:HIS141 2.0 15.8 1.0 N A:HIS141 2.0 14.6 1.0 C A:SER140 2.8 16.8 1.0 CA A:SER140 2.8 19.1 1.0 CG A:HIS141 2.9 14.5 1.0 CE1 A:HIS141 3.0 17.5 1.0 O A:HOH461 3.0 27.6 1.0 CA A:HIS141 3.1 13.7 1.0 CB A:HIS141 3.2 14.5 1.0 OG A:SER140 3.7 21.8 1.0 N A:MET142 3.8 13.3 0.3 CB A:SER140 3.8 19.8 1.0 N A:MET142 3.8 12.2 0.7 C A:HIS141 3.9 12.7 1.0 O A:SER140 4.0 20.1 1.0 CD2 A:HIS141 4.0 16.7 1.0 NE2 A:HIS141 4.0 19.0 1.0 CE1 B:HIS141 5.0 17.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Lectin-Like Ox-Ldl Receptor 1 (P212121) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:16.5 occ:0.60 N B:SER140 1.9 31.9 1.0 N B:HIS141 2.0 22.2 1.0 ND1 B:HIS141 2.0 18.2 1.0 C B:SER140 2.8 26.3 1.0 CA B:SER140 2.9 30.1 1.0 CG B:HIS141 3.0 19.7 1.0 CA B:HIS141 3.0 15.9 1.0 CE1 B:HIS141 3.0 17.6 1.0 O B:HOH524 3.0 39.2 0.8 CB B:HIS141 3.3 20.3 1.0 N B:MET142 3.6 12.4 1.0 C B:HIS141 3.6 15.1 1.0 CE B:MET142 3.9 18.4 1.0 OG B:SER140 4.0 35.6 1.0 CB B:SER140 4.0 33.4 1.0 O B:SER140 4.0 26.9 1.0 O A:SER140 4.0 20.1 1.0 NE2 B:HIS141 4.1 19.0 1.0 CD2 B:HIS141 4.1 21.5 1.0 SD B:MET142 4.2 15.7 1.0 O B:HIS141 4.6 15.7 1.0 OG A:SER140 4.9 21.8 1.0 C A:SER140 4.9 16.8 1.0 CA B:MET142 4.9 11.5 1.0

H.Nar, D.Fiegen, G.Schnapp. A Small-Molecule Inhibitor of Lectin-Like Oxidized Ldl Receptor-1 Acts By Stabilizing An Inactive Receptor Tetramer State Commun Chem 2020.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-020-0321-2